<PAGE>   1
                                                                     EXHIBIT 3.1

                               FIRST AMENDMENT TO
                           SECOND AMENDED AND RESTATED
                        AGREEMENT OF LIMITED PARTNERSHIP
                      OF EOP OPERATING LIMITED PARTNERSHIP

         THIS FIRST AMENDMENT TO SECOND AMENDED AND RESTATED AGREEMENT OF
LIMITED PARTNERSHIP OF EOP OPERATING LIMITED PARTNERSHIP (this "AMENDMENT"),
dated August 21, 2000, is entered into by EQUITY OFFICE PROPERTIES TRUST, a
Maryland real estate investment trust, as the general partner (the "GENERAL
PARTNER") of EOP Operating Limited Partnership, a Delaware limited partnership
(the "PARTNERSHIP"), for itself and on behalf of itself and the Limited Partners
of the Partnership, and those persons whose signatures are set forth on the
signature pages attached hereto.

         WHEREAS, on the date hereof, NORTH LOOP-TREMONT PARTNERSHIP, an
Illinois partnership ("CONTRIBUTOR"), is receiving 94,106 Class B Units of
limited partnership interest in the Partnership ("OP UNITS") in exchange for its
limited partnership interest in ECH-North Loop/Theater District Parking Limited
Partnership ("ECHNLT"), pursuant to a closing under, and as more particularly
described in, that certain Contribution Agreement (the "CONTRIBUTION AGREEMENT")
dated November 6, 1997, by and between the Contributor, the Partnership,
ECH-Chicago Parking Limited Partnership ("ECH") and the constituent partners of
Contributor (the "CONSTITUENT PARTNERS") and that certain Settlement Agreement
and Release of Claims by and between the Partnership, ECH, Contributor and the
Constituent Partners;

         WHEREAS, the principal assets of ECHNLT are the parking garages
(collectively, the "PROPERTIES") commonly known as: (i) the Theater District
Self Park, Chicago, Illinois ("TD SELF PARK"); and (ii) the North Loop
Transportation Center, Chicago, Illinois ("NLTC");

         WHEREAS, pursuant to the authority granted to the General Partner under
the Second Amended and Restated Agreement of Limited Partnership of EOP
Operating Limited Partnership dated as of June 19, 2000, (the "PARTNERSHIP
AGREEMENT"), the General Partner desires to amend the Partnership Agreement to
reflect (i) the admission of the Contributor as an Additional Limited Partner
and the holder of the OP Units and (ii) the agreements by and among the
Partnership and the Contributor as to certain other matters set forth on Exhibit
B to this Amendment; and

         WHEREAS, the Contributor desires to become a party to the Partnership
Agreement and to be bound by all of the terms, conditions and other provisions
of this Amendment, the Exhibits hereto, and the Partnership Agreement;

         NOW, THEREFORE, in consideration of the premises set forth above and
for other good and valuable consideration, the receipt and sufficiency of which
hereby are acknowledged, the General Partner hereby amends the Partnership
Agreement as follows:

<PAGE>   2

         1. RESTATEMENT OF EXHIBIT A. Exhibit A to the Partnership Agreement
hereby is amended to reflect the admission of Contributor as an Additional
Limited Partner to the Partnership hereby. Exhibit "A" attached to this
Amendment contains the name, address, Capital Account, number of Partnership
Units and Percentage Interest of Contributor and shall be deemed attached to,
and an addendum of, Exhibit A to the Partnership Agreement for all relevant
purposes.

         2. AMENDMENT AND RESTATEMENT OF EXHIBIT E. Exhibit E to the Partnership
Agreement is hereby amended by attaching and adding Exhibit B to this Amendment,
which sets forth specific agreements regarding certain additional rights and
obligations of the Contributor, as Exhibit E-7 to the Partnership Agreement.
Further, Exhibit E to the Partnership Agreement shall be restated to designate
Contributor as a Part II Protected Partner. Exhibit E shall be further amended
by adding the following new explanatory note, which shall appear as an
annotation to Part II Protected Partner added to such Exhibit E pursuant to the
preceding sentence of this paragraph 2:

            (7)  Protected Amount is as provided for in Exhibit E-7.

         3. REPRESENTATIONS AND WARRANTIES. The General Partner hereby
represents and warrants to Contributor that the General Partner has the
authority to execute and enter into this Amendment without obtaining the consent
of the Limited Partners.

