<PAGE>   1
                                                                    EXHIBIT 4.16






                                DEPOSIT AGREEMENT
                                    (Class C)

                          Dated as of January 28, 2000


                                     between


                    FIRST SECURITY BANK, NATIONAL ASSOCIATION


                                 as Escrow Agent


                                       and


                      Westdeutsche Landesbank Girozentrale,
                                New York Branch,


                                  as Depositary







<PAGE>   2


DEPOSIT AGREEMENT (Class C) dated as of January 28, 2000 (as amended, modified
or supplemented from time to time, this "Agreement") between First Security
Bank, National Association, a national banking association, as Escrow Agent
under the Escrow and Paying Agent Agreement referred to below (in such capacity,
together with its successors in such capacity, the "Escrow Agent"), and
WESTDEUTSCHE LANDESBANK GIROZENTRALE, a German banking institution organized
under the laws of the State of North Rhine-Westphalia, acting through its New
York Branch as depositary bank (the "Depositary").

                               W I T N E S S E T H

                  WHEREAS, Atlas Air, Inc. ("Atlas") and Wilmington Trust
Company, not in its individual capacity except as otherwise expressly provided
therein, but solely as trustee (in such capacity, together with its successors
in such capacity, 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 pursuant to which the Atlas Air
Pass Through Trust, Series 2000-1C Certificates referred to therein (the
"Certificates") are being issued;

                  WHEREAS, Atlas and Morgan Stanley & Co. Incorporated, Deutsche
Bank Securities Inc. and Salomon Smith Barney Inc. (collectively, the "Placement
Agents" and, together with their respective transferees and assigns as
registered owners of the Certificates, the "Investors") have entered into a
Placement Agreement dated January 20, 2000 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, subject to the terms thereof, from time to time on or prior to the
Delivery Period Termination 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 Escrow Agent, the Placement Agents, the Pass
Through Trustee and Wilmington Trust Company, as paying agent for the Escrow
Agent (in such capacity, together with its successors in such capacity, the
"Paying Agent") concurrently herewith are entering into an Escrow and Paying
Agent Agreement, dated as of the date hereof (as amended, modified or
supplemented from time to time in accordance with the terms thereof, the "Escrow
Agreement");

                  WHEREAS, Atlas and the Depositary concurrently herewith are
entering into an Indemnity Agreement, dated as of the date hereof (the
"Indemnity Agreement"); and

                  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 pursuant to the





<PAGE>   3

Escrow Agreement, subject to withdrawal upon request of and proper certification
by the Pass Through Trustee for the purpose of purchasing Equipment Notes, and
that pending such withdrawal the Net Proceeds be deposited by the Escrow Agent
with the Depositary pursuant to this Agreement, which provides for the
Depositary to pay interest for distribution to the Investors and to establish an
account from which the Escrow Agent shall make withdrawals upon request of and
proper certification by the Pass Through Trustee.

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

                  SECTION 1.1 Acceptance of Depositary. The Depositary hereby
agrees to act as depositary bank as provided herein and in connection therewith
to accept all amounts to be delivered to or held by the Depositary pursuant to
the terms of this Agreement. The Depositary further agrees to hold, maintain and
safeguard the Deposit and the Account (as defined below) during the term of this
Agreement in accordance with the provisions of this Agreement. The Escrow Agent
shall not have any right to withdraw, assign or otherwise transfer moneys held
in the Account except as permitted by this Agreement.

                  SECTION 1.2 Establishment of Account. The Escrow Agent hereby
instructs the Depositary, and the Depositary agrees, to establish the deposit
account listed on Schedule I hereto (the "Account"), in the name of the Escrow
Agent and on the terms and conditions set forth in this Agreement.

                  SECTION 2.1 Deposit. The Escrow Agent shall direct the
Placement Agents to deposit with the Depositary on the date of this Agreement
(the "Deposit Date") in Federal (same day) funds by wire transfer to:
Westdeutsche Landesbank Girozentrale, New York Branch, Reference: Atlas 2000-1C,
and the Depositary shall accept from the Placement Agents, on behalf of the
Escrow Agent, the sum of US$47,937,000. Upon acceptance of such sum, the
Depositary shall (i) establish the deposit specified in Schedule I hereto
maturing on the date set forth therein (the "Deposit") and (ii) credit the
Deposit to the Account as set forth therein. No amount shall be deposited in the
Account other than the related Deposit.

