<PAGE>   1
                                                                    EXHIBIT 4.19


                             NOTE PURCHASE AGREEMENT

                          Dated as of January 28, 2000

                                      Among

                                ATLAS AIR, INC.,

                            WILMINGTON TRUST COMPANY,
                    as Pass Through Trustee under each of the
                          Pass Through Trust Agreement

                            WILMINGTON TRUST COMPANY,
                             as Subordination Agent

                   FIRST SECURITY BANK, NATIONAL ASSOCIATION,
                                 as Escrow Agent

                                       and

                            WILMINGTON TRUST COMPANY,
                                 as Paying Agent



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                        INDEX TO NOTE PURCHASE AGREEMENT

<TABLE>
<CAPTION>
                                                                             Page
                                                                             ----
<S>         <C>                                                              <C>
SECTION 1.  Financing of Aircraft                                               3
SECTION 2.  Conditions Precedent                                                6
SECTION 3.  Representations and Warranties                                      7
SECTION 4.  Covenants                                                          10
SECTION 5.  Notices                                                            11
SECTION 6.  Expenses                                                           11
SECTION 7.  Further Assurances                                                 12
SECTION 8.  Miscellaneous                                                      12
SECTION 9.  Governing Law                                                      13


                                    Schedules

Schedule I   Aircraft and Scheduled Delivery Months
Schedule II  Pass Through Trust Agreements
Schedule III Deposit Agreements
Schedule IV  Escrow and Paying Agent Agreements
Schedule V   Mandatory Document Terms
Schedule VI  Mandatory Economic Terms
Schedule VII Aggregate Amortization Schedule

                                      Annex

Annex A  Definitions

                                    Exhibits

Exhibit A-1 Form of Leased Aircraft Participation Agreement
Exhibit A-2 Form of Lease
Exhibit A-3 Form of Leased Aircraft Indenture
Exhibit A-4 Form of Aircraft Purchase Agreement Assignment
Exhibit A-5 Form of Leased Aircraft Trust Agreement
Exhibit B   Form of Delivery Notice
Exhibit C-1 Form of Owned Aircraft Participation Agreement
Exhibit C-2 Form of Owned Aircraft Indenture
</TABLE>



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                             NOTE PURCHASE AGREEMENT

                  This NOTE PURCHASE AGREEMENT, dated as of January 28, 2000,
among (i) ATLAS AIR, INC., a Delaware corporation (the "Company"), (ii)
WILMINGTON TRUST COMPANY ("WTC"), a Delaware banking corporation, not in its
individual capacity except as otherwise expressly provided herein, but solely as
trustee (in such capacity together with its successors in such capacity, the
"Pass Through Trustee") under each of the four separate Pass Through Trust
Agreements, (iii) WILMINGTON TRUST COMPANY, a Delaware banking corporation, as
subordination agent and trustee (in such capacity together with its successors
in such capacity, the "Subordination Agent") under the Intercreditor Agreement
(as defined below), (iv) FIRST SECURITY BANK, NATIONAL ASSOCIATION, a national
banking association, as Escrow Agent (in such capacity together with its
successors in such capacity, the "Escrow Agent") under each of the Escrow
Agreements (as defined below), and (v) WILMINGTON TRUST COMPANY, a Delaware
banking corporation, as Paying Agent (in such capacity together with its
successors in such capacity, the "Paying Agent") under each of the Escrow
Agreements.

                              W I T N E S S E T H:

                  WHEREAS, capitalized terms used but not defined herein shall
have the meanings ascribed to such terms in Annex A hereto;

                  WHEREAS, the Company has obtained commitments from the
Manufacturer pursuant to the Purchase Agreement for the delivery of the two
aircraft listed in Schedule I hereto (together with any aircraft substituted
therefor in accordance with the Purchase Agreement and this Agreement prior to
the delivery thereof, the "Aircraft");

                  WHEREAS, pursuant to the Pass Through Trust Agreements set
forth in Schedule II hereto, and concurrently with the execution and delivery of
this Agreement, separate grantor trusts (collectively, the "Pass Through Trusts"
and, individually, a "Pass Through Trust") have been created to facilitate
certain of the transactions contemplated hereby, including, without limitation,
the issuance and sale of pass through certificates pursuant thereto
(collectively, the "Certificates") to provide for all or a portion of the
financing of the Aircraft;

                  WHEREAS, the Company has entered into the Placement Agreement
dated January 20, 2000 (the "Placement Agreement") with the several placement
agents (the "Placement Agents") named therein, which provides that the Company
will cause each Pass Through Trustee to issue and sell the Certificates to the
Placement Agents;

                  WHEREAS, concurrently with the execution and delivery of this
Agreement, (i) the Escrow Agents and the Depositary entered into the Deposit
Agreements set forth in Schedule III hereto (the "Deposit Agreements") whereby
the applicable Escrow Agent agreed to direct the Placement Agents to make the
deposit referred to therein on the Issuance Date (each a "Deposit") and to
permit the applicable Pass Through Trustee to re-deposit amounts from time to
time thereafter, (ii) the Company and the Depositary entered into the Indemnity
Agreement, dated as



<PAGE>   4

of the date hereof (the "Indemnity Agreement") and (iii) the Pass Through
Trustees, the Placement Agents, the Paying Agents and the Escrow Agents entered
into the Escrow and Paying Agent Agreements set forth in Schedule IV hereto (the
"Escrow Agreements") whereby, among other things, (a) the Placement Agents
agreed to deliver an amount equal to the amount of the Deposits to the
Depositary on behalf of each applicable Escrow Agent and (b) each Escrow Agent,
upon the Depositary receiving such amount, has agreed to deliver escrow receipts
to be affixed to each Certificate;

                  WHEREAS, prior to the delivery of each Aircraft, the Company
will determine whether to enter into a leveraged lease transaction as lessee
with respect to such Aircraft (a "Leased Aircraft") or to purchase as owner such
Aircraft (an "Owned Aircraft"), and will give to the Pass Through Trustee a
Delivery Notice (as defined below) specifying its election;

                  WHEREAS, upon receipt of a Delivery Notice with respect to an
Aircraft, subject to the terms and conditions of this Agreement, the applicable
Pass Through Trustees will enter into the applicable Financing Agreements
relating to such Aircraft;

                  WHEREAS, upon the delivery of each Aircraft, each Pass Through
Trustee will fund its purchase of Equipment Notes with the proceeds of all or a
portion of the Deposit withdrawn by the applicable Escrow Agent under the
related Deposit Agreement bearing the same interest rate as the Certificates
issued by such Pass Through Trust; and

                  WHEREAS, concurrently with the execution and delivery of this
Agreement, (i) Westdeutsche Landesbank Girozentrale, a German banking
institution organized under the law of the State of North Rhine-Westphalia,
acting through its New York Branch, entered into a revolving credit agreement
for the benefit of the Certificateholders of the Class A Pass Through Trust and
Morgan Stanley Capital Services, Inc. entered into two revolving credit
agreements for the benefit of the Certificateholders of the Class B Pass Through
Trust and the Class C Pass Through Trust, in each case with the Subordination
Agent, as agent for the Pass Through Trustee on behalf of each such Pass Through
Trust (Westdeutsche Landesbank Girozentrale, New York Branch, and Morgan Stanley
Capital Services, Inc. are collectively referred to herein as the "Liquidity
Providers", and the revolving credit agreements as the "Liquidity Facilities")
and (ii) the Pass Through Trustee, the Liquidity Providers and the Subordination
Agent entered into the Intercreditor Agreement, dated as of the date hereof (the
"Intercreditor Agreement");

                  NOW, THEREFORE, in consideration of the foregoing premises and
the mutual agreements herein contained and other good and valuable
consideration, the receipt and adequacy of which are hereby acknowledged, the
parties hereto agree as follows:

                  SECTION 1. Financing of Aircraft. (a) The Company confirms
that it has entered into the Purchase Agreement with the Manufacturer pursuant
to which the Company has agreed to purchase, and the Manufacturer has agreed to
deliver, the Aircraft, all on and subject to terms and conditions specified in
the Purchase Agreement. The currently scheduled delivery dates for the Aircraft
are set forth in Schedule 1. The Company agrees to finance the Aircraft in



                                       2
<PAGE>   5

the manner provided herein, all on and subject to the terms and conditions
hereof and of the relevant Financing Agreements.

