<PAGE>   1
                                                                    EXHIBIT 4.13



                        ESCROW AND PAYING AGENT AGREEMENT
                                    (Class C)

                          Dated as of January 28, 2000

                                      among

                    FIRST SECURITY BANK, NATIONAL ASSOCIATION

                                 as Escrow Agent

                        MORGAN STANLEY & CO. INCORPORATED
                          DEUTSCHE BANK SECURITIES INC.
                            SALOMON SMITH BARNEY INC.

                               as Placement Agents

                            WILMINGTON TRUST COMPANY
                         not in its individual capacity,
                       but solely as Pass Through Trustee
                              for and on behalf of
                      Atlas Air Pass Through Trust 2000-1C

                             as Pass Through Trustee

                                       and

                            WILMINGTON TRUST COMPANY

                                 as Paying Agent



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                                TABLE OF CONTENTS

<TABLE>
<CAPTION>
                                                                                  Page
                                                                                  ----
<S>                                                                             <C>
SECTION 1.    Escrow Agent                                                           2

Section 1.01. Appointment of Escrow Agent                                            2

Section 1.02. Instruction; Etc.                                                      3

Section 1.03. Initial Escrow Amount; Issuance of Escrow Receipts                     4

Section 1.04. Payments to Receiptholders                                             4

Section 1.05. Mutilated, Destroyed, Lost or Stolen Escrow Receipt                    4

Section 1.06. Additional Escrow Amounts                                              5

Section 1.07. Resignation or Removal of Escrow Agent                                 5

Section 1.08. Persons Deemed Owners                                                  6

Section 1.09. Further Assurances                                                     6

SECTION 2.    Paying Agent                                                           6

Section 2.01. Appointment of Paying Agent                                            6

Section 2.02. Establishment of Paying Agent Account                                  6

Section 2.03. Payments from Paying Agent Account                                     7

Section 2.04. Withholding Taxes                                                      8

Section 2.05. Resignation or Removal of Paying Agent                                 8

Section 2.06. Notice of Prepayment Withdrawal and Final Withdrawal                   9

SECTION 3.    Payments                                                               9

SECTION 4.    Other Actions                                                         10

SECTION 5.    Representations and Warranties of the Escrow Agent                    10

SECTION 6.    Representations and Warranties of the Paying Agent                    11
</TABLE>


<PAGE>   3

<TABLE>
<CAPTION>
                                                                                  Page
                                                                                  ----
<S>                                                                             <C>
SECTION 7.  Indemnification                                                         12

SECTION 8.  Amendment, Etc.                                                         12

SECTION 9.  Notices                                                                 13

SECTION 10. Transfer                                                                14

SECTION 11. Entire Agreement                                                        14

SECTION 12. Governing Law                                                           14

SECTION 13. Waiver of Jury Trial Right                                              14

SECTION 14. Counterparts                                                            15

Exhibit A   Escrow Receipt

Exhibit B   Withdrawal Certificate

Exhibit C   Prepayment Withdrawal Certificate
</TABLE>


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                  ESCROW AND PAYING AGENT AGREEMENT (Class C) dated as of
January 28, 2000 (as amended, modified or supplemented from time to time, this
"Agreement") among 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"); MORGAN STANLEY & CO. INCORPORATED, DEUTSCHE
BANK SECURITIES INC. and SALOMON SMITH BARNEY INC., as Placement Agents of the
Certificates referred to below (the "Placement Agents" and together with their
respective transferees and assigns as registered owners of the Certificates, the
"Investors") under the Placement Agreement referred to below; WILMINGTON TRUST
COMPANY, a Delaware banking corporation, not in its individual capacity, but
solely as trustee (in such capacity, together with its successors in such
capacity, the "Pass Through Trustee") under the Pass Through Trust Agreement
referred to below; and WILMINGTON TRUST COMPANY, a Delaware banking corporation,
as paying agent hereunder (in such capacity, together with its successors in
such capacity, the "Paying Agent").

                               W I T N E S S E T H

                  WHEREAS, Atlas Air, Inc. ("Atlas") and the Pass Through
Trustee have entered into a Trust Supplement dated the date hereof to the Pass
Through Trust Agreement, dated as of January 28, 2000 (together, as amended,
modified or supplemented from time to time in accordance with the terms thereof,
the "Pass Through Trust Agreement") relating to Atlas Air Pass Through Trust
2000-1C (the "Pass Through Trust") pursuant to which the Atlas Air Pass Through
Trust, Series 2000-1C Certificates referred to therein (the "Certificates") are
being issued;

                  WHEREAS, Atlas and the Placement Agents have entered into a
Placement Agreement dated as of January 20, 2000 (as amended, modified or
supplemented from time to time in accordance with the terms thereof, the
"Placement Agreement") pursuant to which the Pass Through Trustee will issue and
sell the Certificates to the Placement Agents;

                  WHEREAS, Atlas, the Pass Through Trustee, certain other pass
through trustees and certain other persons concurrently herewith are entering
into the Note Purchase Agreement, dated as of the date hereof (the "Note
Purchase Agreement"), pursuant to which the Pass Through Trustee has agreed to
acquire from time to time on or prior to the Cut-Off Date (as defined in the
Note Purchase Agreement) equipment notes (the "Equipment Notes") issued to
finance the acquisition of aircraft by Atlas, as lessee or as owner, utilizing a
portion of the proceeds from the sale of the Certificates (the "Net Proceeds");

                  WHEREAS, the Placement Agents and the Pass Through Trustee
intend that the Net Proceeds be held in escrow by the Escrow Agent on behalf of
the Investors, subject to withdrawal upon request by the Pass Through Trustee
and satisfaction of the conditions set forth in the Note Purchase Agreement for
the purpose of purchasing Equipment Notes, and that pending such withdrawal the
Net Proceeds be deposited on behalf of the Escrow Agent with Westdeutsche
Landesbank Girozentrale, acting through its New York Branch, as Depositary (the
"Depositary") under the Deposit Agreement, dated as of the date hereof between
the Depositary

<PAGE>   5

and the Escrow Agent relating to the Pass Through Trust (as amended, modified or
supplemented from time to time in accordance with the terms thereof, the
"Deposit Agreement"), pursuant to which, among other things, the Depositary will
pay interest for distribution to the Investors and establish accounts from which
the Escrow Agent shall make withdrawals upon request of and proper certification
by the Pass Through Trustee;

                  WHEREAS, the Escrow Agent wishes to appoint the Paying Agent
to pay amounts required to be distributed to the Investors in accordance with
this Agreement; and

                  WHEREAS, capitalized terms used but not defined herein shall
have the meanings ascribed to such terms in the Pass Through Trust Agreement.