                  SECTION 2.2 Interest. The Depositary shall pay interest on the
balance of the Deposit from and including the date of deposit to but excluding
the date of withdrawal at the rate of 9.702% per annum (computed on the basis of
a year of twelve 30-day months) payable to the Paying Agent on behalf of the
Escrow Agent semi-annually in arrears on each January 2 and July 2, commencing
on July 2, 2000 (each, an "Interest Payment Date"), and on the date of each
Prepayment Withdrawal and the Final Withdrawal (as defined below), all in
accordance with the terms of this Agreement (whether or not any portion of the
Deposit is withdrawn on an Interest Payment Date); provided, however, that in
the event that no Registration Event (as defined in the Registration Rights
Agreement) occurs on or prior to the 210th day after the date of the issuance of
the Certificates (the "Registration Date"), the interest rate per annum paid by
the Depositary on each Deposit shall be increased by 0.50%, effective from and
including the 210th day after the date of issuance of the Certificates, to but
excluding the date on which a Registration Event



<PAGE>   4

occurs; and provided, further, that in the event that a Shelf Registration
Statement (as defined in the Registration Rights Agreement) ceases to be
effective for more than 60 days, whether or not consecutive, during any 12-month
period at any time before the earlier of (a) the second anniversary of the
effective date of the Shelf Registration Statement or (b) the sale pursuant to
the Shelf Registration Statement of all the Certificates covered thereby, the
interest rate per annum paid by the Depositary on each Deposit shall be
increased by 0.50% per annum from the 61st day of the applicable 12-month period
such Shelf Registration Statement ceases to be effective until such time as the
Shelf Registration Statement again becomes effective. Interest accrued on any
portion of the Deposit when withdrawn pursuant to a Notice of Purchase
Withdrawal (as defined below) shall be paid on the next Interest Payment Date,
notwithstanding any intervening Final Withdrawal.

                  SECTION 2.3 Withdrawals. (a) On and after the date seven days
after the establishment of the Deposit, the Escrow Agent may, by providing at
least one Business Day's prior notice of withdrawal to the Depositary in the
form of Exhibit A hereto (a "Notice of Purchase Withdrawal"), withdraw all or a
portion of the Deposit, except that at any time prior to the actual withdrawal
of the Deposit, the Escrow Agent or the Pass Through Trustee may, by notice to
the Depositary, cancel such withdrawal (including on the scheduled date
therefor), and thereafter the Deposit shall continue to be maintained by the
Depositary in accordance with the original terms thereof. Following such
withdrawal the balance in the Account shall be reduced by the amount of the
withdrawal. As used herein, "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, Salt Lake City, Utah or
Wilmington, Delaware. If a Notice of Purchase Withdrawal is related to a single
aircraft, the amount of withdrawal specified therein shall not exceed the
maximum principal amount of the Equipment Notes for such aircraft, as specified
in the Offering Memorandum (as defined in the Note Purchase Agreement).

                  (b) The Escrow Agent may, by providing at least 15 days' prior
notice of withdrawal to the Depositary in the form of Exhibit B hereto (a
"Notice of Prepayment Withdrawal"), withdraw all or a portion of the Deposit
together with all accrued and unpaid interest thereon to but excluding the
specified date of withdrawal (a "Prepayment Withdrawal"), on such date as shall
be specified in such Notice of Prepayment Withdrawal. Following such withdrawal
the balance in the Account shall be reduced by the amount of the withdrawal.
Upon any Prepayment Withdrawal, the Depositary shall pay to the Paying Agent the
amount requested in the related Notice of Prepayment Withdrawal, provided that
after giving pro forma effect to any Prepayment Withdrawal, the remaining amount
of the Deposit shall not be less than the maximum principal amount of the
Equipment Notes issuable in respect of any aircraft scheduled to be delivered
after the date of such Prepayment Withdrawal, as specified in the Offering
Memorandum.

                  (c) The Escrow Agent may, by providing at least 15 days' prior
notice of withdrawal to the Depositary in the form of Exhibit C hereto (a
"Notice of Final Withdrawal"), withdraw the entire amount of the Deposit
together with the all accrued and unpaid interest on the Deposit to but
excluding the specified date of withdrawal (a "Final Withdrawal"), on such




<PAGE>   5

date as shall be specified in such Notice of Final Withdrawal. Following such
withdrawal the balance in the Account shall be zero and the Depositary shall
close such Account. If a Notice of Final Withdrawal has not been given 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 on such date, the Depositary shall pay the amount of the Final
Withdrawal to the Paying Agent on January 16, 2001 (or if the December 31, 2000
date has been extended as set forth in this sentence, the fifteenth day after
the Delivery Period Termination Date).

