<PAGE>   1
                                                                   EXHIBIT 10.96

                                                                  EXECUTION COPY

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                               DEPOSIT AGREEMENT
                                   (Class A)

                          Dated as of February 9, 1998


                                    between


                   FIRST SECURITY BANK, NATIONAL ASSOCIATION


                                as Escrow Agent


                                      and


                              ABN AMRO BANK N.V.,
                       acting through its Chicago Branch,


                                 as Depositary


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<PAGE>   2



                 DEPOSIT AGREEMENT (Class A) dated as of February 9, 1998 (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 ABN AMRO Bank N.V., a banking institution organized under the laws
of the Netherlands, acting through its Chicago Branch, as depositary bank ("ABN
AMRO" and, in its capacity as depositary hereunder, 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 the Pass
Through Trust Agreement dated as of February 9, 1998 (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, Inc. Pass
Through Trust 1998-1A-O pursuant to which the Atlas Air, Inc.  Pass Through
Trust, Series 1998-1A Certificates referred to therein (the "Certificates") are
being issued;

                 WHEREAS, Atlas and Morgan Stanley & Co. Incorporated, BT Alex.
Brown Incorporated, Donaldson, Lufkin & Jenrette Securities Corporation and
Goldman, Sachs & Co.  (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 as
of January 27, 1998 pursuant to which the Pass Through Trustee will issue and
sell the Certificates to the Placement Agents;

                 WHEREAS, the Investors are entitled to the benefits of a
Registration Rights Agreement (the "Registration Rights Agreement"), dated as
of the date hereof, pursuant to which the Company will file a registration
statement with the Securities and Exchange Commission registering the
Certificates (or the Exchange Certificates referred to in the Registration
Rights Agreement) under the Securities Act of 1933, as amended;

                 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
<PAGE>   3
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 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 accounts 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 Deposits and the Accounts (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 Accounts except as permitted by this Agreement.

                 SECTION 1.2  Establishment of Accounts.  The Escrow Agent
hereby instructs the Depositary, and the Depositary agrees, to establish the
separate deposit accounts listed on Schedule I hereto and to establish such
additional separate deposit accounts as may be required in connection with the
deposits contemplated by Section 2.4 hereof (each, an "Account" and
collectively, the "Accounts"), each in the name of the Escrow Agent and all on
the terms and conditions set forth in this Agreement.

                 SECTION 2.1  Deposits.  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:  ABN AMRO
Bank N.V., Chicago Branch, Reference:  Atlas 1998-1, and the Depositary shall
accept from the Placement Agents, on behalf of the Escrow Agent, the sum of
US$300,254,000.  Upon acceptance of such sum, the Depositary shall (i)
establish each of the deposits specified in Schedule I hereto maturing on the
respective dates (each such date, as it may be extended from time to time in
accordance with the Indemnity Agreement, through the Delivery Period
Termination Date, a "Maturity


                                       2
<PAGE>   4
Date") set forth therein (including any deposit made pursuant to Section 2.4
hereof, individually, a "Deposit" and, collectively, the "Deposits") and (ii)
credit each Deposit to the related Account as set forth therein.  No amount
shall be deposited in any Account other than the related Deposit.

                 SECTION 2.2  Interest.  The Depositary shall pay interest on
each Deposit from and including the date of deposit to but excluding the
earlier of (x) the date of withdrawal and (y) the Maturity Date thereof at the
rate (the "Public Rate") of 7.38% 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, and on the date of the
Final Withdrawal (as defined below), commencing on July 2, 1998 (each, an
"Interest Payment Date"), all in accordance with the terms of this Agreement
(whether or not any such 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 180th 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 August 9, 1998, to but
excluding the date on which a Registration Event 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 date hereof 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 Deposit that is 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 (as defined
below).

                 SECTION 2.3  Withdrawals.  (a)  On and after the date seven
days after the establishment of any 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 not less
than the entire balance of such Deposit, except that at any time prior to the
actual withdrawal of such 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 such Deposit shall continue to be
maintained by the Depositary in accordance with the original terms thereof.
Following such withdrawal the balance in the related Account shall be zero and
the Depositary shall close such Account.  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, Chicago,
Illinois, Denver, Colorado or Wilmington, Delaware.