                  NOW, THEREFORE, in consideration of the obligations contained
herein, and for other good and valuable consideration, the receipt and
sufficiency of which is hereby acknowledged, the parties hereto hereby agree as
follows:

                  SECTION 1. Escrow Agent.

                  Section 1.01. Appointment of Escrow Agent. Each of the
Placement Agents, for and on behalf of each of the Investors, hereby irrevocably
appoints, authorizes and directs the Escrow Agent to act as escrow agent and
fiduciary hereunder and under the Deposit Agreement for such specific purposes
and with such powers as are specifically delegated to the Escrow Agent by the
terms of this Agreement, together with such other powers as are reasonably
incidental thereto. Any and all money received and held by the Escrow Agent
under this Agreement or the Deposit Agreement shall be held in escrow by the
Escrow Agent in accordance with the terms of this Agreement. This Agreement is
irrevocable and the Investors' rights with respect to any monies received and
held in escrow by the Escrow Agent under this Agreement or the Deposit Agreement
shall only be as provided under the terms and conditions of this Agreement and
the Deposit Agreement. The Escrow Agent (which term as used in this sentence
shall include reference to its affiliates and its own and its affiliates'
officers, directors, employees and agents): (a) shall have no duties or
responsibilities except those expressly set forth in this Agreement; (b) shall
not be responsible to the Pass Through Trustee or the Investors for any
recitals, statements, representations or warranties of any person other then
itself contained in this Agreement or the Deposit Agreement or for the failure
by the Pass Through Trustee, the Investors or any other person or entity (other
than the Escrow Agent) to perform any of its obligations hereunder (whether or
not the Escrow Agent shall have any knowledge thereof); and (c) shall not be
responsible for any action taken or omitted to be taken by it hereunder or
provided for herein or in connection herewith, except for its own willful
misconduct or gross negligence (or simple negligence in connection with the
handling of funds).

                  Section 1.02. Instruction; Etc. The Placement Agents, for and
on behalf of each of the Investors, hereby irrevocably instruct the Escrow
Agent, and the Escrow Agent agrees, (a) to enter into the Deposit Agreement, (b)
to appoint the Paying Agent as provided in this Agreement, (c) upon receipt at
any time and from time to time prior to the Delivery Period Termination Date (as
defined in the Note Purchase Agreement) of a certificate substantially in

<PAGE>   6


the form of Exhibit B hereto (a "Withdrawal Certificate") executed by the Pass
Through Trustee, together with an attached Notice of Purchase Withdrawal in
substantially the form of Exhibit A to the Deposit Agreement duly completed by
the Pass Through Trustee (the "Applicable Notice of Purchase Withdrawal" and the
withdrawal to which it relates, a "Purchase Withdrawal"), immediately to execute
the Applicable Notice of Purchase Withdrawal as Escrow Agent and transmit it to
the Depositary by facsimile transmission in accordance with the Deposit
Agreement; provided that, upon the request of the Pass Through Trustee after
such transmission, the Escrow Agent shall cancel such Applicable Notice of
Purchase Withdrawal, (d) upon receipt at any time and from time to time prior to
the Delivery Period Termination Date of a certificate substantially in the form
of Exhibit C hereto (a "Prepayment Withdrawal Certificate") executed by the Pass
Through Trustee, together with an attached Notice of Prepayment Withdrawal in
substantially the form of Exhibit B to the Deposit Agreement duly completed by
the Pass Through Trustee (the "Applicable Notice of Prepayment Withdrawal" and
the withdrawal to which it relates, a "Prepayment Withdrawal"), immediately to
execute the Applicable Notice of Prepayment Withdrawal as Escrow Agent and
transmit it to the Depositary by facsimile transmission in accordance with the
Deposit Agreement; provided that, upon the request of the Pass Through Trustee
after such transmission, the Escrow Agent shall cancel such Applicable Notice of
Prepayment Withdrawal, and (e) if there are any undrawn amounts in the Account
(as defined in the Deposit Agreement) on the earlier of (i) the Delivery Period
Termination Date and (ii) the date on which the Escrow Agent receives notice
from the Pass Through Trustee that the Pass Through Trustee's obligation to
purchase Equipment Notes under the Note Purchase Agreement has terminated, to
give notice to the Depositary (with a copy to the Paying Agent) substantially in
the form of Exhibit C to the Deposit Agreement requesting a withdrawal of all of
the remaining amount of the Deposit (as defined in the Deposit Agreement),
together with accrued and unpaid interest on the Deposit to the date of
withdrawal, on the 15th day after the date that such notice of withdrawal is
given to the Depositary (or, if not a Business Day, on the next succeeding
Business Day) (a "Final Withdrawal"), provided that if the day scheduled for the
Final Withdrawal in accordance with the foregoing is within 10 days before a
Regular Distribution Date, then the Escrow Agent shall request that such
requested Final Withdrawal be made on such Regular Distribution Date (the date
of such requested withdrawal, the "Final Withdrawal Date"). If for any reason
the Escrow Agent shall have failed to give the Final Withdrawal Notice to the
Depositary on or before December 31, 2000 (provided, that if a labor strike or
work stoppage occurs at The Boeing Company prior to such date, such date shall
be extended by adding thereto the number of days that each such labor strike or
work stoppage continues in effect), and there are unwithdrawn amounts in the
Account (as defined in the Deposit Agreement) on such date, the Final Withdrawal
Date shall be deemed to be January 16, 2001 (or, if the December 31, 2000 date
has been extended as provided in this sentence, the fifteenth day after the
Delivery Period Termination Date).