                  (d) If the Depositary receives a duly completed Notice of
Purchase Withdrawal, Notice of Prepayment Withdrawal or Notice of Final
Withdrawal complying with the provisions of this Agreement, it shall make the
payments specified therein in accordance with the provisions of this Agreement.
No notice of withdrawal shall be given within seven days after the date of the
immediately preceding notice of withdrawal.

                  SECTION 2.4 Re-Deposit. On the date of withdrawal of any
portion of the Deposit, the Escrow Agent, or the Pass Through Trustee on behalf
of the Escrow Agent, shall be entitled to re-deposit with the Depositary any
portion thereof and the Depositary shall accept the same for deposit hereunder.
Any sums so received for deposit shall be deemed not to have been withdrawn for
all purposes hereof.

                  SECTION 3.1 Termination. This Agreement shall terminate on the
later of the date on which (i) all of the Deposit shall have been withdrawn and
paid as provided herein without any re-deposit and (ii) all accrued and unpaid
interest on the Deposit shall have been paid as provided herein, but in no event
prior to the date on which the Depositary shall have performed in full its
obligations hereunder.

                  SECTION 4. Payments. All payments (including, without
limitation, those payments made in respect of Taxes (as defined and provided for
below)) made by the Depositary hereunder shall be paid in United States Dollars
and immediately available funds by wire transfer (i) in the case of accrued
interest on the Deposit payable under Section 2.2 hereof, any Prepayment
Withdrawal or any Final Withdrawal, directly to the Paying Agent at Wilmington
Trust Company, Wilmington, Delaware, ABA # 03-11-000-92, Account No. 50849-0,
Attention: Robert Hines, Reference: Atlas Air 2000-1C, or to such other account
as the Paying Agent may direct from time to time in writing to the Depositary
and the Escrow Agent and (ii) in the case of any withdrawal of all or a portion
of the Deposit pursuant to a Notice of Purchase Withdrawal, directly to or as
directed by the Pass Through Trustee as specified and in the manner provided in
such Notice of Purchase Withdrawal. The Depositary 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 the Deposit howsoever arising. All payments on or in respect of the
Deposit shall be made free and clear of and without reduction for or on account
of any and all taxes, levies or other impositions or charges (collectively,
"Taxes"). However, if the Depositary or the Paying Agent (pursuant to Section
2.04 of the Escrow Agreement) shall be required by law to deduct or withhold any
Taxes from or



<PAGE>   6

in respect of any sum payable hereunder, the Depositary shall (i) make such
deductions or withholding, (ii) pay the full amount deducted or withheld
(including in respect of such additional amounts) to the competent taxation
authority and (iii) if the Taxes required to be deducted or withheld are imposed
by the Federal Republic of Germany or any political subdivision thereof, pay
such additional amounts as may be necessary in order that the actual amount
received by the designated recipient of such sum under this Agreement or the
Escrow Agreement after such deduction or withholding equals the sum it would
have received had no such deduction or withholding been required. If the date on
which any payment due on the Deposit would otherwise fall on a day which is not
a Business Day, such payment shall be made on the next succeeding Business Day,
with the same force and effect as if made on such scheduled date, and no
additional interest shall accrue in respect of such extension.

                  SECTION 5. Representation and Warranties. The Depositary
hereby represents and warrants to Atlas, the Escrow Agent, the Pass Through
Trustee and the Paying Agent that:

                  (a) it is duly organized and validly existing as a German
         public law banking institution under the laws of the State of
         Rhine-Westphalia and is duly qualified to conduct banking business in
         the State of New York through its New York Branch;

                  (b) 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;

                  (c) the execution, delivery and performance of this 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 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;

                  (d) 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;

                  (e) 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;


<PAGE>   7

                  (f) 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, (i) would adversely affect the ability of it to
         perform its obligations under this Agreement or (ii) would call into
         question or challenge the validity of this Agreement or the
         enforceability hereof in accordance with the terms hereof, nor is the
         Depositary 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; and

                  (g) the Depositary will make all payments under this Agreement
         from its own funds and not from funds provided by, or on deposit from,
         Atlas or any of Atlas' subsidiaries.

                  SECTION 6. Transfer. Neither 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 the Escrow
Agreement, 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) permitted assigns.

                  SECTION 7. Amendment, Etc. This Agreement may not be amended,
waived or otherwise modified except by an instrument in writing signed by the
party against whom the amendment, waiver or other modification is sought to be
enforced and by the Pass Through Trustee.