                                       3
<PAGE>   5
                 (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 not less than the entire balance
of any Deposit together with all accrued and unpaid interest on such Deposit 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 related Account shall be zero and
the Depositary shall close such Account.  Upon any Prepayment Withdrawal, the
Depositary shall (i) pay to the Paying Agent an amount equal to excess of the
aggregate amount of all Deposits on deposit immediately prior to such
Prepayment Withdrawal over the sum of the maximum principal amount of Equipment
Notes that may be acquired with funds withdrawn from all Deposits not being
withdrawn pursuant to such Notice of Prepayment Withdrawal and (ii) redeposit
the remainder, if any, of such Prepayment Withdrawal in accordance with Section
2.4 hereof.

                 (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 all of the
remaining Deposits together with the all accrued and unpaid interest on such
Deposits to but excluding the specified date of withdrawal (a "Final
Withdrawal"), on such date as shall be specified in such Notice of Final
Withdrawal.  Following such withdrawal the balance in the related Accounts
shall be zero and the Depositary shall close such Accounts.  If a Notice of
Final Withdrawal has not been given to the Depositary on or before June 29,
1999 (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
but in no event shall any such extension result in a Deposit being held by the
Depositary past such Deposit's then scheduled maturity date (subject to
extension pursuant to the Indemnity Agreement)) and there are unwithdrawn
Deposits on such date, the Depositary shall pay the amount of the Final
Withdrawal to the Paying Agent on 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.

                 SECTION 2.4  Other Accounts.  On the date of withdrawal of any
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; provided,
however, that the Depositary shall have no obligation to accept such amounts
for deposit if Atlas, at or prior to such time, shall not have complied with
the provisions of Section 3(b) of the Indemnity Agreement.  Any sums so
received for deposit shall be established as a new Deposit and credited to a
new Account, all as more fully provided in Section 2.1 hereof, and thereafter
the provisions of this Agreement shall apply thereto as fully and with the same
force and effect as if such Deposit had been





                                       4
<PAGE>   6
established on the Deposit Date except that (i) such Deposit may not be
withdrawn prior to the date seven days after the establishment thereof and (ii)
such Deposit shall mature on December 30, 1998, as such date may be extended
from time to time in accordance with the Indemnity Agreement through the
Delivery Period Termination Date.

                 SECTION 2.5 Reset of Maturity Date.  If a Registration Event
has not occurred on the Registration Date, unless Atlas has complied with
Section 3(c) of the Indemnity Agreement, the Maturity Date for the Deposit then
held by the Depositary with respect to the final Aircraft to be delivered to
Atlas as contemplated by the Note Purchase Agreement shall be reset to the date
(the "Reset Date") that the Depositary reasonably determines to be the date on
which the sum of (x) interest accrued on the balances of all Deposits hereunder
from the date of calculation through the Reset Date at the then current Deposit
Rate plus (y) the balance of the Collateral Account as at such date of
calculation will be equal to the interest that will have accrued on the
Deposits hereunder from such date of calculation through the Reset Date at the
Public Rate (assuming all scheduled payments are made on each Interest Payment
Date occurring on or prior to the Reset Date and each then remaining Deposit is
withdrawn on its then scheduled Maturity Date). The Depositary shall use
reasonable efforts to determine the amounts necessary to determine the Reset
Date, and such determination shall be conclusive absent manifest error. Any
reset of such Maturity Date pursuant to this Section 2.5 shall be without
prejudice to Atlas' right to re-extend such Maturity Date by posting additional
collateral pursuant to Section 3(a) of the Indemnity Agreement.

                 SECTION 3.1  Termination.  This Agreement shall terminate on
the later of the date on which (i) all of the Deposits shall have been
withdrawn and paid as provided herein without any re-deposit and (ii) all
accrued and unpaid interest on the Deposits 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 3.2  Substitute Depositary.  In the event that Atlas
is required under the provisions of Section 9 or Section 10 of the Indemnity
Agreement to make payments in a material amount to the Depositary, Atlas may
elect to terminate the Depositary as a party to this Agreement, the other
Deposit Agreements and the Indemnity Agreement; provided that, concurrently
with such termination, (i) Atlas shall pay the Depositary all amounts
(including, without limitation, amounts, if any, owed under such Section 9 and
Section 10) owed to the Depositary pursuant to any such Agreement through such
date of termination, (ii) another financial institution satisfactory to Atlas
and the Rating Agencies (as defined in the Note Purchase Agreement) shall
agree, as of such date, to assume all rights and obligations of the Depositary
under all such Agreements to be terminated as of such date, and (iii) all
documents and supporting materials necessary to evidence the termination of the
Depositary and the substitution of such other financial institution shall have
been received as of such date.





