<PAGE>

                                                                     Exhibit 4.1

                          CERTIFICATE OF DESIGNATIONS,
                         POWERS, PREFERENCES AND RIGHTS
                   OF THE SERIES A CONVERTIBLE PREFERRED STOCK

                                       OF

                               ANALEX CORPORATION

                         Pursuant to Section 151 of the
                        Delaware General Corporation Law

     Analex Corporation (the "Corporation"), organized and existing under the
laws of the State of Delaware, does, by its President and under its corporate
seal, hereby certify that pursuant to the authority contained in Article Fourth
of its Certificate of Incorporation and in accordance with the provisions of
Section 151 of the Delaware General Corporation Law, its Board of Directors has
adopted the following resolution creating the following classes and series of
the Corporation's $0.02 par value Convertible Preferred Stock and determining
the voting powers, designations, powers, preferences and relative,
participating, optional or other special rights, and the qualifications,
limitations and restrictions thereof, of such classes and series:

     RESOLVED, that, pursuant to authority conferred upon the Board of Directors
by the Certificate of Incorporation of the Corporation (the "Certificate of
Incorporation"), there is hereby created the following series of Preferred
Stock:

     .    12,000,000 shares shall be designated Series A Convertible Preferred
          Stock, par value $0.02 per share (the "Series A Preferred Stock").

     The designations, powers, preferences, and rights and the qualifications,
limitations and restrictions of the Series A Preferred Stock in addition to
those set forth in the Certificate of Incorporation shall be as follows:

          Section 1. Designation and Amount. 12,000,000 shares of the unissued
convertible preferred stock of the Corporation shall be designated as Series A
Convertible Preferred Stock (the "Series A Preferred Stock"). The Series A
Preferred Stock shall initially be issued at a purchase price of $2.23 per share
(the "Series A Original Issue Price").

          Section 2. Rank. The Series A Preferred Stock shall rank: (i) subject
to the requirements of Section 7, junior to any other class or series of capital
stock of the Corporation hereafter created specifically ranking as to dividend
rights, redemption rights, liquidation preference and other rights senior to the
Series A Preferred Stock (the "Senior Securities"); (ii) subject to the
requirements of Section 7, senior to all of the Corporation's common stock, $.02

                                       1

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                                                                     Exhibit 4.1

par value per share (the "Common Stock"); (iii) senior to any class or series of
capital stock of the Corporation hereafter created not specifically ranking as
to dividend rights, redemption rights, liquidation preference and other rights
senior to or on parity with any Series A Preferred Stock of whatever subdivision
(collectively, with the Common Stock, the "Junior Securities"); and (iv) subject
to the requirements of Section 7, on parity with any class or series of capital
stock of the Corporation hereafter created specifically ranking as to dividend
rights, redemption rights, liquidation preference and other rights on a parity
with the Series A Preferred Stock (the "Parity Securities").

          Section 3. Dividends. Beginning on September 30, 2003, and continuing
on the last day of each calendar quarter thereafter, so long as shares of Series
A Preferred Stock remain outstanding, the holders of each share of the Series A
Preferred Stock (the "Holders") shall be entitled, from and after the date of
issuance of such share, to receive, and shall be paid quarterly in arrears in
cash out of funds legally available therefor, cumulative dividends, of an amount
equal to 6% of the Series A Original Issue Price per share, (as appropriately
adjusted for any stock splits, stock dividends, combinations, and the like), per
annum with respect to each share of the Series A Preferred Stock; provided,
however, if, at any time after the date of the initial issuance of the Series A
Preferred Stock (the "Series A Closing") the Corporation's available cash for
operations for the following 12-month period, in each case calculated from the
date such quarterly dividend installment would otherwise be paid, is less than
One Million Dollars ($1,000,000) in excess of the business projections for the
Corporation approved by the Board of Directors of the Corporation (the "Board")
for such 12-month period (which projections will be updated and presented to the
Board for each calendar quarter) or the Corporation's payment of such dividend
in cash will result in an event of default under the Senior Indebtedness (as
defined below), such dividend may, at the option of the Corporation, be paid to
the Holders in shares of the Series A Preferred Stock valued at the Series A
Original Issue Price. The Holders of shares of Series A Preferred Stock shall be
entitled to receive such dividends, immediately after the payment of any
dividends to Senior Securities required by the Corporation's Certificate of
Incorporation, as amended or amended and restated and in effect, including for
this purpose any certificate(s) of designation, (the "Charter") prior and in
preference to any dividends required to be paid to Junior Securities and Common
Stock but in parity with any distribution to the holders of Parity Securities.