                  (b) In furtherance of the foregoing, the Company agrees to
give the parties hereto, the Depositary and each of the Rating Agencies and DCR
not less than two Business Days' prior notice (a "Delivery Notice") of the
scheduled delivery date (the "Scheduled Delivery Date") (or, in the case of a
substitute Delivery Notice under Section 1(d) or (e) hereof, one Business Day's
prior notice) in respect of each Aircraft under the Purchase Agreement, which
notice shall:

                  (i) specify whether the Company has elected to treat such
         Aircraft as a Leased Aircraft or an Owned Aircraft;

                  (ii) specify the Scheduled Delivery Date of such Aircraft
         (which shall be a Business Day before the Cut-off Date and, except as
         provided in Section 1(e) hereof, the date (the "Funding Date") on which
         the financing therefor in the manner provided herein shall be
         consummated);

                  (iii) instruct the Pass Through Trustee to instruct the
         relevant Escrow Agent to provide a Notice of Purchase Withdrawal to the
         Depositary with respect to the Equipment Notes to be issued in
         connection with the financing of such Aircraft;

                  (iv) instruct the Pass Through Trustee to enter into the
         Participation Agreement included in the Financing Agreements with
         respect to such Aircraft in such form and at such a time on or before
         the Funding Date specified in such Delivery Notice and to perform its
         obligations thereunder;

                  (v) specify the aggregate principal amount of each series of
         Equipment Notes to be issued, and purchased by the Pass Through
         Trustee, in connection with the financing of such Aircraft scheduled to
         be delivered on such Funding Date (which shall in all respects comply
         with the Mandatory Economic Terms); and

                  (vi) if such Aircraft is to be a Leased Aircraft, certify that
         the related Owner Participant (A) is not an Affiliate of the Company
         (unless prior Rating Agency Confirmation permitting the use of an
         Affiliate has been obtained) and (B) based on the representations of
         such Owner Participant, is either (1) a Qualified Owner Participant or
         (2) any other person the obligations of which under the Owner
         Participant Agreements (as defined in the applicable Participation
         Agreement) are guaranteed by a Qualified Owner Participant.

                  (c) Upon receipt of a Delivery Notice, the Pass Through
Trustees shall, and shall cause the Subordination Agent to, enter into and
perform their obligations under the Participation Agreement specified in such
Delivery Notice, provided that, (i) the relevant Financing Agreements as
executed and delivered shall not vary the Mandatory Economic Terms and shall
contain the Mandatory Document Terms and (ii) subject to the next two succeeding
sentences, such Participation Agreement and the other Lease Financing Agreements
or Owner



                                       3
<PAGE>   6

Financing Agreements to be entered into pursuant to such Participation Agreement
shall be in the forms thereof annexed hereto in all material respects. The
Leased Aircraft Participation Agreements and other Lease Financing Agreements
may contain modifications, provided, however, that with respect to any material
modifications (other than modifications affecting only the Owner Participant), a
Rating Agency Confirmation shall have been obtained from each Rating Agency by
the Company and delivered by the Company to the applicable Pass Through Trustee
on or before the relevant Delivery Date. If Rating Agency Confirmation shall
have been received with respect to any Financing Agreements and such Financing
Agreements are utilized for subsequent Aircraft (or Substitute Aircraft) without
material modifications, no additional Rating Agency Confirmation shall be
required. Notwithstanding the foregoing, if any Financing Agreement annexed
hereto shall not have been reviewed by either Rating Agency prior to the
Issuance Date, then, prior to the use thereof in connection with the financing
of any Aircraft hereunder, the Company shall obtain from each Rating Agency a
confirmation that the use of such Financing Documents would not result in (x) a
reduction of the rating for any Class of Certificates below the then current
rating for such Class of Certificates or (y) a withdrawal or suspension of the
rating of any Class of Certificates. With respect to each Aircraft, the Company
shall cause Wilmington Trust Company (or such other person that meets the
eligibility requirements to act as loan trustee under the Leased Aircraft
Indenture or Owned Aircraft Indenture) to execute as Loan Trustee the Financing
Agreements relating to such Aircraft to which such Loan Trustee is intended to
be a party, and shall concurrently therewith execute such Financing Agreements
to which the Company is intended to be a party and perform its respective
obligations thereunder. Upon the request of either Rating Agency or of DCR, the
Company shall deliver or cause to be delivered to such requesting entity a true
and complete copy of each Financing Agreement relating to the financing of each
Aircraft together with a true and complete set of the closing documentation
(including legal opinions) delivered to the related Loan Trustee, Subordination
Agent and Pass Through Trustee under the related Participation Agreement.

                  (d) If after giving any Delivery Notice, there shall be a
delay in the delivery of an Aircraft, or if on the Scheduled Delivery Date of an
Aircraft the financing thereof in the manner contemplated hereby shall not be
consummated for whatever reason, the Company shall give the parties hereto
prompt notice thereof. Concurrently with the giving of such notice of
postponement or subsequently, the Company shall give the parties hereto a
substitute Delivery Notice specifying the date to which such delivery and
related financing shall have been re-scheduled (which shall be a Business Day
before the Cut-off Date on which the Escrow Agents shall be entitled to withdraw
all or a portion of the Deposit under each of the applicable Deposit Agreements
to enable each applicable Pass Through Trustee to fund its purchase of the
related Equipment Notes). Upon receipt of any such notice of postponement, each
applicable Pass Through Trustee shall comply with its obligations under Section
5.01 of each of the Trust Supplements and thereafter the financing of the
relevant Aircraft shall take place on the re-scheduled Delivery Date therefor
(all on and subject to the terms and conditions of the relevant Financing
Agreements) unless further postponed as provided herein.

                  (e) Anything in this Section 1 to the contrary
notwithstanding, the Company shall have the right at any time on or before the
Scheduled Delivery Date of any Aircraft, and subsequent to its giving a Delivery
Notice therefor, to postpone the Scheduled Delivery Date of



                                       4
<PAGE>   7

such Aircraft so as to enable the Company to change its election to treat such
Aircraft as a Leased Aircraft or an Owned Aircraft by written notice of such
postponement to the other parties hereto. The Company shall subsequently give
the parties hereto a substitute Delivery Notice complying with the provisions of
Section 1(b) hereof and specifying the new Funding Date for such postponed
Aircraft (which shall be a Business Day occurring before the Cut-off Date and on
which the Escrow Agents shall be entitled to withdraw the Deposit under each of
the applicable Deposit Agreements sufficient to enable each applicable Pass
Through Trustee to fund its purchase of the related Equipment Notes). In
addition, the Company shall have the further right, anything in this Section 1
to the contrary notwithstanding, to accept delivery of an Aircraft under the
Purchase Agreement on the Delivery Date thereof by utilization of bridge
financing of such Aircraft and promptly thereafter give the parties hereto a
Delivery Notice specifying a Funding Date not later than 60 days after the
Delivery Date of such Aircraft and no later than the Cut-off Date and otherwise
complying with the provisions of Section 1(b) hereof. All other terms and
conditions of this Note Purchase Agreement shall apply to the financing of any
such Aircraft on the re-scheduled Funding Date therefor except (i) the
re-scheduled Funding Date shall be deemed the Delivery Date of such Aircraft for
all purposes of this Section 1 and (ii) the related Financing Agreements shall
be amended to reflect the original delivery of such Aircraft to the Company.

                  (f) If the Scheduled Delivery Date for any Aircraft is delayed
(a) more than 30 days beyond the last day of the month set forth opposite such
Aircraft under the heading "Scheduled Delivery Months" in Schedule I hereto or
(b) beyond the Delivery Period Termination Date, the Company may identify for
delivery a substitute aircraft therefor meeting the following conditions (a
"Substitute Aircraft"): (i) a Substitute Aircraft must be a Boeing 747-400F
aircraft manufactured after 1993, so long as after giving effect thereto such
substitution does not vary the Mandatory Economic Terms, and (ii) the Company
shall be obligated to obtain Rating Agency Confirmation in respect of the
replacement of any Aircraft by Substitute Aircraft. Upon the satisfaction of the
conditions set forth above with respect to a Substitute Aircraft, the Aircraft
to be replaced shall cease to be subject to this Agreement and all rights and
obligations of the parties hereto concerning such Aircraft shall cease, and such
Substitute Aircraft shall become and thereafter be subject to the terms and
conditions of this Agreement to the same extent as such Aircraft.

                  (g) The Company shall have no liability for the failure of any
Pass Through Trustee to purchase Equipment Notes with respect to any Aircraft or
Substitute Aircraft, other than the Company's obligation, if any, to pay the
Deposit Make-Whole Premium pursuant to Section 4(a)(i) of this Agreement.

                  (h) The parties agree that if, in connection with the delivery
of an Aircraft or Substitute Aircraft, any Owner Participant who is to be a
party to any Lease Financing Agreement shall not be a "Citizen of the United
States" within the meaning of Section 40102(a)(15) of the Act, then the
applicable Lease Financing Agreements shall be modified, consistent with the
Mandatory Document Terms, to require such Owner Participant to enter into a
voting trust, voting powers, control rights or similar arrangement satisfactory
to the Company that (A) enables such Aircraft or Substitute Aircraft to be
registered in the United States and (B) complies with the FAA regulations issued
under the Act applicable thereto.