                  Section 1.03. Initial Escrow Amount; Issuance of Escrow
Receipts. The Escrow Agent hereby directs the Placement Agents to, and the
Placement Agents hereby acknowledge that on the date hereof they shall,
irrevocably deliver to the Depositary on behalf of the Escrow Agent, an amount
in U.S. dollars ("Dollars") and immediately available funds equal to $47,937,000
for deposit on behalf of the Escrow Agent with the Depositary in accordance with
Section 2.1 of the Deposit Agreement. The Placement Agents hereby instruct the
Escrow Agent,

<PAGE>   7


upon receipt of such sum from the Placement Agents, to confirm such receipt by
executing and delivering to the Pass Through Trustee an Escrow Receipt in the
form of Exhibit A hereto (an "Escrow Receipt"), (a) to be affixed by the Pass
Through Trustee to each Certificate and (b) to evidence the same percentage
interest (the "Escrow Interest") in the Account Amounts (as defined below) as
the Fractional Undivided Interest in the Pass Through Trust evidenced by the
Certificate to which it is to be affixed. The Escrow Agent shall provide to the
Pass Through Trustee for attachment to each Certificate newly issued under and
in accordance with the Pass Through Trust Agreement an executed Escrow Receipt
as the Pass Through Trustee may from time to time request of the Escrow Agent.
Each Escrow Receipt shall be registered by the Escrow Agent in a register (the
"Register") maintained by the Escrow Agent in the same name and same manner as
the Certificate to which it is attached and may not thereafter be detached from
such Certificate to which it is to be affixed prior to the distribution of the
Final Withdrawal (the "Final Distribution"). After the Final Distribution, no
additional Escrow Receipts shall be issued and the Pass Through Trustee shall
request the return to the Escrow Agent for cancellation of all outstanding
Escrow Receipts.

                  Section 1.04. Payments to Receiptholders. All payments and
distributions made to holders of an Escrow Receipt (collectively
"Receiptholders") in respect of the Escrow Receipt shall be made only from
amounts deposited in the Paying Agent Account (as defined below) ("Account
Amounts"). Each Receiptholder, by its acceptance of an Escrow Receipt, agrees
that (a) it will look solely to the Account Amounts for any payment or
distribution due to such Receiptholder pursuant to the terms of the Escrow
Receipt and this Agreement and (b) it will have no recourse to Atlas, the Pass
Through Trustee, the Paying Agent or the Escrow Agent, except as expressly
provided herein or in the Pass Through Trust Agreement. No Receiptholder shall
have any right to vote or in any manner otherwise control the operation and
management of the Paying Agent Account or the obligations of the parties hereto,
nor shall anything set forth herein, or contained in the terms of the Escrow
Receipt, be construed so as to constitute the Receiptholders from time to time
as partners or members of an association.

                  Section 1.05. Mutilated, Destroyed, Lost or Stolen Escrow
Receipt. If (a) any mutilated Escrow Receipt is surrendered to the Escrow Agent
or the Escrow Agent receives evidence to its satisfaction of the destruction,
loss or theft of any Escrow Receipt and (b) there is delivered to the Escrow
Agent and the Pass Through Trustee such security, indemnity or bond, as may be
required by them to hold each of them harmless, then, absent notice to the
Escrow Agent or the Pass Through Trustee that such destroyed, lost or stolen
Escrow Receipt has been acquired by a bona fide purchaser, and provided that the
requirements of Section 8-405 of the Uniform Commercial Code in effect in any
applicable jurisdiction are met, the Escrow Agent shall execute, authenticate
and deliver, in exchange for or in lieu of any such mutilated, destroyed, lost
or stolen Escrow Receipt, a new Escrow Receipt or Escrow Receipts and of like
Escrow Interest in the Account Amounts and bearing a number not
contemporaneously outstanding.

                  In connection with the issuance of any new Escrow Receipt
under this Section 1.05, the Escrow Agent may require the payment of a sum
sufficient to cover any tax or other governmental charge that may be imposed in
relation thereto and any other expenses (including the fees and expenses of the
Pass Through Trustee and the Escrow Agent) connected therewith.


<PAGE>   8

                  Any duplicate Escrow Receipt issued pursuant to this Section
1.05 shall constitute conclusive evidence of the appropriate Escrow Interest in
the Account Amounts, as if originally issued, whether or not the lost, stolen or
destroyed Escrow Receipt shall be found at any time.

                  The provisions of this Section are exclusive and shall
preclude (to the extent lawful) all other rights and remedies with respect to
the replacement or payment of mutilated, destroyed, lost or stolen Escrow
Receipts.

                  Section 1.06. Additional Escrow Amounts. On the date of any
Purchase Withdrawal, the Pass Through Trustee may re-deposit with the Depositary
some or all of the amounts so withdrawn in accordance with Section 2.4 of the
Deposit Agreement.

