Document:

EXHIBIT 4.1.40

                                                                  EXECUTION COPY
                                                           1998 EETC TRANSACTION

                   1998 CLASS A PASS THROUGH TRUST SUPPLEMENT

      THIS PASS  THROUGH  TRUST  SUPPLEMENT  is made as of the 27th day of July,
2004 (this "TRUST  SUPPLEMENT"),  by and between ATLAS AIR, INC. (the "COMPANY")
and WILMINGTON TRUST COMPANY (the "TRUSTEE"),  as Trustee under the Pass Through
Trust  Agreement  dated as of  February  9, 1998,  between  the  Company and the
Trustee with respect to the formation of Atlas Air Pass Through Trust  1998-1A-S
(as amended from time to time, the "TRUST AGREEMENT").

                             PRELIMINARY STATEMENT

      As contemplated by the Restructure Agreements,  dated as of July 27, 2004,
among  the  Company,   the  Trustee  and  the  other   parties   named   therein
(collectively, the "RESTRUCTURE AGREEMENTS"), the Company and the Trustee desire
to enter into this Trust Supplement.

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

1. DEFINED TERMS.

      Capitalized  terms used and not  otherwise  defined  herein shall have the
same meanings given to them in the Trust Agreement.

2. AMENDMENTS TO TRUST AGREEMENT.

      The Trust Agreement is amended as follows:

      (a)   The  following  Section  12.15 is added after  Section  12.14 of the
            Trust Agreement:

            "12.15 ADDITIONAL PROVISIONS REGARDING LEASES AND INDENTURES.

                  (a) The Trustee and the Company acknowledge and agree that (i)
            each of the Leases has been amended by a certain  amendment dated as
            of July 27, 2004  between the Owner  Trustee  named  therein and the
            Company (collectively, the "Lease Amendments"), and (ii) each of the
            Indentures has been amended by a certain supplement dated as of July
            27, 2004  between the Company or the Owner  Trustee (as  applicable)
            named therein and the Mortgagee  named  therein  (collectively,  the
            "Indenture Supplements").  As of the Restructure Agreement Execution
            Date, (x) all  references  herein to the Leases shall mean and refer
            to the  Leases as  amended  by the Lease  Amendments  and as further
            amended  from  time  to  time,  (y)  all  references  herein  to the
            Indentures  shall mean and refer to the Indentures as amended by the
            Indenture  Supplements and as further amended from time to time, and
            (z) all capitalized terms used herein without  definition shall have
            the respective meanings specified in the Leases, as amended by the

<PAGE>

            Lease Amendments, and in the Indentures, as amended by the Indenture
            Supplements.

                  (b) The Trustee and the Company  agree that in addition to the
            duties and  responsibilities  of the Trustee hereunder,  the Trustee
            shall also, on and after the Restructure  Agreement  Execution Date,
            have the following duties and responsibilities:

                        (i) As promptly  as  practical  after,  and in any event
                  within 10 days after, the receipt by the Trustee from the Loan
                  Trustee of any notice regarding any  Enhancements  pursuant to
                  the Leases or the  Indentures,  the Trustee shall  transmit by
                  mail  to  the   Certificateholders   holding  Certificates  in
                  accordance  with Section 313(c) of the Trust  Indenture Act, a
                  copy of such notice.

                        (ii) As promptly as  practical  after,  and in any event
                  within 10 days after, the receipt by the Trustee from the Loan
                  Trustee  of a  request  by the  Company  to sell an  Owned  or
                  Controlled Aircraft as required pursuant to the Leases and the
                  Indentures  upon the  occurrence of a Sale Trigger Event for a
                  cash bid  realizing net cash proceeds of less than the Minimum
                  Sales  Price,  the  Trustee  shall  transmit  by  mail  to the
                  Certificateholders  holding  Certificates  in accordance  with
                  Section  313(c) of the  Trust  Indenture  Act,  a copy of such
                  request.  The Trustee shall follow the Direction of a majority
                  in  interest  of the  Fractional  Undivided  Interests  of the
                  Certificates  with respect to such request.  The Trustee shall
                  not take any action with  respect to such  request  unless and
                  until it receives such a Direction.