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<PAGE>   8

                  (i) Anything herein to the contrary notwithstanding, the
Company shall not have the right, and shall not be entitled, at any time to
request the issuance of Equipment Notes of any series to any Pass Through
Trustee in an aggregate principal amount in excess of the amount of the Deposit
then available for withdrawal in respect of such Equipment Notes by the Escrow
Agent under and in accordance with the provisions of the related Deposit
Agreement.

                  SECTION 2. Conditions Precedent. The obligation of the Pass
Through Trustees to enter into, and to cause the Subordination Agent to enter
into, any Participation Agreement as directed pursuant to a Delivery Notice and
to perform its obligations under such Participation Agreement is subject to
satisfaction of the following conditions:

                  (a) no Triggering Event shall have occurred; and

                  (b) the Company shall have delivered to each such Pass Through
         Trustee and each Liquidity Provider a certificate stating that (i) such
         Participation Agreement and the other Financing Agreements to be
         entered into pursuant to such Participation Agreement do not vary the
         Mandatory Economic Terms and contain the Mandatory Document Terms and
         (ii) any substantive modification of such Financing Agreements from the
         forms thereof attached to this Agreement do not materially and
         adversely affect the Certificateholders, and such certification shall
         be true and correct.

                  Anything herein to the contrary notwithstanding, the
         obligation of each Pass Through Trustee to purchase Equipment Notes
         shall terminate on the Cut-off Date.

                  SECTION 3. Representations and Warranties. (a) The Company
represents and warrants that:

                  (i) the Company is duly incorporated, validly existing and in
         good standing under the laws of the State of Delaware and is a "citizen
         of the United States" as defined in 49 U.S.C. Section 40102 and a U.S.
         Air Carrier, and has the full corporate power, authority and legal
         right under the laws of the State of Delaware to execute and deliver
         this Agreement and each Financing Agreement to which it will be a party
         and to carry out the obligations of the Company under this Agreement
         and each Financing Agreement to which it will be a party;

                  (ii) the execution and delivery by the Company of this
         Agreement and the performance by the Company of its obligations under
         this Agreement have been duly authorized by the Company and will not
         violate its Certificate of Incorporation or by-laws or the provisions
         of any indenture, mortgage, contract or other agreement to which it is
         a party or by which it is bound; and

                  (iii) this Agreement constitutes the legal, valid and binding
         obligation of the Company, enforceable against it in accordance with
         its terms, except as the same may be limited by applicable bankruptcy,
         insolvency, reorganization, moratorium or similar laws



                                       6
<PAGE>   9

         affecting the rights of creditors generally and by general principles
         of equity, whether considered in a proceeding at law or in equity.

                  (b) WTC represents and warrants that:

                  (i) WTC is duly incorporated, validly existing and in good
         standing under the laws of the State of Delaware and is a "citizen of
         the United States" as defined in 49 U.S.C. Section 40102, and has the
         full corporate power, authority and legal right under the laws of the
         State of Delaware and the United States pertaining to its banking,
         trust and fiduciary powers to execute and deliver this Agreement and
         each Financing Agreement to which it will be a party and to carry out
         the obligations of WTC, in its capacity as Subordination Agent, Pass
         Through Trustee or Paying Agent, as the case may be, under this
         Agreement and each Financing Agreement to which it will be a party;

                  (ii) the execution and delivery by WTC, in its capacity as
         Subordination Agent, Pass Through Trustee or Paying Agent, as the case
         may be, of this Agreement and the performance by WTC, in its capacity
         as Subordination Agent, Pass Through Trustee or Paying Agent, as the
         case may be, of its obligations under this Agreement have been duly
         authorized by WTC, in its capacity as Subordination Agent, Pass Through
         Trustee or Paying Agent, as the case may be, and will not violate its
         articles of association or by-laws or the provisions of any indenture,
         mortgage, contract or other agreement to which it is a party or by
         which it is bound; and

                  (iii) this Agreement constitutes the legal, valid and binding
         obligations of WTC, in its capacity as Subordination Agent, Pass
         Through Trustee or Paying Agent, as the case may be, enforceable
         against it in accordance with its terms, except as the same may be
         limited by applicable bankruptcy, insolvency, reorganization,
         moratorium or similar laws affecting the rights of creditors generally
         and by general principles of equity, whether considered in a proceeding
         at law or in equity.

                  (c) The Pass Through Trustee hereby confirms to each of the
other parties hereto that its representations and warranties set forth in
Section 7.15 of the Basic Pass Through Trust Agreement and Section 5.04 of each
Trust Supplement are true and correct as of the date hereof.

                  (d) The Subordination Agent represents and warrants that:

                  (i) the Subordination Agent is duly incorporated, validly
         existing and in good standing under the laws of the State of Delaware,
         and has the full corporate power, authority and legal right under the
         laws of the State of Delaware and the United States pertaining to its
         banking, trust and fiduciary powers to execute and deliver this
         Agreement and each Financing Agreement to which it is or will be a
         party and to perform its obligations under this Agreement and each
         Financing Agreement to which it is or will be a party;



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<PAGE>   10

                  (ii) this Agreement has been duly authorized, executed and
         delivered by the Subordination Agent; this Agreement constitutes the
         legal, valid and binding obligations of the Subordination Agent
         enforceable against it in accordance with its terms, except as the same
         may be limited by applicable bankruptcy, insolvency, reorganization,
         moratorium or similar laws affecting the rights of creditors generally
         and by general principles of equity, whether considered in a proceeding
         at law or in equity;

                  (iii) none of the execution, delivery and performance by the
         Subordination Agent of this Agreement contravenes any law, rule or
         regulation of the State of Delaware or any United States governmental
         authority or agency regulating the Subordination Agent's banking, trust
         or fiduciary powers or any judgment or order applicable to or binding
         on the Subordination Agent and do not contravene the Subordination
         Agent's articles of association or by-laws or result in any breach of,
         or constitute a default under, any agreement or instrument to which the
         Subordination Agent is a party or by which it or any of its properties
         may be bound;

                  (iv) neither the execution and delivery by the Subordination
         Agent of this Agreement nor the consummation by the Subordination Agent
         of any of the transactions contemplated hereby requires the consent or
         approval of, the giving of notice to, the registration with, or the
         taking of any other action with respect to, any Delaware governmental
         authority or agency or any federal governmental authority or agency
         regulating the Subordination Agent's banking, trust or fiduciary
         powers;

                  (v) there are no Taxes payable by the Subordination Agent
         imposed by the State of Delaware or any political subdivision or taxing
         authority thereof in connection with the execution, delivery and
         performance by the Subordination Agent of this Agreement (other than
         franchise or other taxes based on or measured by any fees or
         compensation received by the Subordination Agent for services rendered
         in connection with the transactions contemplated by the Intercreditor
         Agreement or any of the Liquidity Facilities), and there are no Taxes
         payable by the Subordination Agent imposed by the State of Delaware or
         any political subdivision thereof in connection with the acquisition,
         possession or ownership by the Subordination Agent of any of the
         Equipment Notes (other than franchise or other taxes based on or
         measured by any fees or compensation received by the Subordination
         Agent for services rendered in connection with the transactions
         contemplated by the Intercreditor Agreement or any of the Liquidity
         Facilities); and

                  (vi) there are no pending or threatened actions or proceedings
         against the Subordination Agent before any court or administrative
         agency which individually or in the aggregate, if determined adversely
         to it, would materially adversely affect the ability of the
         Subordination Agent to perform its obligations under this Agreement.



                                       8
<PAGE>   11

                  (e) The Escrow Agent represents and warrants that:

                  (i) the Escrow Agent is a national banking association duly
         organized, validly existing and in good standing under the laws of the
         United States and has the full corporate power, authority and legal
         right under the laws of the United States pertaining to its banking,
         trust and fiduciary powers to execute and deliver this Agreement, each
         Deposit Agreement and each Escrow Agreement and to carry out the
         obligations of the Paying Agent under each of the Escrow Agreements;

                  (ii) the execution and delivery by the Escrow Agent of each of
         the Escrow Agreements and the performance by the Escrow Agent of its
         obligations hereunder and thereunder have been duly authorized by the
         Escrow Agent and will not violate its articles of association or
         by-laws or the provisions of any indenture, mortgage, contract or other
         agreement to which it is a party or by which it is bound; and

                  (iii) each of the Escrow Agreements constitutes the legal,
         valid and binding obligations of the Escrow Agent enforceable against
         it in accordance with its terms, except as the same may be limited by
         applicable bankruptcy, insolvency, reorganization, moratorium or
         similar laws affecting the rights of creditors generally and by general
         principles of equity, whether considered in a proceeding at law or in
         equity.