                  Section 1.07. Resignation or Removal of Escrow Agent. Subject
to the appointment and acceptance of a successor Escrow Agent as provided below,
the Escrow Agent may resign at any time by giving 30 days' prior written notice
thereof to the Investors, but may not otherwise be removed except for cause by
the written consent of the Investors with respect to Investors representing
Escrow Interests aggregating not less than a majority in interest in the Account
Amounts (an "Action of Investors"). Upon any such resignation or removal, the
Investors, by an Action of Investors, shall have the right to appoint a
successor Escrow Agent. If no successor Escrow Agent shall have been so
appointed and shall have accepted such appointment within 30 days after the
retiring Escrow Agent's giving of notice of resignation or the removal of the
retiring Escrow Agent, then the retiring Escrow Agent may appoint a successor
Escrow Agent. Any successor Escrow Agent shall be a bank which has an office in
the United States with a combined capital and surplus of at least $100,000,000.
Upon the acceptance of any appointment as Escrow Agent hereunder by a successor
Escrow Agent, such successor Escrow Agent shall enter into such documents as the
Pass Through Trustee shall require and shall thereupon succeed to and become
vested with all the rights, powers, privileges and duties of the retiring Escrow
Agent, and the retiring Escrow Agent shall be discharged from its duties and
obligations hereunder. No resignation or removal of the Escrow Agent shall be
effective unless a written confirmation shall have been obtained from each of
Moody's Investors Service, Inc. and Standard & Poor's Rating Group, a division
of McGraw-Hill Inc. that the replacement of the Escrow Agent with the successor
Escrow Agent will not result in (a) a reduction of the rating for the
Certificates below the then current rating for the Certificates or (b) a
withdrawal or suspension of the rating of the Certificates.

                  Section 1.08. Persons Deemed Owners. Prior to due presentment
of a Certificate for registration of transfer, the Escrow Agent and the Paying
Agent may treat the Person in whose name any Escrow Receipt is registered (as of
the day of determination) as the owner of such Escrow Receipt for the purpose of
receiving distributions pursuant to this Agreement and for all other purposes
whatsoever, and neither the Escrow Agent nor the Paying Agent shall be affected
by any notice to the contrary.

                  Section 1.09. Further Assurances. The Escrow Agent agrees to
take such actions, and execute such other documents, as may be reasonably
requested by the Pass Through

<PAGE>   9


Trustee in order to effectuate the purposes of this Agreement and the
performance by the Escrow Agent of its obligations hereunder.

                  SECTION 2. Paying Agent.

                  Section 2.01. Appointment of Paying Agent. The Escrow Agent
hereby irrevocably appoints and authorizes the Paying Agent to act as its paying
agent hereunder, for the benefit of the Investors, for such specific purposes
and with such powers as are specifically delegated to the Paying Agent by the
terms of this Agreement, together with such other powers as are reasonably
incidental thereto. Any and all money received and held by the Paying Agent
under this Agreement or the Deposit Agreement shall be held in the Paying Agent
Account for the benefit of the Investors. The Paying Agent (which term as used
in this sentence shall include reference to its affiliates and its own and its
affiliates' officers, directors, employees and agents): (a) shall have no duties
or responsibilities except those expressly set forth in this Agreement, and
shall not by reason of this Agreement be a trustee for the Escrow Agent; (b)
shall not be responsible to the Escrow Agent for any recitals, statements,
representations or warranties of any person other then itself contained in this
Agreement or for the failure by the Escrow Agent or any other person or entity
(other than the Paying Agent) to perform any of its obligations hereunder
(whether or not the Paying Agent shall have any knowledge thereof); and (c)
shall not be responsible for any action taken or omitted to be taken by it
hereunder or provided for herein or in connection herewith, except for its own
willful misconduct or gross negligence (or simple negligence in connection with
the handling of funds).

                  Section 2.02. Establishment of Paying Agent Account. The
Paying Agent shall establish a deposit account (the "Paying Agent Account") at
Wilmington Trust Company in the name of the Escrow Agent. It is expressly
understood by the parties hereto that the Paying Agent is acting as the paying
agent of the Escrow Agent hereunder and that no amounts on deposit in the Paying
Agent Account constitute part of the Trust Property.

                  Section 2.03. Payments from Paying Agent Account. The Escrow
Agent hereby irrevocably instructs the Paying Agent, and the Paying Agent agrees
to act, as follows:

                  (a) On each Interest Payment Date (as defined in the Deposit
         Agreement) or as soon thereafter as the Paying Agent has confirmed
         receipt in the Paying Agent Account from the Depositary of any amount
         in respect of accrued interest on the Deposit, the Paying Agent shall
         distribute out of the Paying Agent Account the entire amount deposited
         therein by the Depositary. There shall be so distributed to each
         Receiptholder of record on the 15th day (whether or not a Business Day)
         preceding such Interest Payment Date by check mailed to such
         Receiptholder, at the address appearing in the Register, such
         Receiptholder's pro rata share (based on the Escrow Interest in the
         Account Amounts held by such Receiptholder) of the total amount of
         interest deposited by the Depositary in the Paying Agent Account on
         such date, except that, with respect to Escrow Receipts registered on
         the record date in the name of a nominee of the Depository Trust
         Company ("DTC"), such distribution shall be made by wire transfer in
         immediately available funds to the account designated by DTC.


<PAGE>   10

                  (b) Upon the confirmation by the Paying Agent of receipt in
         the Paying Agent Account from the Depositary of any amount in respect
         of the Final Withdrawal, the Paying Agent shall forthwith distribute
         the entire amount of the Final Withdrawal deposited therein by the
         Depositary. There shall be so distributed to each Receiptholder of
         record on the 15th day (whether or not a Business Day) preceding the
         Final Withdrawal Date by check mailed to such Receiptholder, at the
         address appearing in the Register, such Receiptholder's pro rata share
         (based on the Escrow Interest in the Account Amounts held by such
         Receiptholder) of the total amount in the Paying Agent Account on
         account of such Final Withdrawal, except that, with respect to Escrow
         Receipts registered on the record date in the name of a nominee of DTC,
         such distribution shall be made by wire transfer in immediately
         available funds to the account designated by DTC.

                  (c) If any payment of interest or principal in respect of the
         Final Withdrawal is not received by the Paying Agent within five days
         of the applicable date when due, then it shall be distributed to
         Receiptholders after actual receipt by the Paying Agent on the same
         basis as a Special Payment is distributed under the Pass Through Trust
         Agreement.