                        (iii) As promptly as practical  after,  and in any event
                  within 10 days after, the receipt by the Trustee of any report
                  from the Loan Trustee regarding  Consolidated  Adjusted EBITDA
                  pursuant to the Leases or the  Indentures,  the Trustee  shall
                  transmit   by   mail   to   the   Certificateholders   holding
                  Certificates  in accordance  with Section  313(c) of the Trust
                  Indenture Act, a copy of such report.

                        (iv) As promptly as  practical  after,  and in any event
                  within 10 days after, the receipt by the Trustee from the Loan
                  Trustee of a request by the  Company to amend,  supplement  or
                  waive any of the  provisions of the  Maintenance  Contracts or
                  enter into any additional Maintenance Contracts in replacement
                  (whether in partial  replacement or complete  replacement)  of
                  the  Maintenance  Contracts  pursuant  to  the  Leases  or the
                  Indentures,   the  Trustee  shall  transmit  by  mail  to  the
                  Certificateholders  in accordance  with Section  313(c) of the
                  Trust Indenture Act, a copy of such request. The Trustee shall
                  follow  the  Direction  of  a  majority  in  interest  of  the
                  Fractional   Undivided  Interests  of  the  Certificates  with
                  respect to such request.

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<PAGE>

                        (v) As promptly as practical, and in any event within 10
                  days after,  the  receipt by the  Trustee of any  information,
                  report or certificate  obtained by the Consultant  pursuant to
                  the Leases or the  Indentures,  the Trustee shall  transmit by
                  mail to the  Certificateholders  in  accordance  with  Section
                  313(c)  of  the  Trust  Indenture  Act,  a copy  of  any  such
                  information, report or certificate.

                        (vi)  The  Trustee  shall  follow  the  Direction  of  a
                  majority in interest of the Fractional  Undivided Interests of
                  the  Certificates  with  respect  to  the  designation  of any
                  Special Inspector and with respect to any inspection  pursuant
                  to the Leases or the  Indentures.  As  promptly  as  practical
                  after,  and in any event within 10 days after,  the receipt by
                  the Trustee of copies of any  Aircraft  Documents,  results of
                  any  inspection  or  any  other  information  obtained  by the
                  Special  Inspector  pursuant to the Leases or the  Indentures,
                  the Trustee shall  transmit by mail to the  Certificateholders
                  in accordance  with Section 313(c) of the Trust Indenture Act,
                  copies of any such Aircraft  Documents,  results of inspection
                  or other information.

                        (vii) As promptly as practical  after,  and in any event
                  within 10 days after, the receipt by the Trustee from the Loan
                  Trustee of a request by the  Company to replace a  Maintenance
                  Contractor  pursuant  to the  Leases  or the  Indentures,  the
                  Trustee shall  transmit by mail to the  Certificateholders  in
                  accordance  with Section 313(c) of the Trust  Indenture Act, a
                  copy of such request and a copy of any  proposed  contract and
                  assignment with respect thereto.  The Trustee shall follow the
                  Direction  of a majority in interest of  Fractional  Undivided
                  Interests of the  Certificates  with respect to such  request,
                  contract and assignment. The Trustee shall not take any action
                  with respect to such request,  contract or  assignment  unless
                  and until it receives such a Direction.

                        (viii)  The  Trustee  shall  follow the  Direction  of a
                  majority in interest of Fractional  Undivided Interests of the
                  Certificates  with respect to any choice and  designation of a
                  Consultant  or a Special  Inspector  pursuant to the Leases or
                  the  Indentures.  The  Trustee  shall not take any action with
                  respect to any such choice or designation  unless and until it
                  receives such a Direction.

3. MISCELLANEOUS.

      (a)   The Trustee  accepts the trusts created by the Trust  Agreement,  as
            supplemented  by this Trust  Supplement,  and agrees to perform  the
            same upon the  terms  and  conditions  of the  Trust  Agreement,  as
            supplemented by this Trust Supplement.

      (b)   Except as  expressly  provided in this Trust  Supplement,  the Trust
            Agreement   shall   remain  in  full  force  and   effect,   without
            modification or amendment.

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<PAGE>

      (c)   This Trust  Supplement shall be binding upon, and shall inure to the
            benefit of, the  parties  hereto and the  successors  and assigns of
            each of the parties hereto.