                  (f) The Paying Agent represents and warrants that:

                  (i) the Paying Agent is duly incorporated, validly existing
         and in good standing under the laws of the State of Delaware and has
         the full corporate power, authority and legal right under the laws of
         the United States pertaining to its banking, trust and fiduciary powers
         to execute and deliver this Agreement and each Escrow Agreement and to
         carry out the obligations of the Paying Agent under each of the Escrow
         Agreements;

                  (ii) the execution and delivery by the Paying Agent of each of
         the Escrow Agreements and the performance by the Paying Agent of its
         obligations hereunder and thereunder have been duly authorized by the
         Paying Agent and will not violate its articles of association or
         by-laws or the provisions of any indenture, mortgage, contract or other
         agreement to which it is a party or by which it is bound; and

                  (iii) each of the Escrow Agreements constitutes the legal,
         valid and binding obligations of the Paying Agent enforceable against
         it in accordance with its terms, except as the same may be limited by
         applicable bankruptcy, insolvency, reorganization, moratorium or
         similar laws affecting the rights of creditors generally and by general
         principles of equity, whether considered in a proceeding at law or in
         equity.

                  SECTION 4. Covenants. (a) The Company covenants with each of
the other parties hereto that:

                  (i) on the date that the Depositary is obligated to pay the
         amount of the Final Withdrawal to the Paying Agent pursuant to a
         Deposit Agreement relating to any Trust,



                                       9
<PAGE>   12

         the Company shall pay to the Pass Through Trustee of such Trust no
         later than 12:30 p.m. (New York time) an amount equal to the Deposit
         Make-Whole Premium, if any, required to be paid in respect of such
         Final Withdrawal amount;

                  (ii) subject to Section 4(a)(iv) of this Agreement, the
         Company shall at all times maintain its corporate existence and shall
         not wind up, liquidate or dissolve or take any action, or fail to take
         any action, that would have the effect of any of the foregoing;

                  (iii) the Company shall at all times remain a U.S. Air Carrier
         (as defined in the Financing Agreements) and shall at all times be
         otherwise certificated and registered to the extent necessary to
         entitle (i) in the case of Leased Aircraft, the Owner Trustee (and the
         Loan Trustee as assignee of the Owner Trustee's rights under each
         Lease) to the rights afforded to lessors of aircraft equipment under
         Section 1110 and (ii) in the case of Owned Aircraft, the Loan Trustee
         to the rights afforded to secured parties of aircraft equipment under
         Section 1110;

                  (iv) Section 13.2.1 of the form of each Lease is hereby
         incorporated by reference herein;

                  (v) the Company agrees to provide written notice to each of
         the parties hereto of the occurrence of the Cut-off Date no later than
         one Business Day after the date thereof; and

                  (vi) the Company shall not issue Series D Equipment Notes
         pursuant to any Owned Aircraft Indenture unless it shall have obtained
         written confirmation from each Rating Agency that the issuance of such
         Series D Equipment Notes will not result in (i) a reduction of the
         rating for any Class of Certificates below the then current rating for
         such Class of Certificates or (ii) a withdrawal or suspension of the
         rating of any Class of Certificates.

                  (b) WTC, in its individual capacity, covenants with each of
the other parties to this Agreement that it will, immediately upon obtaining
knowledge of any facts that would cast doubt upon its continuing status as a
"citizen of the United States" as defined in 49 U.S.C. Section 40102 and
promptly upon public disclosure of negotiations in respect of any transaction
which would or might adversely affect such status, notify in writing all parties
hereto of all relevant matters in connection therewith. Upon WTC giving any such
notice, WTC shall, subject to Section 8.02 of any Indenture then entered into,
resign as Loan Trustee in respect of such Indenture.

                  SECTION 5. Notices. Unless otherwise specifically provided
herein, all notices required or permitted by the terms of this Agreement shall
be in English and in writing, and any such notice shall become effective upon
being delivered personally or, if promptly confirmed by mail, when dispatched by
facsimile or other written telecommunication, addressed to such party hereto at
its address or facsimile number set forth below the signature of such party at
the foot of this Agreement.



                                       10
<PAGE>   13

                  SECTION 6. Expenses. (a) The Company agrees to pay to the
Subordination Agent when due an amount or amounts equal to the fees payable to
the relevant Liquidity Provider under Section 2.03 of each Liquidity Facility
and the related Fee Letter (as defined in the Intercreditor Agreement)
multiplied by a fraction the numerator of which shall be the then outstanding
aggregate amount of the Deposits under the Deposit Agreements and the
denominator of which shall be the sum of (x) the then outstanding aggregate
principal amount of the Series A Equipment Notes, Series B Equipment Notes and
Series C Equipment Notes issued under all of the Indentures and (y) the then
outstanding aggregate amount of the Deposits under the Deposit Agreements.

                  (b) So long as no Equipment Notes have been issued in respect
of any Aircraft, the Company agrees to pay (i) to the Subordination Agent when
due (A) the amount equal to interest on any Downgrade Advance payable under
Section 3.07 of each Liquidity Facility minus Investment Earnings while such
Downgrade Advance shall be outstanding, (B) the amount equal to interest on any
Non-Extension Advance payable under Section 3.07 of each Liquidity Facility
minus Investment Earnings while such Non-Extension Advance shall be outstanding
and (C) any other amounts owed to the Liquidity Provider by the Subordination
Agent as borrower under each Liquidity Facility (other than amounts due as
repayment of advances thereunder or as interest on such advances, except to the
extent payable pursuant to clause (A) or (B)), (ii) all compensation and
reimbursement of expenses, disbursements and advances payable by the Company
under the Pass Through Trust Agreements, (iii) all compensation and
reimbursement of expenses and disbursements payable to the Subordination Agent
under the Intercreditor Agreement except with respect to any income or franchise
taxes incurred by the Subordination Agent in connection with the transactions
contemplated by the Intercreditor Agreement and (iv) in the event the Company
requests any amendment to any Operative Agreement, all reasonable fees and
expenses (including, without limitation, fees and disbursements of counsel) of
the Escrow Agent and/or the Paying Agent in connection therewith. For purposes
of this Section 6(b), the terms "Applied Downgrade Advance", "Downgrade
Advance", "Investment Earnings", "Non-Extension Advance" and "Applied
Non-Extension Advance" shall have the meanings specified in each Liquidity
Facility.

                  SECTION 7. Further Assurances. Each party hereto shall duly
execute, acknowledge and deliver, or shall cause to be executed, acknowledged
and delivered, all such further agreements, instruments, certificates or
documents, and shall do and cause to be done such further acts and things, in
any case, as any other party hereto shall reasonably request in connection with
its administration of, or to carry out more effectually the purposes of, or to
better assure and confirm unto it the rights and benefits to be provided under,
this Agreement.

                  SECTION 8. Miscellaneous. (a) Provided that the transactions
contemplated hereby have been consummated, and except as otherwise provided for
herein, the representations, warranties and agreements herein of the Company,
the Subordination Agent, the Escrow Agent, the Paying Agent and the Pass Through
Trustee, and the Company's, the Subordination Agent's, the Escrow Agent's, the
Paying Agent's and the Pass Through Trustee's obligations under any and all
thereof, shall survive the expiration or other termination of this Agreement and
the other agreements referred to herein.



                                       11
<PAGE>   14

                  (b) This Agreement may be executed in any number of
counterparts (and each of the parties hereto shall not be required to execute
the same counterpart). Each counterpart of this Agreement, including a signature
page executed by each of the parties hereto, shall be an original counterpart of
this Agreement, but all of such counterparts together shall constitute one
instrument. Neither this Agreement nor any of the terms hereof may be
terminated, amended, supplemented, waived or modified orally, but only by an
instrument in writing signed by the party against which the enforcement of the
termination, amendment, supplement, waiver or modification is sought. The index
preceding this Agreement and the headings of the various Sections of this
Agreement are for convenience of reference only and shall not modify, define,
expand or limit any of the terms or provisions hereof. The terms of this
Agreement shall be binding upon, and shall inure to the benefit of, the Company
and its successors and permitted assigns, the Pass Through Trustee and its
successors as Pass Through Trustee (and any additional trustee appointed) under
any of the Pass Through Trust Agreements, the Escrow Agent and its successors as
Escrow Agent under the Escrow Agreements, the Paying Agent and its successors as
Paying Agent under the Escrow Agreements and the Subordination Agent and its
successors as Subordination Agent under the Intercreditor Agreement.