                  (d) Upon the confirmation by the Paying Agent of receipt in
         the Paying Agent Account from the Depositary of any amount in respect
         of a Prepayment Withdrawal, the Paying Agent shall forthwith distribute
         the entire amount of such Prepayment Withdrawal upon not less than 15
         days prior notice to the Receiptholders. There shall be distributed to
         each Receiptholder of record on the 15th day (whether or not a Business
         Day) preceding such date of distribution by check mailed to such
         Receiptholder, at the address appearing in the Register, such
         Receiptholder's pro rata share (based on the Escrow Interest in the
         Account Amounts held by such Receiptholder) of the total amount in the
         Paying Agent Account on account of such Prepayment Withdrawal, except
         that, with respect to the Escrow Receipts registered on such record
         date in the name of a nominee of DTC, such distribution shall be made
         by wire transfer in immediately available funds to the account
         designated by DTC.

                  (e) The Paying Agent shall include with any check mailed
         pursuant to this Section any notice required to be distributed under
         the Pass Through Trust Agreement that is furnished to the Paying Agent
         by the Pass Through Trustee.

                  Section 2.04. Withholding Taxes. The Paying Agent shall
exclude and withhold from each distribution of accrued interest on the Deposit
(as defined in the Deposit Agreement) and any amount in respect of any
Prepayment Withdrawal and the Final Withdrawal any and all withholding taxes
applicable thereto as required by law. The Paying Agent agrees to act as such
withholding agent and, in connection therewith, whenever any present or future
taxes or similar charges are required to be withheld with respect to any amounts
payable in respect of the Deposit (as defined in the Deposit Agreement) or the
escrow amounts, to withhold such amounts and timely pay the same to the
appropriate authority in the name of and on behalf of the Receiptholders, that
it will file any necessary withholding tax returns or statements when due,

<PAGE>   11

and that, as promptly as possible after the payment thereof, it will deliver to
each such Receiptholder appropriate documentation showing the payment thereof,
together with such additional documentary evidence as such Receiptholder may
reasonably request from time to time. The Paying Agent agrees to file any other
information reports as it may be required to file under United States law.

                  Section 2.05. Resignation or Removal of Paying Agent. Subject
to the appointment and acceptance of a successor Paying Agent as provided below,
the Paying Agent may resign at any time by giving 30 days' prior written notice
thereof to the Escrow Agent, but may not otherwise be removed except for cause
by the Escrow Agent. Upon any such resignation or removal, the Escrow Agent
shall have the right to appoint a successor Paying Agent. If no successor Paying
Agent shall have been so appointed and shall have accepted such appointment
within 30 days after the retiring Paying Agent's giving of notice of resignation
or the removal of the retiring Paying Agent, then the retiring Paying Agent may
appoint a successor Paying Agent. Any Successor Paying Agent shall be a bank
which has an office in the United States with a combined capital and surplus of
at least $100,000,000. Upon the acceptance of any appointment as Paying Agent
hereunder by a successor Paying Agent, such successor Paying Agent shall enter
into such documents as the Escrow Agent shall require and shall thereupon
succeed to and become vested with all the rights, powers, privileges and duties
of the retiring Paying Agent, and the retiring Paying Agent shall be discharged
from its duties and obligations hereunder.

                  Section 2.06. Notice of Prepayment Withdrawal and Final
Withdrawal. Promptly after receipt by the Paying Agent of notice that the Escrow
Agent has requested a Prepayment Withdrawal or a Final Withdrawal or that a
Prepayment Withdrawal or a Final Withdrawal will be made, the Paying Agent shall
cause notice of such distribution to be mailed to each of the Receiptholders at
its address as it appears in the Register. Such notice shall be mailed not less
than 15 days prior to the distribution date of such Prepayment Withdrawal (the
"Prepayment Withdrawal Date") or of the Final Withdrawal Date, as the case may
be. Such notice shall set forth:

                  (i) the Prepayment Withdrawal or the Final Withdrawal Date, as
         the case may be, and the date for determining Receiptholders of record
         who shall be entitled to receive distributions in respect of the
         Prepayment Withdrawal or Final Withdrawal,

                  (ii) the amount of the payment in respect of the Prepayment
         Withdrawal or Final Withdrawal, as the case may be, for each $1,000
         face amount Certificate (based on information provided by the Pass
         Through Trustee) and the amount thereof constituting the unused portion
         of the Deposit (as defined in the Deposit Agreement) and interest
         thereon, and

                  (iii) if the Prepayment Withdrawal Date or Final Withdrawal
         Date is the same date as a Regular Distribution Date, the total amount
         to be received on such date for each $1,000 face amount Certificate
         (based on information provided by the Pass Through Trustee).


<PAGE>   12

                  Such mailing may include any notice required to be given to
Certificateholders in connection with such distribution pursuant to the Pass
Through Trust Agreement.

                  SECTION 3. Payments. If, notwithstanding the instructions in
Section 4 of the Deposit Agreement that all amounts payable to the Escrow Agent
under the Deposit Agreement be paid by the Depositary directly to the Paying
Agent or the Pass Through Trustee (depending on the circumstances), the Escrow
Agent receives any payment thereunder, then the Escrow Agent shall forthwith pay
such amount in Dollars and in immediately available funds by wire transfer to
(a) in the case of a payment of accrued interest on the Deposit (as defined in
the Deposit Agreement), any Prepayment Withdrawal or any Final Withdrawal,
directly to the Paying Agent Account and (b) in the case of any Purchase
Withdrawal, directly to the Pass Through Trustee or its designee as specified
and in the manner provided in the Applicable Notice of Purchase Withdrawal. The
Escrow Agent hereby waives any and all rights of set-off, combination of
accounts, right of retention or similar right (whether arising under applicable
law, contract or otherwise) it may have against amounts payable to the Paying
Agent howsoever arising.

