AMENDMENT TO THE 1ST AMENDED/RESTATED AGREEMENT OF LIMITED PARTNERSHIP

AMENDMENT NO. 1 TO THE FIRST AMENDED AND RESTATED
AGREEMENT OF LIMITED PARTNERSHIP OF
HOLLY ENERGY PARTNERS, L.P.

     THIS AMENDMENT NO. 1 TO THE FIRST AMENDED AND RESTATED AGREEMENT OF LIMITED PARTNERSHIP OF HOLLY ENERGY PARTNERS, L.P. (this “Amendment”), dated as of February 28, 2005, is entered into and effectuated by HEP Logistics Holdings, L.P., a Delaware limited partnership, as the General Partner, pursuant to authority granted to it in Section 5.6 of the First Amended and Restated Agreement of Limited Partnership of Holly Energy Partners, L.P., dated as of July 13, 2004, as amended (the “Partnership Agreement”). Capitalized terms used but not defined herein are used as defined in the Partnership Agreement.

     WHEREAS, Section 5.6 of the Partnership Agreement provides that the General Partner, without the approval of any Limited Partners, may issue additional Partnership Securities, or classes or series thereof, for any Partnership purpose at any time and from time to time, and may issue such Partnership Securities to such Persons, for such consideration and on such terms and conditions as shall be established by the General Partner; and

     WHEREAS, Section 13.1(g) of the Partnership Agreement provides that the General Partner, without the approval of any Partner (subject to the terms of Section 5.7 of the Partnership Agreement), may amend any provision of the Partnership Agreement necessary or appropriate in connection with the authorization of issuance of any class or series of Partnership Securities pursuant to Section 5.6 of the Partnership Agreement; and

     WHEREAS, the General Partner has determined that the issuance of the Class B Subordinated Units provided for in this Amendment is permitted by Section 5.7 of the Partnership Agreement; and

     WHEREAS, Section 13.1(d)(i) of the Partnership Agreement provides that the General Partner, without the approval of any Limited Partner, may amend any provision of the Partnership Agreement to reflect a change that the General Partner determines does not adversely affect the Limited Partners (including any particular class of Partnership Interests as compared to other classes of Partnership Interests) in any material respect; and

     WHEREAS, the Partnership has entered into (i) a Contribution Agreement, dated as of January 25, 2005 (the “Alon Contribution Agreement”), with Alon Pipeline Logistics, LLC, a Delaware limited liability company (“Alon Pipeline Logistics”), and Alon USA, LP, a Texas limited partnership (“Alon”), and certain other parties named therein, and (ii) a Pipelines and Terminals Agreement, dated as of February 28, 2005 (the “Alon Pipelines Agreement”), with Alon; and

     WHEREAS, the Contribution Agreement obligates the Partnership to issue limited partner interests to be designated as Class B Subordinated Units having the terms set forth herein; and

Amendment No. 1 to Partnership Agreement_ Exhibit 3.1 to Form 8-K (HEP_UBS Transactions).DOC

     WHEREAS, the General Partner deems it in the best interest of the Partnership to effect this Amendment in order to provide for (i) the issuance of Class B Subordinated Units to Alon Pipeline Logistics pursuant to the Contribution Agreement and (ii) such other matters as are provided herein.

     NOW, THEREFORE, it is hereby agreed as follows:

     “ Alon ” means Alon USA, LP, a Texas limited partnership, and its successors and assigns.

      “ALON Event of Default” means an ALON Event of Default specified in Section 16(b)(i) of the Alon Pipelines Agreement in respect of payments due pursuant to the Minimum Volume Commitment which default has not been cured within the time specified in Section 17(a) of the Alon Pipelines Agreement.

     “Alon Pipeline Logistics” means Alon Pipeline Logistics, LLC, a Delaware limited liability company.

      “Alon Potential Event of Default” means a default in respect of payments due pursuant to the Minimum Volume Commitment which would become an Alon Event of Default on the expiration of the time period specified in Section 17(a) of the Alon Pipelines Agreement.

     “ Alon Pipelines Agreement ” means the Pipelines and Terminals Agreement, dated as of February 28, 2005, between the Partnership and Alon.

     “ Class B Subordinated Unit ” means a Unit representing a fractional part of the Partnership Interests of all Limited Partners and Assignees and having the rights and obligations specified with respect to the Class B Subordinated Units in this Agreement. The term “Class B Subordinated Unit” as used herein does not include a Common Unit, Subordinated Unit or Parity Unit. A Class B Subordinated Unit that is convertible into a Common Unit or a Parity Unit shall not constitute a Common Unit or Parity Unit until such conversion occurs.