      (d)   This  Trust  Supplement  shall be  governed  by,  and  construed  in
            accordance with, the laws of the State of New York.

      (e)   This Trust Supplement may be executed in two counterparts and by the
            parties  hereto  on  separate  counterparts,  each of which  when so
            executed  and  delivered  shall  be an  original,  but all of  which
            counterparts  taken  together  shall be deemed to constitute one and
            the same instrument.  A facsimile of an executed  counterpart  shall
            have the same effect as the original executed counterpart.

4. EFFECTIVENESS.

      This Trust  Supplement shall take effect on the Effective Date (as defined
in the Restructure Agreements).

      [Remainder of page intentionally blank. Next page is signature page.]

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<PAGE>

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

                                    ATLAS AIR, INC.

                                    By: /s/ William C. Bradley
                                        ----------------------------------------
                                    Name: William C. Bradley
                                    Title: Vice President & Treasurer

                                    WILMINGTON TRUST COMPANY,
                                    AS TRUSTEE

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

                                      1998 CLASS A PASS THROUGH TRUST SUPPLEMENT

<PAGE>

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

                                    ATLAS AIR, INC.

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

                                    WILMINGTON TRUST COMPANY,
                                    AS TRUSTEE

                                    By: /s/ Anita E. Dallago
                                        ----------------------------------------
                                    Name: Anita E. Dallago
                                    Title: Senior Financial Services Officer

                                      1998 CLASS A PASS THROUGH TRUST SUPPLEMENTEXHIBIT 4.1.41

                                                                  EXECUTION COPY
                                                           1999 EETC TRANSACTION

           AMENDMENT TO 1999 CLASS A-1 PASS THROUGH TRUST SUPPLEMENT

      THIS AMENDMENT TO TRUST  SUPPLEMENT  NO.  1999-1A-1 is made as of the 27th
day of July,  2004 (this  "AMENDMENT"),  by and  between  ATLAS AIR,  INC.  (the
"COMPANY") and WILMINGTON  TRUST COMPANY (the  "TRUSTEE"),  as Trustee under the
Pass Through Trust Agreement dated as of April 1, 1999,  between the Company and
the Trustee with  respect to the  formation  from to time of separate  Atlas Air
Pass Through Trusts (as amended from time to time, the "TRUST AGREEMENT").

                             PRELIMINARY STATEMENT

      The Company and the Trustee are parties to the Trust  Agreement and to the
supplements  thereto,  including Trust  Supplement No. 1999-1A-1 (the "CLASS A-1
SUPPLEMENT"),  pursuant  to which  7.20%  Atlas Air Pass  Through  Certificates,
Series 1999-1A-1,  were issued.  As contemplated by the Restructure  Agreements,
dated as of July 27, 2004, among the Company,  the Trustee and the other parties
named  therein  (collectively,  "RESTRUCTURE  AGREEMENTS"),  the Company and the
Trustee desire to enter into this Amendment.

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

1. DEFINED TERMS.

      Capitalized  terms used and not  otherwise  defined  herein shall have the
same meanings given to them in the Trust Agreement or Class A-1  Supplement,  as
applicable.

2. AMENDMENTS TO CLASS A-1 SUPPLEMENT.

      The Class A-1 Supplement is amended as follows:

      (a) The  following  Section 3.03 is added after  Section 3.02 of the Class
      A-1 Supplement:

            "Section 3.03 ADDITIONAL PROVISIONS REGARDING LEASES AND INDENTURES.

                  (a) The Trustee and the Company acknowledge and agree that (i)
            each of the Leases has been amended by a certain  amendment dated as
            of July 27, 2004  between the Owner  Trustee  named  therein and the
            Company (collectively, the "Lease Amendments"), and (ii) each of the
            Indentures has been amended by a certain supplement dated as of July
            27, 2004  between the Company or the Owner  Trustee (as  applicable)
            named therein and the Mortgagee  named  therein  (collectively,  the
            "Indenture Supplements").  As of the Restructure Agreement Execution
            Date, (x) all references  herein and, with respect to the Applicable
            Trust