         4. DEFINED TERMS. All capitalized terms used in this Amendment and not
otherwise defined shall have the meanings assigned to them in the Partnership
Agreement. Except as modified herein, all terms and conditions of the
Partnership Agreement shall remain in full force and effect, which terms and
conditions the General Partner hereby ratifies and affirms.

         5. TIME IS OF THE ESSENCE. Time is of the essence of each and every
provision of this Amendment.

         IN WITNESS WHEREOF, the undersigned has executed this Amendment as of
the date first set forth above.

                                            EQUITY OFFICE PROPERTIES TRUST, a
                                            Maryland real estate investment
                                            trust, the General Partner of EOP
                                            Operating Limited Partnership and on
                                            behalf of existing Limited Partners


                                            By:    /s/ LAURA GERARD HASSAN
                                               --------------------------------
                                            Name:  LAURA GERARD HASSAN
                                                 ------------------------------
                                            Title: Vice President
                                                  -----------------------------


                                       2
<PAGE>   3


                                     CONTRIBUTOR:

                                     NORTH LOOP-TREMONT PARTNERSHIP, an
                                     Illinois partnership

                                     By:    North Loop Transportation Center
                                            Limited Partnership, an Illinois
                                            limited partnership, as a
                                            Constituent Partner

                                            By:    Richard A. Stein Development
                                                   Company, Inc., an Illinois
                                                   corporation, as its general
                                                   partner and individually in
                                                   its capacity as a Constituent
                                                   Partner


                                                   By: /s/ RICHARD A. STEIN
                                                      --------------------------
                                                      Its:
                                                          ----------------------

                                            By:    Ruvir Corporation, a
                                                   California corporation, as
                                                   its general partner and
                                                   individually in its capacity
                                                   as a Constituent Partner


                                                   By: /s/ G. RICHARD KATZENBACH
                                                      --------------------------
                                                      Its:
                                                          ----------------------

                                            By:    Myron C. Warshauer
                                                   Development Company, Inc. an
                                                   Illinois corporation, as its
                                                   general partner and
                                                   individually in its
                                                   capacity as a Constituent
                                                   Partner


                                                   By: /s/ MYRON C. WARSHAUER
                                                      --------------------------
                                                      Its:
                                                          ----------------------

                                            By:    Bronco Ltd., a California
                                                   limited partnership, as its
                                                   limited partner and
                                                   individually in its capacity
                                                   as a Constituent Partner


                                                   By: /s/ G. RICHARD KATZENBACH
                                                      --------------------------
                                                      Its:
                                                          ----------------------


                                       3
<PAGE>   4


                                            By: /s/ MYRON C. WARSHAUER
                                               ---------------------------------
                                               Myron C. Warshauer, as its
                                               limited partner and individually
                                               in its capacity as a Constituent
                                               Partner


                                            By: /s/ RICHARD A. STEIN
                                               ---------------------------------
                                               Richard A. Stein, as its limited
                                               partner and individually in its
                                               capacity as a Constituent Partner


                                            By: /s/ RICHARD A. HANSON
                                               ---------------------------------
                                               Richard A. Hanson, as its limited
                                               partner and individually in its
                                               capacity as a Constituent Partner

                                     By:    Tremont Theatre Row Partnership, an
                                            Illinois limited partnership, as a
                                            partner and individually in its
                                            capacity as a Constituent Partner

                                            By:    Stein & Company Theatre
                                                   District Self-Park, Inc., an
                                                   Illinois corporation, as its
                                                   general partner and
                                                   individually in its
                                                   capacity as a Constituent
                                                   Partner


                                                   By: /s/ RICHARD A. STEIN
                                                      --------------------------
                                                      Its:
                                                          ----------------------

                                            By:    Ruvir Corporation, a
                                                   California corporation, as
                                                   its general partner and
                                                   individually in its capacity
                                                   as a Constituent Partner


                                                   By: /s/ G. RICHARD KATZENBACH
                                                      --------------------------
                                                      Its:
                                                          ----------------------

                                            By:    Double R/Tremont Partnership,
                                                   an Illinois general
                                                   partnership, as its limited
                                                   partner and individually in
                                                   its capacity as a Constituent
                                                   Partner



                                       4
<PAGE>   5


                                                   By: /s/ RICHARD A. STEIN
                                                      --------------------------
                                                      Its:
                                                          ----------------------