                  SECTION 8. Notices. Unless otherwise expressly specified or
permitted by the terms hereof, all notices, requests, demands, authorizations,
directions, consents, waivers or documents provided or permitted by this
Agreement to be made, given, furnished or filed shall be in writing, mailed by
certified mail, postage prepaid, or by confirmed telecopy and

                  (i)      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

                  (ii)     if to the Depositary, addressed to it at its offices
                           at:

                           WESTDEUTSCHE LANDESBANK GIROZENTRALE
                           1211 Avenue of the Americas
                           New York, NY  10036
                           Attention: Transportation Finance
                           Telecopier: 212-869-7634



<PAGE>   8

                           with a copy to:
                           Attention: Loan Administration
                           Telecopier: 212-302-7946

                  (iii)    in each case, with a copy 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
                           Telecopy:  302-651-8882

                           and 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

                  Whenever any notice in writing is required to be given by
either of the Escrow Agent or the Depositary to the other, such notice shall be
deemed given and such requirement satisfied when such notice is received. Any
party hereto may change the address to which notices to such party will be sent
by giving notice of such change to the other party to this Agreement.

                  On or prior to the execution of this Agreement, the Escrow
Agent has delivered to the Depositary a certificate containing specimen
signatures of the representatives of the Escrow Agent who are authorized to give
notices and instructions with respect to this Agreement. The Depositary may
conclusively rely on such certificate until the Depositary receives written
notice from the Escrow Agent to the contrary.

                  SECTION 9. Obligations Unconditional. The Depositary hereby
acknowledges and agrees that its obligation to repay the Deposit together with
interest thereon as provided herein is absolute, irrevocable and unconditional
and constitutes a full recourse obligation of the Depositary enforceable against
it to the full extent of all of its assets and properties.

                  SECTION 10. Entire Agreement. This Agreement (including all
attachments hereto) sets forth all of the promises, covenants, agreements,
conditions and understandings between the Depositary and the Escrow Agent 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.



<PAGE>   9

                  SECTION 11. Governing Law. This Agreement, and the rights and
obligations of the Depositary and the Escrow Agent with respect to the Deposit,
shall be governed by, and construed in accordance with, the laws of the State of
New York and subject to the provisions of Regulation D of the Board of Governors
of the Federal Reserve System (or any successor), as the same may be modified
and supplemented and in effect from time to time.

                  SECTION 12. Submission to Jurisdiction; Waiver of Jury Trial.
(a) Each of the parties hereto hereby irrevocably and unconditionally:

                  (i) submits for itself and its property in any legal action or
         proceeding relating to this Agreement, or for recognition and
         enforcement of any judgment in respect hereof, to the nonexclusive
         general jurisdiction of the courts of the State of New York, the courts
         of the United States of America for the Southern District of New York,
         and the appellate courts from any thereof;

                  (ii) consents that any such action or proceeding may be
         brought in such courts, and waives any objection that it may now or
         hereafter have to the venue of any such action or proceeding in any
         such court or that such action or proceeding was brought in an
         inconvenient court and agrees not to plead or claim the same;

                  (iii) agrees that service of process in any such action or
         proceeding may be effected by mailing a copy thereof by registered or
         certified mail (or any substantially similar form and mail), postage
         prepaid, to each party hereto at its address set forth in Section 8
         hereof, or at such other address of which the other parties shall have
         been notified pursuant thereto; and

                  (iv) agrees that nothing herein shall affect the right to
         effect service of process in any other manner permitted by law or shall
         limit the right to sue in any other jurisdiction.

                  (b) EACH OF THE DEPOSITARY AND THE ESCROW AGENT ACKNOWLEDGES
AND ACCEPTS THAT IN ANY SUIT, ACTION OR PROCEEDING ARISING OUT OF OR RELATING TO
THIS AGREEMENT SUCH PARTY KNOWINGLY, VOLUNTARILY AND INTENTIONALLY IRREVOCABLY
WAIVES, TO THE GREATEST EXTENT PERMISSIBLE BY LAW, ITS RIGHT TO A TRIAL BY JURY.

                  SECTION 13. Counterparts. This Agreement may be executed in
one or more counterparts, all of which taken together shall constitute one
instrument.

                  SECTION 14. Depositary's Obligations. The Depositary and the
Escrow Agent understand and agree that in connection with this Agreement, the
Depositary is not acting as a fiduciary, agent of other representative of the
Escrow Agent, the Pass Through Trustees, the Placement Agents or anyone else,
and has no and shall have no obligation to monitor, account for or otherwise
concern itself with the source of funds invested hereunder or the application of
such funds or of payments made by the Depositary hereunder and in accordance
with the terms hereof.