                                       5
<PAGE>   7
                 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 Deposits payable under Section 2.2 hereof or any Final
Withdrawal, directly to the Paying Agent at Wilmington Trust Company,
Wilmington, Delaware, ABA# 03-11-000-92, Account No. 44043-0, Attention:
Robert Hines, Reference:  Atlas Air, 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 one or more Deposits 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
Deposits howsoever arising.  All payments on or in respect of each 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 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 Netherlands 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 any Deposit would otherwise fall on a day which is not
a Business Day, such payment shall be made on the next succeeding Business Day,
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 a bank duly organized and validly existing in
         good standing under the laws of the Netherlands and is duly qualified
         to conduct banking business in the State of Illinois through its
         Chicago 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





                                       6
<PAGE>   8
         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;

                 (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 its 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.
Upon the occurrence of the Transfer (as defined below) contemplated by the
Assignment and Assumption Agreement (as defined below), the Pass Through
Trustee shall (without further act) be deemed to have transferred all of its
right, title and interest in and to this Agreement to the trustee of the
Successor Trust (as defined below) and, thereafter, the





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<PAGE>   9
trustee of the Successor Trust shall be deemed to be the "Pass Through Trustee"
hereunder with the rights of the "Pass Through Trustee" hereunder, and each
reference herein to "Atlas Air, Inc. Pass Through Trust 1998-1A-O" shall be
deemed to be a reference to "Atlas Air Inc. Pass Through Trust 1998-1A-S".  The
Escrow Agent and the Depositary hereby acknowledge and consent to the Transfer
contemplated by the Assignment and Assumption Agreement.  For the purposes of
this Section 6, "Transfer" means the transfer contemplated by the Assignment
and Assumption Agreement; "Assignment and Assumption Agreement" means the
Assignment and Assumption Agreement to be entered into between the Pass Through
Trustee and the trustee of the Successor Trust, substantially in the form of
Exhibit E to the Pass Through Trust Agreement; and "Successor Trust" means the
Atlas Air, Inc. Pass Through Trust 1998-1A-S.

                 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





                                       8
<PAGE>   10
         (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:

                 ABN AMRO BANK N.V., Chicago Branch
                 135 South LaSalle Street, Suite 660
                 Chicago, IL  60674-9135

                 Attention:  Claudia Heldring
                 Telecopier:  312-606-8428

                 and

                 ABN AMRO BANK N.V., Chicago Branch
                 181 W. Madison Street
                 Chicago, IL  60602

                 Attention:  Money Markets Desk
                 Telecopier:  312-904-9106

         (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





                                       9
<PAGE>   11
                 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 each 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.

                 SECTION 11.  Governing Law.  This Agreement, and the rights
and obligations of the Depositary and the Escrow Agent with respect to the
Deposits, 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.  Waiver of Jury Trial Right.  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.





                                       10
<PAGE>   12
                 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.





                                       11
<PAGE>   13
                 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   /s/ C. SCOTT NIELSEN
                                            ------------------------------------
                                            Name: C. Scott Nielsen
                                            Title: Vice President



                                       ABN AMRO BANK N.V.,
                                            Chicago Branch
                                            as Depositary


                                       By   /s/ CLAUDIA C. HELDRING
                                            ------------------------------------
                                            Name: Claudia C. Heldring
                                            Title: Vice President


                                       By   /s/ LUKAS van der HOEF
                                            ------------------------------------
                                            Name: Lukas van der Hoef
                                            Title: Vice President
<PAGE>   14
                                                                      Schedule I


                              Schedule of Deposits
                                   (Class A)


<TABLE>
<CAPTION>
         Date       Deposit Amount     Account No.     Maturity Date
         ----       --------------     -----------     -------------
         <S>        <C>                <C>             <C>
         2/9/98                                           7/31/98

         2/9/98                                           8/31/98

         2/9/98                                          10/30/98

         2/9/98                                          11/30/98

         2/9/98                                          12/31/98

</TABLE>

[Note: The portion of proceeds of the sale of Class A Certificates deposited
into each account will be equal to, in the case of the first four accounts, the
maximum principal amount of Equipment Notes that may be purchased with the
funds in each such Deposit and, in the case of the final account, any remaining
proceeds.]
<PAGE>   15
                                                                       EXHIBIT A