                                            By:    Bronco Ltd, a California
                                                   limited partnership, as its
                                                   limited partner and
                                                   individually in its capacity
                                                   as a Constituent Partner


                                                   By: /s/ G. RICHARD KATZENBACH
                                                      --------------------------
                                                      Its:
                                                          ----------------------


                                            By: /s/ MYRON C. WARSHAUER
                                               --------------------------------
                                               Myron C. Warshauer, as its
                                               limited partner and individually
                                               in its capacity as a Constituent
                                               Partner


                                            By: /s/ STANLEY WARSHAUER
                                               ---------------------------------
                                               Stanley Warshauer, as its limited
                                               partner and individually in its
                                               capacity as a Constituent Partner


                                            By: /s/ STEVEN A. WARSHAUER
                                               ---------------------------------
                                               Steven A. Warshauer, as its
                                               limited partner and individually
                                               in its capacity as a Constituent
                                               Partner



                                       5
<PAGE>   6


                                                                       EXHIBIT A



<TABLE>
<CAPTION>
                                                                                  Class B Units
                                                                                 ---------------
                                                                                 Initial Capital        Percentage
    Name and Address of Partner               Partnership Units                      Account             Interest
    ---------------------------               -----------------                  ---------------        ----------
<S>                                           <C>                                <C>                    <C>

</TABLE>




                                      A-1
<PAGE>   7

                                                                       EXHIBIT B


                                   EXHIBIT E-7

               (ECH-NORTH LOOP/THEATER DISTRICT PARKING AGREEMENT)



         BACKGROUND

         On August 21, 2000, in connection with the closing of the Contribution
Agreement by and between North Loop-Tremont Partnership, an Illinois
partnership, ("Contributor"), the Partnership, ECH-Chicago Parking Limited
Partnership ("ECH"), and the Constituent partners of Contributor (the
"Constituent Partners"), dated November 6, 1997 and the Settlement Agreement and
Release of Claims by and between the Partnership, ECH, Contributor and the
Constituent Partners, Contributor received 91,406 Class B units of limited
Partnership Interest in the Partnership (the "ECHNLT Units") in exchange for its
limited partnership interest in ECH-North Loop/Theater District Parking Limited
Partnership. In connection with the issuance of the ECHNLT Units, the First
Amendment to the Agreement (the "FIRST AMENDMENT") was executed adding this
Exhibit E-7 to the Agreement, setting forth specific agreements regarding
additional rights and obligations of the Contributor with respect to the ECHNLT
Units. Such specific agreements are set forth below.

         All Capitalized terms used and not otherwise defined in this Exhibit
E-7 have the meanings assigned in the Agreement.

         SPECIFIC AGREEMENTS

1.       ADMISSION TO PARTNERSHIP. Contributor is hereby admitted to the
         Partnership as an Additional Limited Partner in accordance with Section
         12.2 of the Agreement and hereby agrees to become a party to the
         Agreement and to be bound by all of the terms, conditions and other
         provisions of the Agreement, including, but not limited to, the power
         of attorney set forth in Section 15.11 of the Agreement.

2.       RIGHT TO ASSIGN. Notwithstanding any other provision of this Exhibit
         E-7, the Agreement or the First Amendment, Contributor shall have the
         right to assign at any time and from time to time all or any portion of
         its ECHNLT Units, together with any and all other rights of Contributor
         pursuant to this Exhibit E-7 or the Agreement, to one or more of the
         constituent partners or shareholders, members, partners or
         beneficiaries of constituent partners of Contributor on the date
         hereof, whether direct or indirect, without the need for the consent of
         the General Partner or any other General Partner or Limited Partner and
         without being subject to the right of first refusal set forth in
         Section 11.3.A(a) of the Agreement, but in each case subject to the
         restrictions and conditions set forth in Sections 11.3.C, 11.3.D,
         11.3.E, 11.6.E and 11.6.F of the


