EXHIBIT 10.6

Effective January 14, 2009

ATLAS PIPELINE HOLDINGS

LONG-TERM INCENTIVE PLAN

Amended and Restated as of January 14, 2009

SECTION 1: PURPOSE OF THE PLAN.

The Amended and Restated Atlas Pipeline Holdings Long-Term Incentive Plan (the
“Plan”) is intended to promote the interests of Atlas Pipeline Holdings, L.P., a
Delaware limited partnership (the “Partnership”), by providing to officers,
employees and managing board members of Atlas Pipeline Holdings GP, LLC, a
Delaware limited liability company (the “Company”), and employees of its
Affiliates, consultants and joint venture partners who perform services for the
Company or the Partnership incentive awards for superior performance that are
based on Units. It is also contemplated that the Plan will enhance the ability
of the Company and its Affiliates to attract and retain the services of
individuals who are essential for the growth and profitability of the Company or
the Partnership and to encourage them to devote their best efforts to the
business of the Company or the Partnership, thereby advancing the interests of
the Company and the Partnership.

SECTION 2: DEFINITIONS.

As used in the Plan, the following terms shall have the meanings set forth
below:

“Affiliate” means, with respect to any Person, any other Person that directly or
indirectly through one or more intermediaries controls, is controlled by or is
under common control with, the Person in question. As used herein, the term
“control” means the possession, direct or indirect, of the power to direct or
cause the direction of the management and policies of a Person, whether through
ownership of voting securities, by contract or otherwise.

“Award” means an Option or Phantom Unit granted under the Plan, and shall
include any tandem DERs granted with respect to a Phantom Unit.

“Board” means the Managing Board of the Company.

“Change in Control” means the occurrence of any of the following:

(a) the Company, or an Affiliate of the Parent, ceases to be the general partner
of the Partnership;

(b) a merger, consolidation, share exchange, division or other reorganization or
transaction of the Partnership, the general partner of Atlas Pipeline Partners,
L.P., Atlas Pipeline Partners, L.P., the Company, the Parent or any Affiliate of
the Parent that is a direct or indirect parent of the Company with any entity,
other than a transaction which would result in the voting securities of the
Partnership, the general partner of Atlas Pipeline Partners, L.P., Atlas
Pipeline Partners, L.P., the Company or Parent, as appropriate, outstanding
immediately prior thereto continuing to represent (either by

--------------------------------------------------------------------------------

remaining outstanding or by being converted into voting securities of the
surviving entity) at least 60% of the combined voting power immediately after
such transaction of the surviving entity’s outstanding securities or, in the
case of a division, the outstanding securities of each entity resulting from the
division;

(c) the equity holders of the Partnership, the general partner of Atlas Pipeline
Partners, L.P., the Parent or any Affiliate of the Parent that is a direct or
indirect parent of the Company approve a plan of complete liquidation or
winding-up or an agreement for the sale or disposition (in one transaction or a
series of transactions) of all or substantially all of the Partnership’s, the
Parent’s, the general partner of Atlas Pipeline Partners, L.P., or any such
Affiliate’s assets; or

(d) during any period of 24 consecutive months, individuals who at the beginning
of such period constituted the board of directors of the Company, the Parent or
any Affiliate of the Parent that is a direct or indirect parent of the Company
(including for this purpose any new director whose election or nomination for
election or appointment was approved by a vote of at least  2/3 of the directors
then still in office who were directors at the beginning of such period) cease
for any reason to constitute at least a majority of the board or, in the case of
a spin off of the Parent, if Edward E. Cohen and Jonathan Z. Cohen cease to be
directors of the Parent.

Notwithstanding the foregoing, with respect to any Award that is subject to
Section 409A of the Code, Change in Control shall mean a “change of control
event,” as defined in the regulations and guidance issued under Section 409A of
the Code. In addition, notwithstanding the foregoing, the Committee may specify
a more limited definition of Change in Control for a particular Award, as the
Committee deems appropriate.

“Code” means the Internal Revenue Code of 1986, as amended, or any successor
thereto.

“Committee” means (i) the Board or such committee of the Board or the board of
an Affiliate of the Partnership appointed by the Board to administer the Plan or
(ii) with respect to Awards that are intended to be “qualified performance-based
compensation” under Section 162(m) of the Code, a committee that consists of two
or more persons appointed by the Board, all of whom shall be “outside directors”
as defined under Section 162(m) of the Code and related Treasury regulations.

“DER” means a right, granted in tandem with a specific Phantom Unit, to receive
an amount in cash equal to, and at the same time as, the cash distributions made
by the Partnership with respect to a Unit during the period such Phantom Unit is
outstanding.