                  (c) This Agreement is not intended to, and shall not, provide
any person not a party hereto (other than the Placement Agents and each of the
beneficiaries of Section 6 hereof) with any rights of any nature whatsoever
against any of the parties hereto, and no person not a party hereto (other than
the Placement Agents and each of the beneficiaries of Section 6 hereof) shall
have any right, power or privilege in respect of, or have any benefit or
interest arising out of, this Agreement.

                  SECTION 9. Governing Law. THIS AGREEMENT SHALL BE GOVERNED BY,
AND CONSTRUED IN ACCORDANCE WITH, THE LAWS OF THE STATE OF NEW YORK. THIS
AGREEMENT IS BEING DELIVERED IN THE STATE OF NEW YORK.

                            [SIGNATURE PAGES FOLLOW]



                                       12
<PAGE>   15

                  IN WITNESS WHEREOF, the parties hereto have caused this
Agreement to be duly executed by their respective officers thereunto duly
authorized as of the day and year first above written.

                                  ATLAS AIR, INC.


                                  By:
                                     --------------------------------
                                  Name:
                                  Title:

                                  Address: 538 Commons Drive
                                           Golden, Colorado  80401
                                           Attention: Chief Financial Officer
                                           Facsimile: (303) 526-5051

                                  WILMINGTON TRUST COMPANY,
                                    not in its individual capacity, except as
                                    otherwise expressly provided herein, but
                                    solely as Pass Through Trustee, Loan
                                    Trustee, Subordination Agent and Paying
                                    Agent, as applicable

                                  By:
                                     --------------------------------
                                  Name:
                                  Title:

                                  Address: One Rodney Square
                                           1100 North Market Street
                                           Wilmington, Delaware
                                           19890-0001
                                           Attention: Corporate Trust Admin.

                                  FIRST SECURITY BANK, NATIONAL ASSOCIATION,
                                     as Escrow Agent


                                  By:
                                     --------------------------------
                                  Name:
                                  Title:

                                  Address: 79 South Main Street
                                           Salt Lake City, Utah 84111
                                           Attention: Corporate Trust Department



                                       13
<PAGE>   16

                                  SCHEDULE I to
                             Note Purchase Agreement

                     AIRCRAFT AND SCHEDULED DELIVERY MONTHS

<TABLE>
<CAPTION>
                                    Scheduled                  Expected
                                     Delivery                Registration               Manufacturer's
Aircraft Type                          Month                    Number                  Serial Number
-------------                          -----                    ------                  -------------
<S>                                 <C>                      <C>                        <C>
Boeing 747-400F                     July 2000                   N409MC                      30558
Boeing 747-400F                     August 2000                 N412MC                      30559
</TABLE>



<PAGE>   17

                                 SCHEDULE II to
                             Note Purchase Agreement

                                TRUST SUPPLEMENTS


Trust Supplement dated as of the Issuance Date between the Company and the Pass
Through Trustee in respect of Atlas Air Pass Through Trust, Series 2000-1A.

Trust Supplement dated as of the Issuance Date between the Company and the Pass
Through Trustee in respect of Atlas Air Pass Through Trust, Series 2000-1B.

Trust Supplement dated as of the Issuance Date between the Company and the Pass
Through Trustee in respect of Atlas Air Pass Through Trust, Series 2000-1C.



<PAGE>   18

                                 SCHEDULE III to
                             Note Purchase Agreement

                               DEPOSIT AGREEMENTS


Deposit Agreement (Class A) dated as of the Issuance Date between the Depositary
and the Escrow Agent.

Deposit Agreement (Class B) dated as of the Issuance Date between the Depositary
and the Escrow Agent.

Deposit Agreement (Class C) dated as of the Issuance Date between the Depositary
and the Escrow Agent.



<PAGE>   19

                                 SCHEDULE IV to
                             Note Purchase Agreement

                       ESCROW AND PAYING AGENT AGREEMENTS


Escrow and Paying Agent Agreement (Class A) dated as of the Issuance Date among
the Escrow Agent, the Placement Agents, the Pass Through Trustee and the Paying
Agent.

Escrow and Paying Agent Agreement (Class B) dated as of the Issuance Date among
the Escrow Agent, the Placement Agents, the Pass Through Trustee and the Paying
Agent.

Escrow and Paying Agent Agreement (Class C) dated as of the Issuance Date among
the Escrow Agent, the Placement Agents, the Pass Through Trustee and the Paying
Agent.



<PAGE>   20

                                  SCHEDULE V to
                             Note Purchase Agreement

             MANDATORY DOCUMENT TERMS FOR LEASE FINANCING AGREEMENTS

o    May not modify in any material adverse respect the Granting Clause of the
     Trust Indenture Form so as to deprive the Note Holders, the Loan
     Participants or the Indenture Indemnitees of a first priority security
     interest in and mortgage lien on the Aircraft and the Lease or to eliminate
     any of the obligations secured thereby or otherwise modify in any material
     adverse respect as regards the interests of the Note Holders, the
     Subordination Agent, the Liquidity Providers or the Mortgagee the
     provisions of Article II or III or Section 4.02, 4.03, 4.04, 5.02, 5.06,
     9.01(b), 10.04, 10.11 or 10.12 of the Trust Indenture Form.

o    May not modify in any material adverse respect as regards the interests of
     the Note Holders, the Subordination Agent, the Liquidity Providers or the
     Mortgagee the provisions of Section 3.2.1(e), 3.3(c), 4.7, the final
     sentence of 7.1.1, 10.3.1(d)(ii), 13.3, 16, 18.3 or 18.7(a) or Clause D of
     Annex D of the Lease Form or otherwise modify the terms of the Lease Form
     so as to deprive the Mortgagee of rights expressly granted to the
     "Mortgagee" therein.

o    May not modify in any material adverse respect as regards the interests of
     the Note Holders, the Subordination Agent, the Liquidity Providers or the
     Mortgagee the provisions of Section 5.1.9, 5.1.10, 5.1.11, 5.1.12, 7.5, 12,
     15.8(a) or 15.9 of the Participation Agreement Form or of the provisions of
     Section 5.1.2(xxiii) or 10.1.1(a)(iv) of the Participation Agreement Form
     so as to eliminate the requirement to deliver to the Loan Participant or
     the Mortgagee, as the case may be, the legal opinions to be provided to
     such Persons thereunder (recognizing that the lawyers rendering such
     opinions may be changed) or of the provisions of Section 7.6.11(a)(ii) of
     the Participation Agreement Form as regards the rights of the Mortgagee
     thereunder or otherwise modify the terms of the Participation Agreement
     Form to deprive the Trustees, the Subordination Agent, the Liquidity
     Providers or the Mortgagee of any indemnity or right of reimbursement in
     its favor for Expenses or Taxes.

o    May not modify, in any material adverse respect as regards the interests of
     the Note Holders, the Subordination Agent, the Liquidity Providers or the
     Mortgagee, the definition of "Make Whole Amount" in Annex A to the
     Participation Agreement Form.

 Notwithstanding the foregoing, any such Mandatory Document Term may be modified
  to correct or supplement any such provision which may be defective or to cure
  any ambiguity or correct any mistake, provided that any such action shall not
       materially adversely affect the interests of the Note Holders, the
       Subordination Agent, the Liquidity Providers, the Mortgagee or the
                              Certificateholders.



<PAGE>   21

                                 SCHEDULE VI to
                             Note Purchase Agreement

                            MANDATORY ECONOMIC TERMS

Equipment Notes

Obligor: Atlas Air, Inc. or an Owner Trust

Maximum Principal Amount:

     The aggregate principal amount of all Equipment Notes issued with respect
     to an Aircraft shall not exceed the maximum principal amount of Equipment
     Notes indicated for such Aircraft as set forth in the Offering Memorandum
     in "Summary--Equipment Notes and the Aircraft" under the column "Maximum
     Principal Amount of Equipment Notes".

Aggregate Maximum Principal Amount:

For all Boeing 747-400F Aircraft    $217,317,000

The aggregate original principal amount of all Equipment Notes for all Aircraft
shall not exceed the aggregate face amount of all Certificates issued on the
Issuance Date.

The aggregate original principal amount of all Equipment Notes of any series
shall not exceed the aggregate face amount of all Certificates of the related
Class issued on the Issuance Date.