          Section 4. Liquidation Preference.

               (a) In the event of any liquidation, dissolution or winding up of
the Corporation, either voluntary or involuntary, the Holders shall be entitled
to be paid out of the assets of the Corporation available for distribution to
its stockholders, whether from capital, surplus or earnings, immediately after
any distributions to Senior Securities required by the Charter, and prior and in
preference to any distribution to Junior Securities and Common Stock but in
parity with any distribution to the holders of Parity Securities, an amount per
share equal to the sum of the Series A Original Issue Price (as appropriately
adjusted for any stock splits,

                                       2

<PAGE>

                                                                     Exhibit 4.1

stock dividends, combinations, and the like) and any accrued but unpaid dividend
on the Series A Preferred Stock. If upon the occurrence of such event, and after
the payment in full of the preferential amounts with respect to the Senior
Securities, the assets and funds available to be distributed among the holders
of the Series A Preferred Stock and any Parity Securities shall be insufficient
to permit the payment to such holders of the full preferential amounts due to
the holders of the Series A Preferred Stock and the Parity Securities,
respectively, then the entire assets and funds of the Corporation legally
available for distribution shall be distributed among the holders of the Series
A Preferred Stock and the Parity Securities, pro rata, based on the amount each
such holder would receive if such full preferential amounts were paid unless
otherwise provided in the Charter.

               (b) Upon the completion of the distribution required by Section
4(a), if assets remain in the Corporation, they shall be distributed in
accordance with the Charter.

               (c) Upon the completion of the distributions required by Section
4(a) and Section 4(b), if assets remain in the Corporation, they shall be
distributed pro rata, on an as-converted to Common Stock basis, to the holders
of the Common Stock.

               (d) A sale, conveyance or disposition of all or substantially all
of the capital stock or assets of the Corporation or a merger, consolidation or
other transaction or series of related transactions (whether involving the
Corporation or a subsidiary thereof) in which the Corporation's stockholders
immediately prior to such transaction do not retain a majority of the voting
power in the surviving entity (a "Transaction"), shall be deemed to be a
liquidation, dissolution or winding up within the meaning of this Section 4,
unless the holders of a majority of the then outstanding shares of the Series A
Preferred Stock vote affirmatively or consent in writing that such transaction
shall not be treated as a liquidation, dissolution or winding up within the
meaning of this Section 4.

               (e) Prior to the closing of a Transaction described in Section
4(d) which would constitute a liquidation, dissolution or winding up within the
meaning of this Section 4, the Corporation shall, at its sole option, either (i)
make all distributions of cash or other property that it is required to make to
the Holders pursuant to the first sentence of Section 4(a), (ii) set aside
sufficient funds or other property from which the distributions required to be
made to such Holders can be made, or (iii) in connection with a sale of all or
substantially all the assets of the Corporation, establish an escrow or other
similar arrangement with a third party pursuant to which the proceeds payable to
the Corporation from a sale of all or substantially all the assets of the
Corporation will be used to make the liquidating payments to such Holders
immediately after the consummation of such sale. In the event that the
Corporation is unable to fully comply with any of the foregoing alternatives,
the Corporation shall either: (x) cause such closing to be postponed until the
Corporation complies with one of the foregoing alternatives, or (y) cancel such
Transaction, in which event the rights of the Holders shall be the same as
existing immediately prior to

                                       3

<PAGE>

                                                                     Exhibit 4.1

such proposed Transaction.