                  SECTION 4. Other Actions. The Escrow Agent shall take such
other actions under or in respect of the Deposit Agreement (including, without
limitation, the enforcement of the obligations of the Depositary thereunder) as
the Investors, by an Action of Investors, may from time to time request.

                  SECTION 5. Representations and Warranties of the Escrow Agent.
The Escrow Agent represents and warrants to Atlas, the Investors, the Paying
Agent and the Pass Through Trustee as follows:

                  (i) it is a national banking association duly organized and
         validly existing in good standing under the laws of the United States
         of America;

                  (ii) it has full power, authority and legal right to conduct
         its business and operations as currently conducted and to enter into
         and perform its obligations under this Agreement and the Deposit
         Agreement;

                  (iii) the execution, delivery and performance of each of this
         Agreement and the Deposit Agreement have been duly authorized by all
         necessary corporate action on the part of it and do not require any
         stockholder approval, or approval or consent of any trustee or holder
         of any indebtedness or obligations of it, and each such document has
         been duly executed and delivered by it and constitutes its legal, valid
         and binding obligations enforceable against it in accordance with the
         terms hereof or thereof except as such enforceability may be limited by
         bankruptcy, insolvency, moratorium, reorganization or other similar
         laws or equitable principles of general application to or affecting the
         enforcement of creditors' rights generally (regardless of whether such
         enforceability is considered in a proceeding in equity or at law);


<PAGE>   13


                  (iv) no authorization, consent or approval of or other action
         by, and no notice to or filing with, any United States federal or state
         governmental authority or regulatory body governing its banking and
         fiduciary powers is required for the execution, delivery or performance
         by it of this Agreement or the Deposit Agreement;

                  (v) neither the execution, delivery or performance by it of
         this Agreement or the Deposit Agreement, nor compliance with the terms
         and provisions hereof or thereof, conflicts or will conflict with or
         results or will result in a breach or violation of any of the terms,
         conditions or provisions of, or will require any consent or approval
         under, any law, governmental rule or regulation or the charter
         documents, as amended, or bylaws, as amended, of it or any similar
         instrument binding on it or any order, writ, injunction or decree of
         any court or governmental authority against it or by which it or any of
         its properties is bound or any indenture, mortgage or contract or other
         agreement or instrument to which it is a party or by which it or any of
         its properties is bound, or constitutes or will constitute a default
         thereunder or results or will result in the imposition of any lien upon
         any of its properties; and

                  (vi) there are no pending or, to its knowledge, threatened
         actions, suits, investigations or proceedings (whether or not
         purportedly on behalf of it) against or affecting it or any of its
         property before or by any court or administrative agency which, if
         adversely determined, (A) would adversely affect the ability of it to
         perform its obligations under this Agreement or the Deposit Agreement
         or (B) would call into question or challenge the validity of this
         Agreement or the Deposit Agreement or the enforceability hereof or
         thereof in accordance with the terms hereof or thereof, nor is the
         Escrow Agent in default with respect to any order of any court,
         governmental authority, arbitration board or administrative agency so
         as to adversely affect its ability to perform its obligations under
         this Agreement or the Deposit Agreement.

                  SECTION 6. Representations and Warranties of the Paying Agent.
The Paying Agent represents and warrants to Atlas, the Investors, the Escrow
Agent and the Pass Through Trustee as follows:

                  (i) it is a Delaware banking company duly organized and
         validly existing in good standing under the laws of its jurisdiction of
         incorporation;

                  (ii) it has full power, authority and legal right to conduct
         its business and operations as currently conducted and to enter into
         and perform its obligations under this Agreement;

                  (iii) the execution, delivery and performance of this
         Agreement has been duly authorized by all necessary corporate action on
         the part of it and does

<PAGE>   14

         not require any stockholder approval, or approval or consent of any
         trustee or holder of any indebtedness or obligations of it, and such
         document has been duly executed and delivered by it and constitutes its
         legal, valid and binding obligations enforceable against it in
         accordance with the terms hereof except as such enforceability may be
         limited by bankruptcy, insolvency, moratorium, reorganization or other
         similar laws or equitable principles of general application to or
         affecting the enforcement of creditors' rights generally (regardless of
         whether such enforceability is considered in a proceeding in equity or
         at law);

                  (iv) no authorization, consent or approval of or other action
         by, and no notice to or filing with, any United States federal or state
         governmental authority or regulatory body is required for the
         execution, delivery or performance by it of this Agreement;

                  (v) neither the execution, delivery or performance by it of
         this Agreement, nor compliance with the terms and provisions hereof,
         conflicts or will conflict with or results or will result in a breach
         or violation of any of the terms, conditions or provisions of, or will
         require any consent or approval under, any law, governmental rule or
         regulation or the charter documents, as amended, or bylaws, as amended,
         of it or any similar instrument binding on it or any order, writ,
         injunction or decree of any court or governmental authority against it
         or by which it or any of its properties is bound or any indenture,
         mortgage or contract or other agreement or instrument to which it is a
         party or by which it or any of its properties is bound, or constitutes
         or will constitute a default thereunder or results or will result in
         the imposition of any lien upon any of its properties; and

                  (vi) there are no pending or, to its knowledge, threatened
         actions, suits, investigations or proceedings (whether or not
         purportedly on behalf of it) against or affecting it or any of its
         property before or by any court or administrative agency which, if
         adversely determined, (A) would adversely affect the ability of it to
         perform its obligations under this Agreement or (B) would call into
         question or challenge the validity of this Agreement or the
         enforceability hereof in accordance with the terms hereof, nor is the
         Paying Agent in default with respect to any order of any court,
         governmental authority, arbitration board or administrative agency so
         as to adversely affect its ability to perform its obligations under
         this Agreement.