Initial Loan to Aircraft Value with respect to an Aircraft (with the value of
any Aircraft equal to the value (the "Assumed Appraised Value") for such
Aircraft set forth in the Offering Memorandum in "Summary--Equipment Notes and
the Aircraft" under the column "Appraised Base Value"):



<PAGE>   22

Series A: not in excess of 39.0%
Series B: not in excess of 53.0%
Series C: not in excess of 68.0%

Loan to Aircraft Value for each series of Equipment Notes issued in respect of
each Aircraft (computed as of the date of issuance thereof on the basis of the
Assumed Appraised Value of such Aircraft and the Depreciation Assumption, as
defined in the Offering Memorandum) as of any Regular Distribution Date
(assuming no default in the payment of the Equipment Notes):

Series A: not in excess of 39.0%
Series B: not in excess of 53.0%
Series C: not in excess of 68.0%

Initial Average Life (in years) of each series of Equipment Notes for each
Boeing 747-400F Aircraft from the Issuance Date:

Series A: not less than 11.0 years or more than 13.5 years
Series B: not less than 6.5 years or more than 9.5 years
Series C: not less than 2.5 years or more than 4.25 years

Average Life (in years):

     As of the Delivery Period Termination Date, the average life of each Class
     of Certificates from the Issuance Date (computed without regard to the
     acceleration of any Equipment Notes and after giving effect to any special
     distribution on the Certificates thereafter required in respect of unused
     Deposits):

Class A: not less than 11.0 years or more than 13.5 years
Class B: not less than 7.5 years or more than 9.0 years
Class C: not less than 3.0 years or more than 4.0 years

Final Expected Regular Distribution Date:

Series A: January 2, 2020
Series B: January 2, 2016
Series C: January 2, 2010

Debt Rate (computed on the basis of a 360-day year consisting of twelve 30-day
months, payable semi-annually in arrears):

Series A: 8.707%
Series B: 9.057%
Series C: 9.702%

The interest rate applicable to each Series of Equipment Notes must be equal to
the rate applicable to the Certificates issued by the corresponding Pass Through
Trust.



<PAGE>   23

Past Due Rates: Debt Rate plus 2% per annum

Payment Dates:  January 2 and July 2

Make-Whole Amounts: As provided in Article II of the form of Trust Indenture
     marked as Exhibit A-3 of the Note Purchase Agreement (the "Trust Indenture
     Form") or the Owned Aircraft Indenture marked as Exhibit C-2 of the Note
     Purchase Agreement

Redemption and
Purchase: As provided in Article II of the Trust Indenture Form


Lease

Term: The Base Lease Term shall expire by its terms on or after final maturity
     date of the related Series A Equipment Notes

LeasePayment Dates: January 2 and July 2, provided that rent under a Lease may
     also be paid at the election of Atlas Air upon the commencement of such
     Lease and on any other date agreed between Atlas Air and the Owner
     Participant that occurs after the latest maturity date of the Equipment
     Notes issued in connection with the acquisition of the Aircraft to which
     such Lease relates

Minimum Rent: Basic Rent due and payable on each Lease Payment Date shall be at
     least sufficient to pay in full, as of such Lease Payment Date (assuming
     timely payment of the related Equipment Notes prior to such Date), the
     aggregate principal amount of scheduled installments due on the related
     Equipment Notes outstanding on such Lease Payment Date, together with
     accrued and unpaid interest thereon

Supplemental Rent: Sufficient to cover the sums described in clauses (a) through
     (d) of such term as defined in Annex A to the form of Lease (the "Lease
     Form") marked as Exhibit A-2 of the Note Purchase Agreement

Stipulated Loss
Value: At all times equal to or greater than the then outstanding principal
     amount of the related Equipment Notes together with accrued interest
     thereon

Termination Value: At all times equal to or greater than the then outstanding
     principal amount of the related Equipment Notes together with accrued
     interest thereon

All-risk Hull
Insurance: Not less than the Stipulated Loss Value or, in the case of an Owned
     Aircraft, not less than the unpaid principal amount of the related
     Equipment Notes, subject to Lessees right to self-insure on terms no more
     favorable to Lessee in any material respect than those set forth in
     Section G of Annex D to the Lease Form



<PAGE>   24

Minimum Liability
Insurance Amount: As set forth in Schedule 1 to the Lease Form

Past Due Rate: As set forth in Schedule 1 to the Lease Form

SLV Rate: As set forth in Schedule 1 to the Lease Form

Participation Agreement

     Mortgagee, Subordination Agent, Liquidity Providers, Guarantor, Pass
         Through Trustees, Escrow Agents and Note Holders shall be indemnified
         against Expenses and Taxes to the extent set forth in Section 9 of the
         form of the Participation Agreement marked as Exhibit A-1 to the Note
         Purchase Agreement (the "Participation Form"), Lease Form and Trust
         Indenture Form.



<PAGE>   25

                                 SCHEDULE VII to
                             Note Purchase Agreement

                         AGGREGATE AMORTIZATION SCHEDULE

<TABLE>
<CAPTION>
                     2000-1A Trust         2000-1B Trust         2000-1C Trust
                  Scheduled Principal   Scheduled Principal   Scheduled Principal
      Date              Payment               Payment               Payment
      ----              -------               -------               -------
<S>               <C>                   <C>                   <C>
January 2, 2001   $        10,384,326   $         8,948,200   $         9,587,400
January 2, 2002                     0                     0             5,787,514
January 2, 2003               832,183                     0             7,698,129
January 2, 2004             3,739,203                     0             5,637,012
January 2, 2005             3,739,203                     0             6,553,968
January 2, 2006             3,739,203               379,549             7,183,589
January 2, 2007             3,739,203             7,032,058                     0
January 2, 2008             3,739,203             4,993,949                     0
January 2, 2009             3,739,203               636,279             2,360,008
January 2, 2010             3,739,203                     0             3,129,380
January 2, 2011             3,739,203             3,550,493                     0
January 2, 2012             3,739,203             4,311,527                     0
January 2, 2013             3,739,203             4,480,179                     0
January 2, 2014             3,739,203             5,495,282                     0
January 2, 2015             3,739,203             4,813,484                     0
January 2, 2016             3,739,203               100,000                     0
January 2, 2017             3,739,203                     0                     0
January 2, 2018            21,177,982                     0                     0
July 2, 2018               20,473,746                     0                     0
January 2, 2019            19,321,921                     0                     0
January 2, 2020               100,000                     0                     0
</TABLE>



<PAGE>   26

                                   ANNEX A to
                            Note Purchase Agreement

                                   DEFINITIONS

         "Act" means 49 U.S.C. Section 40101-46507.

         "Adjusted Treasury Yield" means the Treasury Yield plus, in the case of
a distribution to holders of (i) Class A Certificates, 195 basis points, (ii)
Class B Certificates, 230 basis points and, (iii) Class C Certificates, 310
basis points.

         "Affiliate" means, with respect to any person, any other person
directly or indirectly controlling, controlled by or under common control with
such person. For purposes of this definition, "control" means the power,
directly or indirectly, to direct or cause the direction of the management and
policies of such person, whether through the ownership of voting securities or
by contract or otherwise and "controlling," "controlled by" and "under common
control with" have correlative meanings.

         "Aircraft" has the meaning set forth in the second recital to the Note
Purchase Agreement.

         "Aircraft Purchase Agreement Assignment" means a Purchase Agreement and
Engine Warranties Assignment substantially in the form of Exhibit A-4 to the
Note Purchase Agreement.

         "Assumed Amortization Schedule" means Schedule VII to the Note Purchase
Agreement.

         "Average Life Date" means, for any Equipment Note, the date which
follows the time of determination by a period equal to the Remaining Weighted
Average Life of such Equipment Note.

         "Bankruptcy Code" means the United States Bankruptcy Code, 11 U.S.C.
Section 102 et seq.

         "Basic Pass Through Trust Agreement" means the Pass Through Trust
Agreement dated as of January 28, 2000 between the Company and the Pass Through
Trustee, as such agreement may be supplemented, amended or modified, but does
not include any Trust Supplement.

         "Business Day" means any day, other than a Saturday, Sunday or other
day on which commercial banks are authorized or required by law to close in New
York, New York, Denver, Colorado, Wilmington, Delaware or Salt Lake City, Utah.

         "Certificateholder" means the Person in whose name a Certificate is
registered in the Register.

         "Certificates" has the meaning set forth in the third recital to the
Note Purchase Agreement.



<PAGE>   27

         "Class" means the class of Certificates issued by each Pass Through
Trust.

         "Class A Pass Through Trust" means the Atlas Air Pass Through Trust,
2000-1A.

         "Class B Pass Through Trust" means the Atlas Air Pass Through Trust,
2000-1B.

         "Class C Pass Through Trust" means the Atlas Air Pass Through Trust,
2000-1C.

         "Company" means Atlas Air, Inc., a Delaware corporation.

         "Corporate Trust Office" with respect to any Pass Through Trustee or
any Loan Trustee, means the office of such trustee in the city at which at any
particular time its corporate trust business shall be principally administered.

         "Cut-Off Date" means the earlier of (a) the day after the Delivery
Period Termination Date and (b) the date on which a Triggering Event occurs.

         "DCR" means Duff & Phelps Credit Rating Co.