                         NOTICE OF PURCHASE WITHDRAWAL

ABN AMRO BANK N.V., Chicago Branch
135 South LaSalle Street, Suite 660
Chicago, IL  60674-9135

Attention:  Claudia Heldring
Telecopier:  312-606-8428


ABN AMRO BANK N.V., Chicago Branch
181 W. Madison Street
Chicago, IL  60602

Attention:  Money Markets Desk
Telecopier:  312-904-9106

Gentlemen:

                 Reference is made to the Deposit Agreement (Class A) dated as
of February 9, 1998 (the "Deposit Agreement") between First Security Bank,
N.A., as Escrow Agent, and ABN AMRO Bank N.V., Chicago Branch, as Depositary
(the "Depositary").

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

                 The undersigned hereby directs the Depositary to pay the
proceeds of the Deposit to ________________, Account No. _____, Reference:
_________ on _________ __, 199_, 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: _______ __, 199_
<PAGE>   16
                                                                       EXHIBIT B

                        NOTICE OF PREPAYMENT WITHDRAWAL

ABN AMRO BANK N.V., Chicago Branch
135 South LaSalle Street, Suite 660
Chicago, IL  60674-9135

Attention:  Claudia Heldring
Telecopier:  312-606-8428


ABN AMRO BANK N.V., Chicago Branch
181 W. Madison Street
Chicago, IL  60602

Attention:  Money Markets Desk
Telecopier:  312-904-9106

Gentlemen:

                 Reference is made to the Deposit Agreement (Class A) dated as
of February 9, 1998 (the "Deposit Agreement") between First Security Bank,
N.A., as Escrow Agent, and ABN AMRO Bank N.V., Chicago Branch, as Depositary
(the "Depositary").

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

                 The undersigned hereby directs the Depositary (i) to pay to
the Paying Agent at Wilmington Trust Company, ABA# 03-11-000-92, Account
No.44043-0, Reference:  Atlas Air, out of the proceeds of the Deposit and
accrued interest thereon, $________, representing the amount equal to excess of
(x) the aggregate amount of all Deposits on deposit immediately prior to such
withdrawal over (y) the sum of the maximum principal amount of Equipment Notes
that may be acquired with funds withdrawn from all Deposits not being withdrawn
pursuant to this Notice of Prepayment Withdrawal and (ii) to redeposit
<PAGE>   17
in accordance with Section 2.4 of the Deposit Agreement the remainder, if any,
of the amount withdrawn pursuant hereto.


                                       FIRST SECURITY BANK,
                                       -    NATIONAL ASSOCIATION,
                                            as Escrow Agent


                                       By
                                            ------------------------------------
                                            Name:
                                            Title:
Dated: _______ __, 199_
<PAGE>   18
                                                                       EXHIBIT C

                           NOTICE OF FINAL WITHDRAWAL


ABN AMRO BANK N.V., Chicago Branch
135 South LaSalle Street, Suite 660
Chicago, IL  60674-9135

Attention:  Claudia Heldring
Telecopier:  312-606-8428


ABN AMRO BANK N.V., Chicago Branch
181 W. Madison Street
Chicago, IL  60602

Attention:  Money Markets Desk
Telecopier:  312-904-9106

Gentlemen:

                 Reference is made to the Deposit Agreement (Class A) dated as
of February 9, 1998 (the "Deposit Agreement") between First Security Bank,
N.A., as Escrow Agent, and ABN AMRO Bank N.V., Chicago Branch, as Depositary
(the "Depositary").

                 In accordance with Section 2.3(b) of the Deposit Agreement,
the undersigned hereby requests the withdrawal of the entire amount of all
Deposits.

                 The undersigned hereby directs the Depositary to pay the
proceeds of the Deposits and accrued interest thereon to the Paying Agent at
Wilmington Trust Company, ABA# 03-11-000-92, Account No. 44043-0, Reference:
Atlas Air.


                                       FIRST SECURITY BANK,
                                            NATIONAL ASSOCIATION,
                                            as Escrow Agent


                                       By
                                            ------------------------------------
                                            Name:
                                            Title:
Dated: _______ __, 199_