EXHIBIT 3.1

                                                               EXECUTION VERSION

                  AMENDMENT NO. 2 TO FIRST AMENDED AND RESTATED
                       AGREEMENT OF LIMITED PARTNERSHIP OF
                           HOLLY ENERGY PARTNERS, L.P.

      THIS AMENDMENT NO. 2 TO THE FIRST AMENDED AND RESTATED AGREEMENT OF
LIMITED PARTNERSHIP OF HOLLY ENERGY PARTNERS, L.P. (this "Amendment"), dated as
of July 6, 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 13.1(d)(i) 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 13.1(d)(i) of the Partnership Agreement provides that the
General Partner, without the approval of any Limited Partners, 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, acting pursuant to the power and authority granted to it under
Section 13.1(d)(i) of the Partnership Agreement, the General Partner has
determined that the following amendment to the Partnership Agreement does not
adversely affect the Limited Partners (including any particular class of
Partnership Interests) in any material respect.

      NOW, THEREFORE, it is hereby agreed as follows:

A.    Amendment. The Partnership Agreement is hereby amended as follows:

      Section 7.11 is hereby amended and restated in its entirety as follows:

      7.11 Purchase or Sale of Partnership Securities. The General Partner may
cause the Partnership to purchase or otherwise acquire Partnership Securities;
provided that, except as permitted pursuant to Section 4.10, the General Partner
may not cause any Group Member to purchase Subordinated Units during the
Subordination Period. Such Partnership Securities shall be held by the
Partnership as treasury securities unless they are expressly cancelled by action
of an appropriate officer of the General Partner. As long as Partnership
Securities are held by any Group Member, such Partnership Securities shall not
be considered Outstanding for any purpose, except as otherwise provided herein.
The General Partner or any Affiliate of the General Partner may also purchase or
otherwise acquire and sell or otherwise dispose of Partnership Securities for
its own account, subject to the provisions of Articles IV and X.

B. Agreement in Effect. Except as hereby amended, the Partnership Agreement
shall remain in full force and effect.

                  AMENDMENT NO. 2 TO FIRST AMENDED AND RESTATED
                       AGREEMENT OF LIMITED PARTNERSHIP OF
                           HOLLY ENERGY PARTNERS, L.P.



C. Governing Law. This Amendment shall be governed by, and interpreted in
accordance with, the laws of the State of Delaware, all rights and remedies
being governed by such laws without regard to principles of conflicts of laws.

D. Severability. Each provision of this Amendment shall be considered severable
and if for any reason any provision or provisions herein are determined to be
invalid, unenforceable or illegal under any existing or future law, such
invalidity, unenforceability or illegality shall not impair the operation of or
affect those portions of this Amendment that are valid, enforceable and legal.

            [THE REMAINDER OF THIS PAGE IS INTENTIONALLY LEFT BLANK]

                  AMENDMENT NO. 2 TO FIRST AMENDED AND RESTATED
                       AGREEMENT OF LIMITED PARTNERSHIP OF
                           HOLLY ENERGY PARTNERS, L.P.

                                       2



      IN WITNESS WHEREOF, this Amendment has been executed as of the date first
written above.

                               HEP LOGISTICS HOLDINGS, L.P.

                               By:    HOLLY LOGISTIC SERVICES, L.L.C.,
                                      its General Partner

                               By:    /s/ Stephen J. McDonnell
                                      ------------------------------------------
                               Name:  Stephen J. McDonnell
                               Title: Vice President and Chief Financial Officer

                                 SIGNATURE PAGE
                  AMENDMENT NO. 2 TO FIRST AMENDED AND RESTATED
                       AGREEMENT OF LIMITED PARTNERSHIP OF
                           HOLLY ENERGY PARTNERS, L.P.