“Disability” means an illness or injury that lasts at least 6 months, is
expected to be permanent and renders the Participant unable to substantially
carry out his or her duties to the Company or any of its Affiliates, as
determined by the Committee.

“Employee” means any officer or employee of the Company, its Affiliates,
consultants or joint venture partners who performs services for the Company or
the Partnership or in furtherance of our or the Partnership’s business.

 

2

--------------------------------------------------------------------------------

“Exchange Act” means the Securities Exchange Act of 1934, as amended.

“Fair Market Value” means the closing sales price of a Unit on the applicable
date (or if there is no trading in the Units on such date, the closing sales
price on the last date Units were traded). In the event Units are not publicly
traded at the time a determination of fair market value is required to be made
hereunder, the determination of fair market value shall be made in good faith by
the Committee.

“Manager” means a “non-employee director” of the Company as defined in Rule
16b-3 under the Exchange Act.

“Option” means an option to purchase Units granted under the Plan.

“Parent” means Atlas America, Inc., a Delaware corporation.

“Participant” means any Employee or Manager granted an Award under the Plan.

“Partnership Agreement” means the Agreement of Limited Partnership of Atlas
Pipeline Holdings, L.P., as amended from time to time.

“Person” means an individual or a corporation, limited liability company,
partnership, joint venture, trust, unincorporated organization, association,
government agency or political subdivision thereof or other entity.

“Phantom Unit” means a phantom (notional) unit granted under the Plan which upon
vesting entitles the Participant to receive a Unit or its then Fair Market Value
in cash, as determined by the Committee.

“Restricted Period” means the period established by the Committee with respect
to an Award during which the Award remains subject to forfeiture or is not
exercisable by the Participant.

“Rule 16b-3” means Rule 16b-3 promulgated by the SEC under the Exchange Act, or
any successor rule or regulation thereto as in effect from time to time.

“SEC” means the Securities and Exchange Commission, or any successor thereto.

“Securities Act” means the Securities Act of 1933, as amended.

“Unit” means a common unit of limited partner interest of the Partnership.

SECTION 3: ADMINISTRATION.

The Plan shall be administered by the Committee. A majority of the Committee
shall constitute a quorum, and the acts of a majority of the members of the
Committee who are present at any meeting thereof at which a quorum is present,
or acts unanimously approved by the members of the Committee in writing, shall
be the acts of the Committee. Subject to the following and any applicable law,
the Committee, in its sole discretion, may delegate any or all of its powers and
duties under the Plan, including the power to grant Awards under the Plan, to
the Chief

 

3

--------------------------------------------------------------------------------

Executive Officer of the Company, subject to such limitations on such delegated
powers and duties as the Committee may impose, if any; provided, however, that
such delegation shall not limit the Chief Executive Officer’s right to receive
Awards under the Plan. Notwithstanding the foregoing, the Chief Executive
Officer may not grant Awards to, or take any action with respect to any Award
previously granted to, himself or a Person who is an Employee or Manager subject
to Rule 16b-3. Subject to the terms of the Plan and applicable law, and in
addition to other express powers and authorizations conferred on the Committee
by the Plan, the Committee shall have full power and authority to: (i) designate
Participants; (ii) determine the type or types of Awards to be granted to a
Participant; (iii) determine the terms and conditions of any Award;
(iv) determine whether, to what extent, and under what circumstances Awards may
be settled, exercised, canceled, or forfeited; (v) interpret and administer the
Plan and any instrument or agreement relating to an Award made under the Plan;
(vi) establish, amend, suspend, or waive such rules and regulations and appoint
such agents as it shall deem appropriate for the proper administration of the
Plan; and (vii) make any other determination and take any other action that the
Committee deems necessary or desirable for the administration of the Plan.
Unless otherwise expressly provided in the Plan, all designations,
determinations, interpretations, and other decisions under or with respect to
the Plan or any Award shall be within the sole discretion of the Committee, may
be made at any time and shall be final, conclusive, and binding upon all
Persons, including the Company, the Partnership, any Affiliate, any Participant,
and any beneficiary of any Award. All Awards under the Plan shall be made
conditional upon the Participant’s acknowledgement, in writing or by acceptance
of the Award, that all decisions and determinations of the Committee shall be
final and binding on the Participant, his or her beneficiaries and any other
person having or claiming an interest in such Award. Awards made under a
particular Section of the Plan need not be uniform as among Participants.

SECTION 4: UNITS.