          Section 5. Conversion of Series A Preferred Stock. The Corporation and
the record Holders of the Series A Preferred Stock shall have conversion rights
as follows:

               (a) Right to Convert. Each record Holder of Series A Preferred
Stock shall be entitled to convert whole shares of Series A Preferred Stock for
the Common Stock issuable upon conversion of the Series A Preferred Stock, as
follows: each outstanding share of Series A Preferred Stock is convertible, at
any time at the option of the holder thereof, into one fully-paid and
non-assessable share of Common Stock, subject to adjustment as provided in
Section 5(d) hereof. Each share of Series A Preferred Stock shall be convertible
into such number of fully paid and nonassessable shares of Common Stock as
obtained by (i) multiplying the number of shares of Series A Preferred Stock so
to be converted by, initially, the applicable Series A Original Issue Price and
(ii) dividing the result by the conversion price equal to, initially, the
applicable Series A Original Issue Price per share or, in case an adjustment of
such price has taken place pursuant to this Section 5, then by the conversion
price as last adjusted and in effect at the date any share or shares of Series A
Preferred Stock are surrendered for conversion (such price, or such price last
adjusted, hereafter referred to as the "Conversion Price"). Accrued but unpaid
dividends will be paid in cash upon any such conversion.

               (b) Automatic Conversion.

               (i) After the date that is 18 months following the Series A
Closing, each share of outstanding Series A Preferred Stock shall be
automatically converted into Common Stock at the Conversion Price then in effect
(A) on the date on which the average closing price for the immediately preceding
twenty (20) consecutive trading days of the Common Stock trading on the American
Stock Exchange (or other stock exchange approved by the holders of a majority of
the then outstanding shares of Series A Preferred Stock) exceeds
two-and-one-half (2.5) times the Conversion Price or (B) on the sixty-first
(61st) day following the date on which the Corporation delivers a Notice of
Conversion (as defined below) pursuant to Section 5(c) below to each Holder and
offers to pay to such Holder an amount per share equal to or greater than
two-and-one-half (2.5) times the Conversion Price (the "Cash Offer") for each
share of the Series A Preferred Stock held by such Holder if such Holder does
not accept such offer by written notice of acceptance to the Corporation within
60 days of the date of such Notice of Conversion. Except as otherwise provided
Section 3 above, accrued but unpaid dividends shall be paid in cash on any such
automatic conversion. For the avoidance of doubt, only the shares of Series A
Preferred Stock held by Holders that do not accept the Cash Offer within 60 days
of the Notice of Conversion with respect thereto shall be automatically
converted in accordance with Section 5(b)(i)(B) and those Holders that do accept
the Cash Offer shall have their shares of Series A Preferred Stock repurchased
by the Corporation pursuant to the terms of the Cash Offer.

                                       4

<PAGE>

                                                                     Exhibit 4.1

               (ii) Each share of outstanding Series A Preferred Stock
automatically shall be converted into Common Stock at the Conversion Price then
in effect on any date after the Series A Closing that a majority of the then
outstanding shares of Series A Preferred Stock agree in writing shall be the
conversion date of all of the then outstanding shares of Series A Preferred
Stock. Except as provided otherwise in Section 3 above, accrued but unpaid
dividends will be paid in cash on any such conversion.

               (iii) Notwithstanding anything to the contrary herein, no shares
of outstanding Series A Preferred Stock shall be automatically converted into
Common Stock pursuant to this Section 5(b) unless at the time of such proposed
conversion the Corporation shall have on file with the Securities and Exchange
Commission an effective registration statement with respect to the shares of
Common Stock issued or issuable to the Holders (A) on conversion of the Series A
Preferred Stock then issued or issuable to such Holders, (B) on conversion of
the secured subordinated convertible promissory notes dated on or about the date
of this Certificate of Designations issued pursuant to the Note Purchase
Agreement (the "Notes") and (C) on exercise of all of the warrants to purchase
Common Stock of the Corporation dated on or about the date of this Certificate
of Designations issued pursuant to the Note Purchase Agreement (the "Warrants")
and such shares of Common Stock have been approved by and listed on the American
Stock Exchange (or other stock exchange approved by the holders of a majority of
the then outstanding shares of Series A Preferred Stock).