                  SECTION 7. Indemnification. Except for actions expressly
required of the Escrow Agent or the Paying Agent hereunder, each of the Escrow
Agent and the Paying Agent shall in all cases be fully justified in failing or
refusing to act hereunder unless it shall have been indemnified by the party
requesting such action in a manner reasonably satisfactory to it against any and
all liability and expense which may be incurred by it by reason of taking or
continuing to take any such action. In the event Atlas requests any amendment to
any Operative Agreement (as defined in the Note Purchase Agreement), the Pass
Through Trustee agrees to pay all reasonable fees and expenses (including,
without limitation, fees and disbursements of counsel) of the Escrow Agent and
the Paying Agent in connection therewith.


<PAGE>   15

                  SECTION 8. Amendment, Etc. Upon request of the Pass Through
Trustee and approval by an Action of Investors, the Escrow Agent shall enter
into an amendment to this Agreement, so long as such amendment does not
adversely affect the rights or obligations of the Escrow Agent or the Paying
Agent, provided that upon request of the Pass Through Trustee and without any
consent of the Investors, the Escrow Agent shall enter into an amendment to this
Agreement for any of the following purposes:

                  (1) to correct or supplement any provision in this Agreement
         which may be defective or inconsistent with any other provision herein
         or to cure any ambiguity or correct any mistake or to modify any other
         provision with respect to matters or questions arising under this
         Agreement, provided that any such action shall not materially adversely
         affect the interests of the Investors; or

                  (2) to comply with any requirement of the SEC, applicable law,
         rules or regulations of any exchange or quotation system on which the
         Certificates are listed or any regulatory body; or

                  (3) to evidence and provide for the acceptance of appointment
         under this Agreement of a successor Escrow Agent, successor Paying
         Agent or successor Pass Through Trustee.

                  SECTION 9. Notices. Unless otherwise expressly provided
herein, any notice or other communication under this Agreement shall be in
writing (including by facsimile) and shall be deemed to be given and effective
upon receipt thereof. All notices shall be sent to

                  (i)      if to the Investors, as their respective names shall
                           appear in the Register;

                  (ii)     if to the Escrow Agent, addressed to at its office
                           at:

                           FIRST SECURITY BANK, NATIONAL ASSOCIATION
                           79 South Main Street
                           Salt Lake City, UT 84111

                           Attention:  Corporate Trust Department
                           Telecopier:  801-246-5053

                  (iii)    if to the Pass Through Trustee, addressed to it at
                           its office at:

                           WILMINGTON TRUST COMPANY
                           One Rodney Square
                           1100 N. Market Street
                           Wilmington, DE  19890-0001

                           Attention:  Corporate Trust Administration
                           Telecopier:  302-651-8882

<PAGE>   16


                  (iv)     if to the Paying Agent, addressed to it at its office
                           at:

                           WILMINGTON TRUST COMPANY
                           One Rodney Square
                           1100 N. Market Street
                           Wilmington, DE  19890-0001
                           Attention:  Corporate Trust Administration
                           Telecopier:  302-651-8882

                  (v)      in each case with a copy to Atlas, addressed to it at
                           its office at:

                           ATLAS AIR, INC.
                           538 Commons Drive
                           Golden, CO  80401

                           Attention:  Chief Financial Officer
                           Telecopier:  303-526-5051

(or at such other address as any such party may specify from time to time in a
written notice to the other parties). On or prior to the execution of this
Agreement, the Pass Through Trustee has delivered to the Escrow Agent a
certificate containing specimen signatures of the representatives of the Pass
Through Trustee who are authorized to give notices and instructions with respect
to this Agreement. The Escrow Agent may conclusively rely on such certificate
until the Escrow Agent receives written notice from the Pass Through Trustee to
the contrary.

                  SECTION 10. Transfer. No party hereto shall be entitled to
assign or otherwise transfer this Agreement (or any interest herein) other than
(in the case of the Escrow Agent) to a successor escrow agent under Section 1.07
hereof or (in the case of the Paying Agent) to a successor paying agent under
Section 2.05 hereof, and any purported assignment in violation thereof shall be
void. This Agreement shall be binding upon the parties hereto and their
respective successors and (in the case of the Escrow Agent and the Paying Agent)
their respective permitted assigns.

                  SECTION 11. Entire Agreement. This Agreement sets forth all of
the promises, covenants, agreements, conditions and understandings among the
Escrow Agent, the Paying Agent, the Placement Agents and the Pass Through
Trustee with respect to the subject matter hereof, and supersedes all prior and
contemporaneous agreements and undertakings, inducements or conditions, express
or implied, oral or written.

                  SECTION 12. Governing Law. This Agreement shall be governed
by, and construed in accordance with, the laws of the State of New York.

                  SECTION 13. Waiver of Jury Trial Right. EACH OF THE ESCROW
AGENT, THE PAYING AGENT, THE INVESTORS AND THE PASS THROUGH

<PAGE>   17

TRUSTEE ACKNOWLEDGES AND ACCEPTS THAT IN ANY SUIT, ACTION OR PROCEEDING ARISING
OUT OF OR RELATING TO THIS AGREEMENT SUCH PARTY IRREVOCABLY WAIVES ITS RIGHT TO
A TRIAL BY JURY.

                  SECTION 14. Counterparts. This Agreement may be executed in
one or more counterparts, all of which taken together shall constitute one
instrument.



<PAGE>   18



                  IN WITNESS WHEREOF, the Escrow Agent, the Paying Agent, the
Placement Agents and the Pass Through Trustee have caused this Escrow and Paying
Agent Agreement (Class C) to be duly executed as of the day and year first above
written.