(a) Units Available. Subject to adjustment as provided in Section 4(c), the
number of Units with respect to which Phantom Units and Options may be granted
under the Plan is 2,100,000. If any Option or Phantom Unit is forfeited or
otherwise terminates or is canceled or paid without the delivery of Units, then
the Units covered by such Award, to the extent of such forfeiture, termination,
payment or cancellation, shall again be Units with respect to which Awards may
be granted.

(b) Sources of Units Deliverable under Awards. Any Units delivered pursuant to
an Award shall consist, in whole or in part, of Units newly issued by the
Partnership, Units acquired in the open market or from any Affiliate of the
Partnership or the Company, or any other Person, or any combination of the
foregoing, as determined by the Committee in its discretion.

(c) Adjustments. In the event that any distribution (whether in the form of
cash, Units, other securities or other property), recapitalization, split,
reverse split, reorganization, merger, consolidation, split-up, spin-off,
combination, repurchase, or exchange of Units or other securities of the
Partnership, issuance of warrants or other rights to purchase Units or other
securities of the Partnership, or other similar transaction or event affects the
Units such that an adjustment is necessary in order to prevent dilution or
enlargement of the benefits or potential benefits intended to be made available
under the Plan, then the Committee shall equitably adjust (i) the number and
type of Units (or other securities or property) with respect to which Awards may
be granted, (ii)

 

4

--------------------------------------------------------------------------------

the number and type of Units (or other securities or property) subject to
outstanding Awards, and (iii) the grant or exercise price with respect to any
Award; provided, however, that the number of Units subject to any Award shall
always be a whole number. The Committee may make provision for a cash payment to
the holder of an outstanding Award.

SECTION 5: ELIGIBILITY.

Any Employee or Manager shall be eligible to be designated a Participant and
receive an Award under the Plan.

SECTION 6: AWARDS.

(a) Options. The Committee shall have the authority to determine the Employees
and Managers to whom Options shall be granted, the number of Units to be covered
by each Option, the exercise price therefor, the Restricted Period and the
conditions and limitations applicable to the exercise of the Option, as the
Committee shall determine, that are not inconsistent with the provisions of the
Plan.

(i) Exercise Price. The exercise price per Unit purchasable under an Option
shall be determined by the Committee at the time the Option is granted and may
be more or less than its Fair Market Value as of the date of grant.

(ii) Time and Method of Exercise. The Committee shall determine the Restricted
Period and the method or methods by which payment of the exercise price may be
made or deemed to have been made, which may include, without limitation, cash,
check acceptable to the Board, a “cashless-broker” exercise through procedures
approved by the Board, a recourse note from the Participant in a form acceptable
to the Board, or any combination thereof, having a fair market value on the
exercise date equal to the relevant exercise price.

(b) Phantom Units. The Committee shall have the authority to determine the
Employees and Managers to whom Phantom Units shall be granted, the number of
Phantom Units to be granted to each such Participant, the Restricted Period, the
conditions under which the Phantom Units may become vested or forfeited, whether
DERs are granted with respect to an Award and such other terms and conditions,
as the Committee may determine, that are not inconsistent with the provisions of
the Plan.

(c) General.

(i) Forfeiture. Except as otherwise provided in the terms of the Award, upon
termination of a Participant’s employment with the Company or its Affiliates or
membership on the Board during the applicable Restricted Period, all Options and
unvested Phantom Units shall be forfeited by the Participant; provided, however,
that if the reason for the termination is the Participant’s death or Disability,
all Options awarded to the Participant shall become exercisable and all Phantom
Units shall vest automatically. The Committee may, in its discretion, waive in
whole or in part any forfeiture.

(ii) Awards May Be Granted Separately or Together. Awards may, in the discretion
of the Committee, be granted either alone or in addition to, in tandem with, or
in substitution for any other Award granted under the Plan or any award granted
under any other plan of the Company or any Affiliate.

 

5

--------------------------------------------------------------------------------

(iii) Limits on Transfer of Awards.

(A) Except as provided in (C) below, each Option shall be exercisable only by
the Participant during the Participant’s lifetime, or by the person to whom the
Participant’s rights shall pass by will or the laws of descent and distribution.

(B) Except as provided in (C) below, no Award and no right under any such Award
may be assigned, alienated, pledged, attached, sold or otherwise transferred or
encumbered by a Participant and any such purported assignment, alienation,
pledge, attachment, sale, transfer or encumbrance shall be void and
unenforceable against the Partnership, the Company or any Affiliate thereof.