         "Delivery Date" means the Business Day on which an Aircraft is
delivered to and accepted by the Company.

         "Delivery Period Termination Date" means December 31, 2000, provided
that, if a labor strike occurs at the Manufacturer on or prior to such date,
such date shall be extended by adding thereto the number of days that such
strike continued in effect.

         "Deposit Agreements" has the meaning set forth in the fifth recital to
the Note Purchase Agreement.

         "Deposit Make-Whole Premium" means, with respect to the distribution of
unused Deposits to holders of any Class of Certificates, as of any date of
determination, an amount equal to the excess, if any, of (a) the present value
of the excess of (i) the scheduled payment of principal and interest to maturity
of the related series of Equipment Notes, assuming the maximum principal amount
thereof (the "Maximum Amount") minus the sum of (x) such Class of Certificates'
proportionate share (in the same proportion that the amount of unused Deposit
with respect to such Class of Certificates bears to the unused Deposits with
respect to all Classes of Certificates, disregarding for this purpose unused
Deposits attributable to any Non- Delivery Redemption Amount) of the Par
Redemption Amount and (y) the portion of the Non-Delivery Redemption Amount
attributable to such Class, were issued, on each remaining Regular Distribution
Date for such Class under the Assumed Amortization Schedule over (ii) the
scheduled payment of principal and interest to maturity of the Equipment Notes
actually acquired by the Pass Through Trustee for such Class on each such
Regular Distribution Date, such present value computed by discounting such
excess on a semiannual basis on each Regular Distribution Date (assuming a
360-day year of twelve 30-day months) using a discount rate equal to the



<PAGE>   28

Adjusted Treasury Yield over (b) the amount of such unused Deposits to be (and
that have been) distributed to the holders of such Certificates minus the sum of
(x) such Class of Certificates' proportionate share of the Par Redemption Amount
and (y) the portion of the Non-Delivery Redemption Amount attributable to such
Class, plus accrued and unpaid interest on such net amount to but excluding such
date of determination from and including the preceding Regular Distribution Date
(or if such date of determination precedes the first Regular Distribution Date,
the Issuance Date).

         "Depositary" means Westdeutsche Landesbank Girozentrale, a German
banking institution organized under the law of the State of North
Rhine-Westphalia, acting through its New York Branch.

         "Deposits" has the meaning set forth in the fifth recital to the Note
Purchase Agreement.

         "Equipment Notes" means and includes any equipment notes issued under
any Indenture in the form specified in Section 2.01 thereof (as such form may be
varied pursuant to the terms of such Indenture) and any Equipment Note issued
under any Indenture in exchange for or replacement of any other Equipment Note.

         "Escrow Agent" has the meaning set forth in the first paragraph of the
Note Purchase Agreement.

         "Escrow Agreements" has the meaning set forth in the fifth recital to
the Note Purchase Agreement.

         "FAA" means the Federal Aviation Administration of the United States.

         "Final Withdrawal" with respect to each Escrow Agreement, has the
meaning set forth in Section 1.02 thereof.

         "Financing Agreements" means, collectively, the Lease Financing
Agreements and the Owner Financing Agreements.

         "Funding Date" has the meaning set forth in the Section 1(b) of the
Note Purchase Agreement.

         "Government Entity" means (a) any federal, state, provincial or similar
government, and any body, board, department, commission, court, tribunal,
authority, agency or other instrumentality of any such government or otherwise
exercising any executive, legislative, judicial, administrative or regulatory
functions of such government or (b) any other government entity having
jurisdiction over any matter contemplated by the Operative Agreements or
relating to the observance or performance of the obligations of any of the
parties to the Operative Agreements.

         "Guarantee Agreement" has the meaning set forth in the Intercreditor
Agreement.



<PAGE>   29

         "Guarantor" has the meaning set forth in the Intercreditor Agreement.

         "H.15(519)" means the weekly statistical release designated as such, or
any successor publication, published by the Board of Governors of the Federal
Reserve System.

         "Indentures" means, collectively, the Leased Aircraft Indentures and
the Owned Aircraft Indentures.

         "Intercreditor Agreement" has the meaning set forth in the ninth
recital to the Note Purchase Agreement.

         "Issuance Date" means the date of the original issuance of the
Certificates.

         "Law" means (a) any constitution, treaty, statute, law, decree,
regulation, order, rule or directive of any Government Entity, and (b) any
judicial or administrative interpretation or application of, or decision under,
any of the foregoing.

         "Lease" means a Lease Agreement substantially in the form of Exhibit
A-2 to the Note Purchase Agreement.

         "Lease Financing Agreements" means, collectively, the Aircraft Purchase
Agreement Assignment, the Leased Aircraft Participation Agreement, the Lease,
the Leased Aircraft Indenture, the Equipment Notes issued thereunder and the
Trust Agreement relating to the financing of a Leased Aircraft.

         "Leased Aircraft" means an Aircraft subject to a Lease.

         "Leased Aircraft Indenture" means a Trust Indenture and Mortgage
substantially in the form of Exhibit A-3 to the Note Purchase Agreement.

         "Leased Aircraft Participation Agreement" means a Participation
Agreement substantially in the form of Exhibit A-1 to the Note Purchase
Agreement.

         "Liquidity Facilities" has the meaning set forth in the ninth recital
to the Note Purchase Agreement.

         "Liquidity Providers" has the meaning set forth in the ninth recital to
the Note Purchase Agreement.

         "Loan Trustee" means the "Mortgagee" as defined in the Financing
Agreements.

         "Mandatory Document Terms" means the terms set forth on Schedule V to
the Note Purchase Agreement.



<PAGE>   30

         "Mandatory Economic Terms" means the terms set forth on Schedule VI to
the Note Purchase Agreement.

         "Manufacturer" means The Boeing Company, a Delaware corporation, solely
in its capacity as manufacturer of seller of the Aircraft.

         "Non-Delivery Redemption Amount" means the aggregate amount of Deposits
relating to Aircraft that are or will not be delivered by the Manufacturer prior
to the Delivery Period Termination Date due to any reason not occasioned by the
Company's fault or negligence.

         "Note Purchase Agreement" means the Note Purchase Agreement to which
this Annex A is attached.

         "Notice of Purchase Withdrawal" with respect to each Deposit Agreement,
has the meaning set forth in Section 2.3 thereof.

         "Offering Memorandum" means the Offering Memorandum dated January 20,
2000 relating to the Certificates.

         "Operative Agreements" means, collectively, the Pass Through Trust
Agreements, the Escrow Agreements, the Deposit Agreements, the Liquidity
Facilities, the Guarantee Agreements, the Intercreditor Agreement, the Trust
Agreements, the Equipment Notes, the Certificates and the Financing Agreements.

         "Owned Aircraft" means an Aircraft subject to an Owned Aircraft
Indenture.

         "Owned Aircraft Indenture" means a Trust Indenture and Mortgage
substantially in the form of Exhibit C-2 to the Note Purchase Agreement.

         "Owned Aircraft Participation Agreement" means a Participation
Agreement substantially in the form of Exhibit C-1 to the Note Purchase
Agreement.

         "Owner Financing Agreements" means, collectively, the Owned Aircraft
Participation Agreement, the Owned Aircraft Indenture and the Equipment Notes
issued thereunder.

         "Owner Participant" means, with respect to any Leased Aircraft, the
Person named as the Owner Participant in the Participation Agreement with
respect to such Leased Aircraft.

         "Owner Trust" means with respect to any Leased Aircraft, the trust
created by the "Trust Agreement" referred to in the Leased Aircraft Indenture
related thereto.

         "Owner Trustee" means with respect to any Leased Aircraft, the "Owner
Trustee" party to the "Trust Agreement" referred to in the Leased Aircraft
Indenture related thereto.

         "Par Redemption Amount" means $5 million.



<PAGE>   31

         "Participation Agreements" means, collectively, the Leased Aircraft
Participation Agreements and the Owned Aircraft Participation Agreements.

         "Pass Through Trust" has the meaning set forth in the third recital to
the Note Purchase Agreement.

         "Pass Through Trust Agreement" means each of the four separate Trust
Supplements, together in each case with the Basic Pass Through Trust Agreement,
each dated as of the Issuance Date, by and between the Company and the Pass
Through Trustee.

         "Pass Through Trustee" has the meaning set forth in the first paragraph
of the Note Purchase Agreement.

         "Paying Agent" has the meaning set forth in the first paragraph of the
Note Purchase Agreement.

         "Person" means any individual, firm, partnership, joint venture, trust,
trustee, Government Entity, organization, association, corporation, government
agency, committee, department, authority and other body, corporate or
incorporate, whether having distinct legal status or not, or any member of any
of the same.