                                      B-1
<PAGE>   8

         Agreement. Upon the delivery of written notice of such an assignment to
         the General Partner, each assignee of ECHNLT Units pursuant to the
         immediately preceding sentence shall be admitted to the Partnership as
         a Substituted Limited Partner owning the ECHNLT Units so assigned and
         having all of the rights of a Limited Partner under the Agreement, the
         First Amendment thereto and this Exhibit E-7, subject only to such
         assignee executing and delivering to the Partnership an acceptance of
         all of the terms and conditions of the Agreement and such other
         documents or instruments as the General Partner may reasonably require
         to effect such admission, in accordance with Section 11.4.B of the
         Agreement. Each permitted assignee of any of the ECHNLT Units issued to
         the Contributor pursuant to the Contribution Agreement that is admitted
         as a Substituted Limited Partner in accordance with this Section 2 or
         Article XI of the Agreement, for so long as such Person owns any such
         ECHNLT Units, is referred to in this Exhibit E-7 as an "INDIRECT EQUITY
         HOLDER." Upon satisfaction of the condition described in the second
         sentence of this Section 2, the General Partner shall amend Exhibit A
         to the Agreement in the manner described in Section 11.4.C of the
         Agreement. For purposes of Section 8.6 of the Agreement, Contributor
         and each Indirect Equity Holder shall be entitled to exercise its right
         to require the Partnership to redeem all or any portion of the ECHNLT
         Units at any time on or after the first anniversary date of the
         issuance of the ECHNLT Units to Contributor.

3.       PRE-CONTRIBUTION GAIN. Contributor shall be allocated gain in
         accordance with Section 704(c) of the Code upon the sale, transfer,
         conveyance or disposition, directly or indirectly, of either or both
         Properties (as such term is defined in the First Amendment) (such gain
         being hereinafter referred to as "PRE-CONTRIBUTION GAIN").
         Notwithstanding anything contained in the Agreement to the contrary,
         the Pre-Contribution Gain allocable to Contributor pursuant to Section
         704(c) of the Code in connection with any sale, transfer, conveyance or
         disposition, directly or indirectly, of the Properties shall be, in
         aggregate and as of the date hereof, $12,424,927 in respect of the TD
         Self Park (as such term is defined in the First Amendment) and
         $35,127,926 in respect of NLTC (as such term is defined in the First
         Amendment), as each such amount is hereafter reduced in accordance with
         the provisions of Section 704(c) of the Code and Exhibit C, Paragraph 2
         of the Agreement. The provisions of Exhibit C, Paragraph 2 to the
         Agreement shall be applicable with respect to the allocation of income,
         gain, loss and deduction pursuant to Section 704(c) of the Code to
         Contributor.

4.       ALLOCATIONS. Notwithstanding any contrary provision in the Agreement,
         for purposes of allocating items of income, gain, loss and deduction
         with respect to the Properties in the manner required by Section 704(c)
         of the Code, the Partnership shall employ, and shall cause any entity
         controlled by the Partnership which holds title to any of the
         Properties to employ, the "traditional method" as set forth in
         Regulation Section 1.704-3(b).

5.       OBLIGATION TO RESTORE DEFICIT CAPITAL ACCOUNTS. Contributor shall be a
         Part II Protected Partner pursuant to the Agreement for all relevant
         purposes. The Protected Amount allocable to Contributor pursuant to the
         Agreement shall be the amount


                                      B-2
<PAGE>   9

         designated on Schedule 1 to this Exhibit E-7 as the Protected Amount
         for Contributor. Notwithstanding anything contained in the Agreement to
         the contrary, any Indirect Equity Holder that is admitted as a
         Substitute Limited Partner pursuant to, and in accordance with, Section
         2 to this Exhibit E-7 above shall be admitted as a Part II Protected
         Partner if and only if all of the following conditions are satisfied:
         (i) such Indirect Equity Holder shall expressly assume, in writing, all
         of the liabilities and obligations of a Part II Protected Partner
         pursuant to the Agreement for the benefit of the General Partner and
         the Partnership (such written assumption agreement, an "ASSUMPTION
         AGREEMENT"); (ii) such Indirect Equity Holder shall designate its
         Protected Amount in the Assumption Agreement, which Protected Amount
         shall be approved by Contributor (or the applicable immediate
         predecessor-in-interest to such Indirect Equity Holder) in writing; and
         (iii) the aggregate Protected Amount, at any time, allocated to
         Contributor and any and all Indirect Equity Holders allocated a
         Protected Amount pursuant to this sentence shall not exceed the
         Protected Amount presently allocated to Contributor on Schedule 1 to
         this Exhibit E-7.



                                      B-3
<PAGE>   10


                                                       SCHEDULE 1 TO EXHIBIT E-7


<TABLE>
<CAPTION>
  PART II PROTECTED PARTNER                            PROTECTED AMOUNT
  -------------------------                            ----------------
<S>                                                    <C>
</TABLE>

                                      B-4