(C) To the extent specifically provided by the Committee with respect to an
Option grant, an Option may be transferred by a Participant without
consideration to immediate family members or related family trusts, limited
partnerships or similar entities or on such terms and conditions as the
Committee may from time to time establish. In addition, Awards may be
transferred by will and the laws of descent and distribution.

(iv) Unit Certificates. All certificates for Units or other securities of the
Partnership delivered under the Plan pursuant to any Award or the exercise
thereof shall be subject to such stop transfer orders and other restrictions as
the Committee may deem advisable under the Plan or the rules, regulations, and
other requirements of the SEC, any stock exchange upon which such Units or other
securities are then listed, and any applicable federal or state laws, and the
Committee may cause a legend or legends to be put on any such certificates to
make appropriate reference to such restrictions.

(v) Delivery of Units or Other Securities and Payment by Participant of
Consideration. Notwithstanding anything in the Plan or any grant agreement to
the contrary, delivery of Units pursuant to the exercise or vesting of an Award
may be deferred for any period during which, in the good faith determination of
the Committee, the Partnership is not reasonably able to obtain or issue Units
pursuant to such Award without violating the rules or regulations of any
applicable law or securities exchange. No Units or other securities shall be
delivered pursuant to any Award until payment in full of any amount required to
be paid pursuant to the Plan or the applicable Award grant agreement (including,
without limitation, any exercise price or tax withholding) is received by the
Partnership.

(vi) Rule 16b-3. It is intended that the Plan and any Award made to a
Participant subject to Section 16 of the Exchange Act meet all of the
requirements of Rule 16b-3. If any provision of the Plan or any such Award would
disqualify the Plan or such Award under, or would otherwise not comply with Rule
16b-3, such provision or Award shall be construed or deemed amended to conform
to Rule 16b-3.

(vii) Status of Original Issue Units. The Partnership intends, but shall not be
obligated, to register for sale under the Securities Act the Units acquirable
pursuant to Awards, and to keep such registration effective throughout the
period any Awards are in effect. In the

 

6

--------------------------------------------------------------------------------

absence of such effective registration or an available exemption from
registration under the Securities Act, delivery of Units acquirable pursuant to
Awards shall be delayed until registration of such Units is effective or an
exemption from registration under the Securities Act is available. In the event
exemption from registration under the Securities Act is available, a Participant
(or a Participant’s estate or personal representative in the event of the
Participant’s death or incapacity), if requested by the Partnership to do so,
will execute and deliver to the Partnership in writing an agreement containing
such provisions as the Partnership may require to assure compliance with
applicable securities laws. No sale or disposition of Units acquired pursuant to
an Award by a Participant shall be made in the absence of an effective
registration statement under the Securities Act with respect to such Units
unless an opinion of counsel satisfactory to the Partnership that such sale or
disposition will not constitute a violation of the Securities Act or any other
applicable securities laws is first obtained.

(viii) Change in Control. Upon a Change in Control, unless the Committee
determines otherwise in the terms of the Award, all Awards shall automatically
vest and become payable or exercisable, as the case may be, in full. In the
event of a Change in Control, unless the Committee determines otherwise in the
terms of the Award, all Restricted Periods shall terminate and all performance
criteria, if any, shall be deemed to have been achieved at the maximum level. To
the extent an Option that has become fully vested and exercisable is not
exercised upon a Change in Control, the Committee may, in its discretion, cancel
such Award without payment. The Committee may also, in its discretion, provide
for a replacement grant with respect to such property and on such terms as it
deems appropriate.

SECTION 7: AMENDMENT AND TERMINATION.

Except to the extent prohibited by applicable law:

(a) Amendments to the Plan. Except as required by the rules of the principal
securities exchange on which the Units are traded and subject to Section 7(b)
below, the Board or the Committee may amend, alter, suspend, discontinue, or
terminate the Plan in any manner without the consent of any partner,
Participant, other holder or beneficiary of an Award, or other Person.

(b) Amendments to Awards. Subject to Section 7(a), the Committee may waive any
conditions or rights under, amend any terms of, or alter any Award theretofore
granted, provided no change, other than pursuant to Section 7(c), in any Award
shall materially reduce the benefit to a Participant without the consent of such
Participant.

(c) Adjustment of Awards upon the Occurrence of Certain Unusual or Nonrecurring
Events. The Committee is hereby authorized to make adjustments in the terms and
conditions of, and the criteria included in, Awards in recognition of unusual or
nonrecurring events (including, without limitation, the events described in
Section 4(c) of the Plan) affecting the Partnership or the financial statements
of the Partnership, or of changes in applicable laws, regulations, or accounting
principles, whenever the Committee determines that such adjustments are
appropriate in order to prevent dilution or enlargement of the benefits or
potential benefits intended to be made available under the Plan.