     “ Class B Subordination Period ” means the period commencing on February 28, 2005 and ending on the first to occur of the following dates:

     (a) the first day of any Quarter beginning after March 31, 2010 in respect of which no ALON Event of Default existed with respect to each of the three consecutive, non-overlapping four-Quarter periods immediately preceding such date; provided , however , that if an Alon Potential Event of Default exists on such date, but is cured prior to its becoming an Alon Event of Default, the Class B Subordination Period shall end on the first Business Day after such cure; and

Amendment No. 1 to First Amended and Restated
Agreement of Limited Partnership of
Holly Energy Partners, L.P.

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     (b) the date on which the General Partner is removed as general partner of the Partnership upon the requisite vote by holders of Outstanding Units under the circumstances where Cause does not exist and Units held by the General Partner and its Affiliates are not voted in favor of such removal.

     “ Minimum Volume Commitment ” has the meaning set forth in the Alon Pipelines Agreement.

     The term “Common Unit” does not refer to a Subordinated Unit or a Class B Subordinated Unit prior to its conversion into a Common Unit pursuant to the terms hereof.

     “ Common Unit Arrearage ” means, with respect to any Common Unit, whenever issued, as to any Quarter within the Subordination Period or the Class B Subordination Period, the excess, if any, of (a) the Minimum Quarterly Distribution with respect to a Common Unit in respect of such Quarter over (b) the sum of all Available Cash distributed with respect to a Common Unit in respect of such Quarter pursuant to Section 6.4(a)(i).

     “ Cumulative Common Unit Arrearage ” means, with respect to any Common Unit, whenever issued, and as of the end of any Quarter, the excess, if any, of (a) the sum resulting from adding together the Common Unit Arrearage as to an Initial Common Unit for each of the Quarters within the Subordination Period or the Class B Subordination Period ending on or before the last day of such Quarter over (b) the sum of any distributions theretofore made pursuant to Section 6.4(a)(ii) and the second sentence of Section 6.5 with respect to an Initial Common Unit (including any distributions to be made in respect of the last of such Quarters).

     “ Limited Partner Interest ” means the ownership interest of a Limited Partner or Assignee in the Partnership, which may be evidenced by Common Units, Subordinated Units, Class B Subordinated Units, Incentive Distribution Rights or other Partnership Securities or a combination thereof or interest therein, and includes any and all benefits to which such Limited Partner or Assignee is entitled as provided in this Agreement, together with all obligations of such Limited Partner or Assignee to comply with the terms and provisions of this Agreement; provided , however , that when the term “Limited Partner Interest” is used herein in the context of any vote or other approval, including without limitation Articles XIII and XIV, such term shall not, solely for such purpose, include any holder of an Incentive Distribution Right except as may otherwise be required by law.

     “ Partnership Security ” means any class or series of equity interest in the Partnership (but excluding any options, rights, warrants and appreciation rights relating to an equity interest in the Partnership), including without limitation, Common Units, Subordinated Units, Class B Subordinated Units and Incentive Distribution Rights.

Amendment No. 1 to First Amended and Restated
Agreement of Limited Partnership of
Holly Energy Partners, L.P.

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     “ Remaining Net Positive Adjustments ” means as of the end of any taxable period, (i) with respect to the Unitholders holding Common Units, Subordinated Units or Class B Subordinated Units, the excess of (a) the Net Positive Adjustments of the Unitholders holding Common Units, Subordinated Units or Class B Subordinated Units as of the end of such period over (b) the sum of those Partners’ Share of Additional Book Basis Derivative Items for each prior taxable period, (ii) with respect to the General Partner (as holder of the General Partner Interest), the excess of (a) the Net Positive Adjustments of the General Partner as of the end of such period over (b) the sum of the General Partner’s Share of Additional Book Basis Derivative Items with respect to the General Partner Interest for each prior taxable period, and (iii) with respect to the holders of Incentive Distribution Rights, the excess of (a) the Net Positive Adjustments of the holders of Incentive Distribution Rights as of the end of such period over (b) the sum of the Share of Additional Book Basis Derivative Items of the holders of the Incentive Distribution Rights for each prior taxable period.

     “ Share of Additional Book Basis Derivative Items ” means in connection with any allocation of Additional Book Basis Derivative Items for any taxable period, (i) with respect to the Unitholders holding Common Units, Subordinated Units or Class B Subordinated Units, the amount that bears the same ratio to such Additional Book Basis Derivative Items as the Unitholders’ Remaining Net Positive Adj