<PAGE>

            created hereby,  in the Basic Agreement to the Leases shall mean and
            refer to the  Leases  as  amended  by the  Lease  Amendments  and as
            further  amended from time to time, (y) all  references  herein and,
            with respect to the Applicable  Trust created  hereby,  in the Basic
            Agreement to the  Indentures  shall mean and refer to the Indentures
            as amended by the Indenture  Supplements and as further amended from
            time to time,  and (z) all  capitalized  terms used herein and, with
            respect  to the  Applicable  Trust  created  hereby,  in  the  Basic
            Agreement  without  definition  shall have the  respective  meanings
            specified in the Leases, as amended by the Lease Amendments,  and in
            the Indentures, as amended by the Indenture Supplements.

                  (b) The Trustee and the Company  agree that in addition to the
            duties and  responsibilities  of the  Trustee  hereunder  and,  with
            respect to the  Applicable  Trust  created  hereby,  under the Basic
            Agreement,  the  Trustee  shall also,  on and after the  Restructure
            Agreement   Execution   Date,   have  the   following   duties   and
            responsibilities:

                        (i) As promptly  as  practical  after,  and in any event
                  within 10 days after, the receipt by the Trustee from the Loan
                  Trustee of any notice regarding any  Enhancements  pursuant to
                  the Leases or the  Indentures,  the Trustee shall  transmit by
                  mail  to  the   Certificateholders   holding  Certificates  in
                  accordance  with Section 313(c) of the Trust  Indenture Act, a
                  copy of such notice.

                        (ii) As promptly as  practical  after,  and in any event
                  within 10 days after, the receipt by the Trustee from the Loan
                  Trustee  of a  request  by the  Company  to sell an  Owned  or
                  Controlled Aircraft as required pursuant to the Leases and the
                  Indentures  upon the  occurrence of a Sale Trigger Event for a
                  cash bid  realizing net cash proceeds of less than the Minimum
                  Sales  Price,  the  Trustee  shall  transmit  by  mail  to the
                  Applicable  Certificateholders holding Applicable Certificates
                  in accordance  with Section 313(c) of the Trust Indenture Act,
                  a copy of such request. The Trustee shall follow the Direction
                  of  a  majority  in  interest  of  the  Fractional   Undivided
                  Interests of the Applicable  Certificates with respect to such
                  request. The Trustee shall not take any action with respect to
                  such request unless and until it receives such a Direction.

                        (iii) As promptly as practical  after,  and in any event
                  within 10 days after, the receipt by the Trustee of any report
                  from the Loan Trustee regarding  Consolidated  Adjusted EBITDA
                  pursuant to the Leases or the  Indentures,  the Trustee  shall
                  transmit by mail to the Applicable  Certificateholders holding
                  Applicable  Certificates  in accordance with Section 313(c) of
                  the Trust Indenture Act, a copy of such report.

                        (iv) As promptly as  practical  after,  and in any event
                  within 10 days after, the receipt by the Trustee from the Loan
                  Trustee of a request by the  Company to amend,  supplement  or
                  waive any of the provisions of the

                                       2
<PAGE>

                  Maintenance Contracts or enter into any additional Maintenance
                  Contracts in  replacement  (whether in partial  replacement or
                  complete replacement) of the Maintenance Contracts pursuant to
                  the Leases or the  Indentures,  the Trustee shall  transmit by
                  mail to the Applicable  Certificateholders  in accordance with
                  Section  313(c) of the  Trust  Indenture  Act,  a copy of such
                  request.  The Trustee shall follow the Direction of a majority
                  in  interest  of the  Fractional  Undivided  Interests  of the
                  Applicable Certificates with respect to such request.

                        (v) As promptly as practical, and in any event within 10
                  days after,  the  receipt by the  Trustee of any  information,
                  report or certificate  obtained by the Consultant  pursuant to
                  the Leases or the  Indentures,  the Trustee shall  transmit by
                  mail to the Applicable  Certificateholders  in accordance with
                  Section 313(c) of the Trust  Indenture Act, a copy of any such
                  information, report or certificate.