 

7

--------------------------------------------------------------------------------

SECTION 8: GENERAL PROVISIONS.

(a) No Rights to Award. No Person shall have any claim to be granted any Award
under the Plan, and there is no obligation for uniformity of treatment of
Participants. The terms and conditions of Awards need not be the same with
respect to each Participant.

(b) Withholding. The Company or any Affiliate is authorized to withhold from any
Award, from any payment due or transfer made under any Award or from any
compensation or other amount owing to a Participant the amount (in cash, Units,
other securities. Units that would otherwise be issued pursuant to such Award or
other property) of any applicable taxes payable in respect of the grant of an
Award, its exercise, the lapse of restrictions thereon, or any payment or
transfer under an Award or under the Plan and to take such other action as may
be necessary in the opinion of the Company or Affiliate to satisfy its
withholding obligations for the payment of such taxes.

(c) No Right to Employment. The grant of an Award shall not be construed as
giving a Participant the right to be retained in the employ of the Company or
any Affiliate or to remain on the Board. Further, the Company or an Affiliate
may at any time dismiss a Participant from employment, free from any liability
or any claim under the Plan, unless otherwise expressly provided in the Plan or
in any Award agreement.

(d) Governing Law. The validity, construction, and effect of the Plan and any
rules and regulations relating to the Plan shall be determined in accordance
with the laws of the State of Delaware and applicable federal law.

(e) Severability. If any provision of the Plan or any Award is or becomes or is
deemed to be invalid, illegal, or unenforceable in any jurisdiction or as to any
Person or Award, or would disqualify the Plan or any Award under any law deemed
applicable by the Committee, such provision shall be construed or deemed amended
to conform to the applicable laws, or if it cannot be construed or deemed
amended without, in the determination of the Committee, materially altering the
intent of the Plan or the Award, such provision shall be stricken as to such
jurisdiction, Person or Award and the remainder of the Plan and any such Award
shall remain in full force and effect.

(f) Compliance with Other Laws. The Committee may refuse to issue or transfer
any Units or other consideration under an Award if, in its sole discretion, it
determines that the issuance or transfer or such Units or such other
consideration might violate any applicable law or regulation, the rules of the
principal securities exchange on which the Units are then traded, or entitle the
Partnership or an Affiliate to recover the same under Section 16(b) of the
Exchange Act, and any payment tendered to the Partnership by a Participant,
other holder or beneficiary in connection with the exercise of such Award shall
be promptly refunded to the relevant Participant, holder or beneficiary. It is
intended that, to the extent applicable, Awards made under the Plan comply with
the requirements of section 409A of the Code and the regulations thereunder. To
the extent that any legal requirement of section 409A of the Code as set forth
in the Plan ceases to be required under section 409A of the Code, that Plan
provision shall cease to apply.

 

8

--------------------------------------------------------------------------------

(g) No Trust or Fund Created. Neither the Plan nor any Award shall create or be
construed to create a trust or separate fund of any kind or a fiduciary
relationship between the Partnership, the Company or any participating Affiliate
and a Participant or any other Person.

(h) No Fractional Units. No fractional Units shall be issued or delivered
pursuant to the Plan or any Award, and the Committee shall determine whether
cash, other securities, or other property shall be paid or transferred in lieu
of any fractional Units or whether such fractional Units or any rights thereto
shall be canceled, terminated, or otherwise eliminated.

(i) Headings. Headings are given to the sections and subsections of the Plan
solely as a convenience to facilitate reference. Such headings shall not be
deemed in any way material or relevant to the construction or interpretation of
the Plan or any provision thereof.

(j) Facility Payment. Any amounts payable hereunder to any Person under legal
disability or who, in the judgment of the Committee, is unable to properly
manage his financial affairs, may be paid to the legal representative of such
Person, or may be applied for the benefit of such Person in any manner which the
Committee may select, and the Company shall be relieved of any further liability
for payment of such amounts.

SECTION 9: TERM OF THE PLAN.

The Plan shall be effective on the date of its approval by the Unit holders and
shall continue until the date terminated by the Board or Units are no longer
available for the grant of Awards under the Plan, whichever occurs first.
However, unless otherwise expressly provided in the Plan or in an applicable
Award agreement, any Award granted prior to such termination, and the authority
of the Board or the Committee to amend, alter, adjust, suspend, discontinue, or
terminate any such Award or to waive any conditions or rights under such Award,
shall extend beyond such termination date.

 

9