         "Purchase Agreement" means the Purchase Agreement dated June 9, 1997
between the Company and the Manufacturer (including all exhibits thereto,
together with all letter agreements entered into that by their terms constitute
part of any such Purchase Agreement).

         "Qualified Owner Participant" means any bank, trust company, insurance
company, financial institution or corporation (other than, without the Company's
consent, a commercial air carrier, a commercial aircraft operator, a freight
forwarder or Affiliate of any of the foregoing), in each case with a combined
capital and surplus or net worth of at least $50,000,000.

         "Rating Agencies" means Moody's Investors Service, Inc. and Standard &
Poor's Ratings Services, a division of The McGraw-Hill Companies, Inc.

         "Rating Agency Confirmation" means, with respect to any Financing
Agreement that has been modified in any material respect from the forms thereof
attached to the Note Purchase Agreement (other than modifications affecting only
the Owner Participant) or with respect to Substitute Aircraft, a written
confirmation from each Rating Agency that the use of such Financing Agreement
with such modifications or the substituting of such Substitute Aircraft for an
Aircraft, whichever of the foregoing shall in a particular case require
confirmation from such rating agencies, would not result in (i) a reduction of
the rating for any Class of Certificates below the then current rating for such
Class of Certificates or (ii) a withdrawal or suspension of the rating of any
Class of Certificates.



<PAGE>   32

         "Register" means the register maintained pursuant to Sections 3.04 and
7.12 of the Basic Pass Through Trust Agreement with respect to each Pass Through
Trust.

         "Regular Distribution Dates" shall mean January 2 and July 2 of each
year, commencing July 2, 2000.

         "Remaining Weighted Average Life" means, on a given date with respect
to any Equipment Note, the number of days equal to the quotient obtained by
dividing (a) the sum of each of the products obtained by multiplying (i) the
amount of each then remaining scheduled payment of principal of such Equipment
Note by (ii) the number of days from and including such determination date to
but excluding the date on which such payment of principal is scheduled to be
made, by (b) the then outstanding principal amount of such Equipment Note.

         "Section 1110" means 11 U.S.C. Section 1110 of the Bankruptcy Code or
any successor or analogous Section of the federal bankruptcy Law in effect from
time to time.

         "Series A Equipment Notes" means Equipment Notes issued under an
Indenture and designated as "Series A" thereunder.

         "Series B Equipment Notes" means Equipment Notes issued under an
Indenture and designated as "Series B" thereunder.

         "Series C Equipment Notes" means Equipment Notes issued under an
Indenture and designated as "Series C" thereunder.

         "Series D Equipment Notes" means Equipment Notes issued under an Owned
Aircraft Indenture and designated as "Series D" thereunder.

         "Subordination Agent" has the meaning set forth in the first paragraph
of the Note Purchase Agreement.

         "Substitute Aircraft" has the meaning set forth in Section 1(f) of the
Note Purchase Agreement.

         "Taxes" means all license, recording, documentary, registration and
other similar fees and all taxes, levies, imposts, duties, charges, assessments
or withholdings of any nature whatsoever imposed by any Taxing Authority,
together with any penalties, additions to tax, fines or interest thereon or
additions thereto.

         "Taxing Authority" means any federal, state or local government or
other taxing authority in the United States, any foreign government or any
political subdivision or taxing authority thereof, any international taxing
authority or any territory or possession of the United States or any taxing
authority thereof.



<PAGE>   33

         "Treasury Yield" means, at the date of determination, with respect to
any Equipment Note, the interest rate (expressed as a decimal and, in the case
of United States Treasury bills, converted to a bond equivalent yield)
determined to be the per annum rate equal to the semi-annual yield to maturity
for United States Treasury securities maturing on the Average Life Date of such
Equipment Note and trading in the public securities markets either as determined
by interpolation between the most recent weekly average yield to maturity for
two series of United States Treasury securities trading in the public securities
markets, (A) one maturing as close as possible to, but earlier than, the Average
Life Date of such Equipment Note and (B) the other maturing as close as possible
to, but later than, the Average Life Date of such Equipment Note, in each case
as published in the most recent H.15(519) or, if a weekly average yield to
maturity for United States Treasury securities maturing on the Average Life Date
of such Equipment Note is reported on the most recent H.15(519), such weekly
average yield to maturity as published in such H.15(519).

         "Triggering Event" has the meaning assigned to such term in the
Intercreditor Agreement.

         "Trust Agreement" means a Trust Agreement substantially in the form of
Exhibit A-5 to the Note Purchase Agreement.

         "Trust Supplement" means an agreement supplemental to the Basic Pass
Through Trust Agreement pursuant to which (i) a separate trust is created for
the benefit of the holders of the Pass Through Certificates of a class, (ii) the
issuance of the Pass Through Certificates of such class representing fractional
undivided interests in such trust is authorized and (iii) the terms of the Pass
Through Certificates of such class are established.

         "WTC" has the meaning set forth in the first paragraph of the Note
Purchase Agreement.



<PAGE>   34

                                 EXHIBIT A-1 to
                             Note Purchase Agreement

                 FORM OF LEASED AIRCRAFT PARTICIPATION AGREEMENT



<PAGE>   35

                                 EXHIBIT A-2 to
                             Note Purchase Agreement

                                  FORM OF LEASE



<PAGE>   36

                                 EXHIBIT A-3 to
                             Note Purchase Agreement

                        FORM OF LEASED AIRCRAFT INDENTURE



<PAGE>   37

                                 EXHIBIT A-4 to
                             Note Purchase Agreement

                 FORM OF AIRCRAFT PURCHASE AGREEMENT ASSIGNMENT



<PAGE>   38

                                 EXHIBIT A-5 to
                             Note Purchase Agreement

                     FORM OF LEASED AIRCRAFT TRUST AGREEMENT



<PAGE>   39

                                  EXHIBIT B to
                             Note Purchase Agreement

                             FORM OF DELIVERY NOTICE

[DATE]
Wilmington Trust Company
One Rodney Square
1100 North Market Street
Wilmington, Delaware 19890-0001
Attention: Corporate Trust Administration

First Security Bank, National Association
79 South Main Street
Salt Lake City, Utah 84111
Attention: Corporate Trust Department

Moody's Investors Service, Inc.
99 Church Street
New York, N.Y. 10007
Attention:

Standard & Poor's Ratings Services
55 Water Street
New York, N.Y. 10041
Attention:

Duff & Phelps Credit Rating Co.
17 State Street, 12th Floor
New York, NY 10004
Attention:

Re: Atlas Air, Inc.

Gentlemen:

         Reference is made to the Note Purchase Agreement dated as of January
28, 2000 (the "Note Purchase Agreement") among Atlas Air, Inc. ("Atlas"),
Wilmington Trust Company, as Pass Through Trustee under each of the Pass Through
Trust Agreements, as Subordination Agent and as Paying Agent, and First Security
Bank, National Association, as Escrow Agent.

         In accordance with Section 1(b) of the Note Purchase Agreement, the
undersigned hereby notifies you as follows:

         (i) Delivery of an Aircraft, and the consummation of the financing
         therefor, will take place on _________, which is a Business Day before
         the Cut-off Date.



<PAGE>   40

         (ii) Atlas will treat the Aircraft as a [Leased] [Owned] Aircraft.

         (iii) [The Owner Participant (a) is not an Affiliate of the Company and
         (b) based on the representations of the Owner Participant, is a
         Qualified Owner Participant or is a person the obligations of which
         under the Owner Participant Agreements are guaranteed by a Qualified
         Owner Participant].(1)

         (iv) The aggregate principal amount of Series A Equipment Notes to be
         issued and purchased by the Pass Through Trustee is $[_______].

         (v) The aggregate principal amount of Series B Equipment Notes to be
         issued and purchased by the Pass Through Trustee is $[_______].

         (vi) The aggregate amount of Series C Equipment Notes to be issued and
         purchased by the Pass Though Trustee is $[_______].

         The undersigned hereby directs the Pass Through Trustee to (a) instruct
the Escrow Agent to provide Notices of Purchase Withdrawal to the Depositary in
respect of the Equipment Notes to be issued as specified above and (b) enter
into the Participation Agreement included in the Financing Agreements with
respect to the Aircraft on the date specified in clause (i) above and to perform
its obligations thereunder.

                                       ATLAS AIR, INC.


                                       By:
                                          --------------------------------------
                                          Title:

--------
(1) Include for Leased Aircraft only



<PAGE>   41

                                 EXHIBIT C-1 to
                             Note Purchase Agreement

                 FORM OF OWNED AIRCRAFT PARTICIPATION AGREEMENT



<PAGE>   42

                                 EXHIBIT C-2 to
                             Note Purchase Agreement

                        FORM OF OWNED AIRCRAFT INDENTURE