                        (vi)  The  Trustee  shall  follow  the  Direction  of  a
                  majority in interest of the Fractional  Undivided Interests of
                  the Applicable Certificates with respect to the designation of
                  any  Special  Inspector  and with  respect  to any  inspection
                  pursuant  to the  Leases or the  Indentures.  As  promptly  as
                  practical  after,  and in any event within 10 days after,  the
                  receipt by the  Trustee of copies of any  Aircraft  Documents,
                  results of any inspection or any other information obtained by
                  the   Special   Inspector   pursuant  to  the  Leases  or  the
                  Indentures,   the  Trustee  shall  transmit  by  mail  to  the
                  Applicable   Certificateholders  in  accordance  with  Section
                  313(c) of the Trust Indenture Act, copies of any such Aircraft
                  Documents, results of inspection or other information.

                        (vii) As promptly as practical  after,  and in any event
                  within 10 days after, the receipt by the Trustee from the Loan
                  Trustee of a request by the  Company to replace a  Maintenance
                  Contractor  pursuant  to the  Leases  or the  Indentures,  the
                  Trustee   shall   transmit   by   mail   to   the   Applicable
                  Certificateholders  in accordance  with Section  313(c) of the
                  Trust  Indenture Act, a copy of such request and a copy of any
                  proposed  contract and assignment  with respect  thereto.  The
                  Trustee  shall follow the  Direction of a majority in interest
                  of   Fractional   Undivided   Interests   of  the   Applicable
                  Certificates  with  respect  to  such  request,  contract  and
                  assignment. The Trustee shall not take any action with respect
                  to such request,  contract or  assignment  unless and until it
                  receives such a Direction.

                        (viii)  The  Trustee  shall  follow the  Direction  of a
                  majority in interest of Fractional  Undivided Interests of the
                  Applicable   Certificates  with  respect  to  any  choice  and
                  designation of a Consultant or a Special Inspector pursuant to
                  the Leases or the  Indentures.  The Trustee shall not take any
                  action with respect to any such choice or  designation  unless
                  and until it receives such a Direction.

                                       3
<PAGE>

3. MISCELLANEOUS.

      (a)   The Trustee  accepts the trusts created by the Trust  Agreement,  as
            supplemented  by  the  Class  A-1  Supplement  as  amended  by  this
            Amendment,  and  agrees  to  perform  the same  upon the  terms  and
            conditions of the Trust Agreement,  as supplemented by the Class A-1
            Supplement as amended by this Amendment.

      (b)   Except to the  extent  that the Class A-1  Supplement  is  expressly
            amended  by this  Amendment,  the  Trust  Agreement  and  Class  A-1
            Supplement   shall   remain  in  full  force  and  effect,   without
            modification or amendment.

      (c)   This Amendment shall be binding upon, and shall inure to the benefit
            of, the parties hereto and the successors and assigns of each of the
            parties hereto.

      (d)   This  Amendment  shall be governed by, and  construed in  accordance
            with, the laws of the State of New York.

      (e)   This  Amendment  may  be  executed  in two  counterparts  and by the
            parties  hereto  on  separate  counterparts,  each of which  when so
            executed  and  delivered  shall  be an  original,  but all of  which
            counterparts  taken  together  shall be deemed to constitute one and
            the same instrument.  A facsimile of an executed  counterpart  shall
            have the same effect as the original executed counterpart.

4. EFFECTIVENESS.

      This Amendment  shall take effect on the Effective Date (as defined in the
Restructure Agreements).

     [Remainder of page intentionally blank. Next page is signature page.]

                                       4
<PAGE>

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

                                    ATLAS AIR, INC.

                                    By: /s/ William C. Bradley
                                        ----------------------------------------
                                    Name: William C. Bradley
                                    Title: Vice President & Treasurer

                                    WILMINGTON TRUST COMPANY,
                                    AS TRUSTEE

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

                       AMENDMENT TO 1999 CLASS A-1 PASS THROUGH TRUST SUPPLEMENT

<PAGE>

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

                                    ATLAS AIR, INC.

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

                                    WILMINGTON TRUST COMPANY,
                                    AS TRUSTEE

                                    By: /s/ Anita E. Dallago
                                        ----------------------------------------
                                    Name: Anita E. Dallago
                                    Title: Senior Financial Services Officer

                       AMENDMENT TO 1999 CLASS A-1 PASS THROUGH TRUST SUPPLEMENT

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