<PAGE>   10

                  IN WITNESS WHEREOF, the Escrow Agent and the Depositary have
caused this Deposit Agreement to be duly executed as of the day and year first
above written.


                                        FIRST SECURITY BANK,
                                             NATIONAL ASSOCIATION,
                                             as Escrow Agent


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



                                        WESTDEUTSCHE LANDESBANK
                                        GIROZENTRALE, New York Branch,
                                             as Depositary


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


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

<PAGE>   11



         Schedule I


                                     Deposit
                                    (Class C)


<TABLE>
<CAPTION>
Date                           Deposit Amount               Account No.                 Maturity Date
----------------               --------------               -----------                 ----------------
<S>                            <C>                          <C>                         <C>
January 28, 2000               $47,937,000                  712-000 3                   January 16, 2001
</TABLE>




<PAGE>   12



                                    EXHIBIT A

                          NOTICE OF PURCHASE WITHDRAWAL

                      WESTDEUTSCHE LANDESBANK GIROZENTRALE
                           1211 Avenue of the Americas
                               New York, NY 10036

                        Attention: Transportation Finance
                            Telecopier: 212-869-7634

                         Attention: Loan Administration
                            Telecopier: 212-302-7946


                              Ladies and Gentlemen:

                  Reference is made to the Deposit Agreement (Class C) dated as
of January 28, 2000 (the "Deposit Agreement") between First Security Bank, N.A.,
as Escrow Agent, and Westdeutsche Landesbank Girozentrale, New York Branch, as
Depositary (the "Depositary").

                  In accordance with Section 2.3(a) of the Deposit Agreement,
the undersigned hereby requests the withdrawal of the following amount of the
Deposit: $_______, Account No. ____________.

                  The undersigned hereby directs that on _______________, the
Depositary pay $___________ of the proceeds of the Deposit to ________________,
Account No. _____, Reference: Atlas Air upon the telephonic request of a
representative reasonably believed by the Depositary to be that of the Pass
Through Trustee.


                                             FIRST SECURITY BANK,
                                             NATIONAL ASSOCIATION,
                                                 as Escrow Agent


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

Dated: _______ __, ____

<PAGE>   13



                                    EXHIBIT B

                         NOTICE OF PREPAYMENT WITHDRAWAL

                      WESTDEUTSCHE LANDESBANK GIROZENTRALE
                           1211 Avenue of the Americas
                               New York, NY 10036

                        Attention: Transportation Finance
                            Telecopier: 212-869-7634

                         Attention: Loan Administration
                            Telecopier: 212-302-7946

                  Reference is made to the Deposit Agreement (Class C) dated as
of January 28, 2000 (the "Deposit Agreement") between First Security Bank, N.A.,
as Escrow Agent, and Westdeutsche Landesbank Girozentrale, New York Branch, as
Depositary (the "Depositary").

                  In accordance with Section 2.3(b) of the Deposit Agreement,
the undersigned hereby requests the withdrawal of the following amount of the
Deposit: $_______, Account No. ____________.

                  The undersigned hereby directs that on _______ the Depositary
pay $________ of the proceeds of such Deposit and accrued interest thereon to
the Paying Agent at Wilmington Trust Company, ABA# [ ], Account No.[ ],
Reference: Atlas Air.




                                             FIRST SECURITY BANK,
                                             NATIONAL ASSOCIATION,
                                                 as Escrow Agent


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

Dated: _______ __, ____

<PAGE>   14



                                    EXHIBIT C

                           NOTICE OF FINAL WITHDRAWAL

WESTDEUTSCHE LANDESBANK GIROZENTRALE
1211 Avenue of the Americas
New York, NY 10036

Attention: Transportation Finance
Telecopier: 212-869-7634

Attention: Loan Administration
Telecopier: 212-302-7946

Ladies and Gentlemen:

                  Reference is made to the Deposit Agreement (Class C) dated as
of January 28, 2000 (the "Deposit Agreement") between First Security Bank, N.A.,
as Escrow Agent, and Westdeutsche Landesbank Girozentrale, New York Branch, as
Depositary (the "Depositary").

                  In accordance with Section 2.3(c) of the Deposit Agreement,
the undersigned hereby requests the withdrawal of the entire amount of the
Deposit on _____________.

                  The undersigned hereby directs the Depositary to pay the
proceeds of the Deposit and accrued interest thereon to the Paying Agent at
Wilmington Trust Company, ABA# [     ], Account No. [       ], Reference:
Atlas Air.


                                        FIRST SECURITY BANK,
                                             NATIONAL ASSOCIATION,
                                             as Escrow Agent


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

Dated: _______ __, ____