                                 FIRST SECURITY BANK, NATIONAL ASSOCIATION,
                                 as Escrow Agent



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



<PAGE>   19



                                 MORGAN STANLEY & CO. INCORPORATED
                                 DEUTSCHE BANK SECURITIES INC.
                                 SALOMON SMITH BARNEY INC.,
                                 as Placement Agents

                                 By:  MORGAN STANLEY & CO. INCORPORATED


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

                                 WILMINGTON TRUST COMPANY, not in its
                                 individual capacity, but solely as Pass
                                 Through Trustee for and on behalf of Atlas
                                 Air Pass Through Trust 2000-1C


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


                                 WILMINGTON TRUST COMPANY,
                                 as Paying Agent


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


<PAGE>   20



         EXHIBIT A

                     ATLAS AIR, INC. 2000-1C ESCROW RECEIPT

                                     No. __

                  This Escrow Receipt evidences a fractional undivided interest
in amounts ("Account Amounts") from time to time deposited into a certain paying
agent account (the "Paying Agent Account") described in the Escrow and Paying
Agent Agreement (Class C) dated as of January 28, 2000 (as amended, modified or
supplemented from time to time, the "Escrow and Paying Agent Agreement") among
First Security Bank, National Association, as Escrow Agent (in such capacity,
together with its successors in such capacity, the "Escrow Agent"), Morgan
Stanley & Co. Incorporated, Deutsche Bank Securities Inc. and Salomon Smith
Barney Inc., as Placement Agents, Wilmington Trust Company as Pass Through
Trustee (in such capacity, together with its successors in such capacity, the
"Pass Through Trustee") and Wilmington Trust Company, as paying agent (in such
capacity, together with its successors in such capacity, the "Paying Agent").
Capitalized terms not defined herein shall have the meanings assigned to them in
the Escrow and Paying Agent Agreement.

                  This Escrow Receipt is issued under and is subject to the
terms, provisions and conditions of the Escrow and Paying Agent Agreement. By
virtue of its acceptance hereof the holder of this Escrow Receipt assents and
agrees to be bound by the provisions of the Escrow and Paying Agent Agreement
and this Escrow Receipt.

                  This Escrow Receipt represents a fractional undivided interest
in amounts deposited from time to time in the Paying Agent Account, and grants
or represents no rights, benefits or interests of any kind in respect of any
assets or property other than such amounts. This Escrow Receipt evidences the
same percentage interest in the Account Amounts as the Fractional Undivided
Interest in the Pass Through Trust evidenced by the Certificate to which this
Escrow Receipt is affixed.

                  All payments and distributions made to Receiptholders in
respect of the Escrow Receipt shall be made only from Account Amounts deposited
in the Paying Agent Account. The holder of this Escrow Receipt, by its
acceptance of this Escrow Receipt, agrees that it will look solely to the
Account Amounts for any payment or distribution due to it pursuant to this
Escrow Receipt and that it will not have any recourse to Atlas, the Pass Through
Trustee, the Paying Agent or the Escrow Agent, except as expressly provided
herein or in the Pass Through Trust Agreement. No Receiptholder of this Escrow
Receipt shall have any right to vote or in any manner otherwise control the
operation and management of the Paying Agent Account, nor shall anything set
forth herein, or contained in the terms of this Escrow Receipt, be construed so
as to constitute the Receiptholders from time to time as partners or members of
an association.

                  This Escrow Receipt may not be assigned or transferred except
in connection with the assignment or transfer of the Certificate to which this
Escrow Receipt is affixed. After payment to the holder hereof of its Escrow
Interest in the Final Distribution, upon the request of

<PAGE>   21


the Pass Through Trustee, the holder hereof will return this Escrow Receipt to
the Pass Through Trustee.

                  The Paying Agent may treat the person in whose name the
Certificate to which this Escrow Receipt is attached as the owner hereof for all
purposes, and the Paying Agent shall not be affected by any notice to the
contrary.

                  THIS ESCROW RECEIPT SHALL BE GOVERNED BY AND CONSTRUED IN
ACCORDANCE WITH THE LAWS OF THE STATE OF NEW YORK.

                  IN WITNESS WHEREOF, the Escrow Agent has caused this Escrow
Receipt to be duly executed.

Dated: ______________, ____



                                 FIRST SECURITY BANK, NATIONAL ASSOCIATION,
                                 as Escrow Agent


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




<PAGE>   22


         EXHIBIT B

                             WITHDRAWAL CERTIFICATE
                                    (Class C)

First Security Bank, National Association,
as Escrow Agent
79 South Main Street
Salt Lake City, UT 84111
Attention: Corporate Trust Services

Dear Sirs:

                  Reference is made to the Escrow and Paying Agent Agreement,
dated as of January 28, 2000 (the "Agreement"). We hereby certify to you that
the conditions to the obligations of the undersigned to execute a Participation
Agreement pursuant to the Note Purchase Agreement have been satisfied. Pursuant
to Section 1.02(c) of the Agreement, please execute the attached Notice of
Purchase Withdrawal and immediately transmit by facsimile to the Depositary, at
_________, Attention: ____________________________.


                                 Very truly yours,

                                 WILMINGTON TRUST COMPANY,
                                 not in its individual capacity but
                                 solely as Pass Through Trustee


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


Dated:
      ----------------

<PAGE>   23



         EXHIBIT C

                        PREPAYMENT WITHDRAWAL CERTIFICATE
                                    (Class C)

First Security Bank, National Association,
as Escrow Agent
79 South Main Street
Salt Lake City, UT 84111
Attention: Corporate Trust Services

Dear Sirs:

                  Reference is made to the Escrow and Paying Agent Agreement,
dated as of January 28, 2000 (the "Agreement"). The undersigned has been
notified by Atlas Air, Inc. that it has received written notice from The Boeing
Company that the delivery date for the Aircraft in respect of which the attached
Notice of Prepayment Withdrawal is to be given will be delayed beyond the
Delivery Period Termination Date. Pursuant to Section 1.02(d) of the Agreement,
please execute the attached Notice of Prepayment Withdrawal and immediately
transmit by facsimile to the Depositary, at ____________, Attention: _________.


                                 Very truly yours,

                                 WILMINGTON TRUST COMPANY,
                                 not in its individual capacity but
                                 solely as Pass Through Trustee


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