               (c) Mechanics of Conversion. In order to convert Series A
Preferred Stock into full shares of Common Stock if (i) such conversion is
pursuant to Section 5(a), the Holder shall (A) fax a copy of a fully executed
notice of conversion ("Notice of Conversion") to the Corporation at the office
of the Corporation or to the Corporation's designated transfer agent (the
"Transfer Agent") for the Series A Preferred Stock stating that the Holder
elects to convert, which notice shall specify the date of conversion, the number
of shares of Series A Preferred Stock to be converted, the Conversion Price and
a calculation of the number of shares of Common Stock issuable upon such
conversion (together with a copy of the front page of each certificate to be
converted) and (B) surrender to a common courier for either overnight or two (2)
day delivery to the office of the Corporation or its transfer agent, the
original certificates representing the Series A Preferred Stock being converted
(the "Preferred Stock Certificates"), duly endorsed for transfer, and (ii) such
conversion is pursuant to Section 5(b), the Corporation shall fax a copy of a
Notice of Conversion to the Holders stating that the shares of Series A
Preferred Stock have been automatically converted into Common Stock, which
notice shall specify the date of such automatic conversion, the number of shares
of Series A Preferred Stock that have been converted, the Conversion Price and a
calculation of the number of shares of Common Stock issuable upon such
conversion (together with a copy of the front page of each certificate to be
converted); provided, however, that the Corporation's failure to issue a Notice
of Conversion shall not effect the automatic conversion of such shares of Series
A Preferred Stock and the automatic cancellation of the certificates
representing such shares of Series A Preferred Stock. In the event of an
automatic conversion pursuant to Section 5(b), the outstanding shares

                                       5

<PAGE>

                                                                     Exhibit 4.1

of Series A Preferred Stock shall be converted automatically without any further
action by the Holders of such shares and whether or not the certificates
representing such shares are surrendered to the Corporation or its transfer
agent and the Corporation shall not be obligated to issue certificates
evidencing the shares of Common Stock issuable upon such conversion unless
either the Preferred Stock Certificates are delivered to the Corporation or the
Transfer Agent as provided above, or the Holder notifies the Corporation or its
Transfer Agent that such certificates have been lost, stolen or destroyed
(subject to the requirements of Section 5(c)(i) below).

                    (i) Lost or Stolen Certificates. Upon receipt by the
Corporation of evidence of the loss, theft, destruction or mutilation of any
Preferred Stock Certificates representing shares of Series A Preferred Stock,
and (in the case of loss, theft or destruction) of indemnity or security
reasonably satisfactory to the Corporation, and upon surrender and cancellation
of the Preferred Stock Certificates, if mutilated, the Corporation shall execute
and deliver new Preferred Stock Certificates of like tenor and date. However,
the Corporation shall not be obligated to re-issue such lost or stolen Preferred
Stock Certificates if the Holder contemporaneously requests the Corporation to
convert such Series A Preferred Stock into Common Stock or if such shares of
Series A Preferred Stock have been automatically converted into Common Stock.

                    (ii) Delivery of Common Stock Upon Conversion. The
Corporation no later than 6:00 p.m. (New York City time) on the third (3rd)
business day after receipt by the Corporation or its transfer agent of all
necessary documentation duly executed and in proper form required for
conversion, including the original Preferred Stock Certificates to be converted
(or after provision for security or indemnification in the case of lost, stolen
or destroyed certificates, if required), shall issue and surrender to a common
courier for either overnight or (if delivery is outside the United States) two
(2) day delivery to the Holder as shown on the stock records of the Corporation
a certificate for the number of shares of Common Stock to which the Holder shall
be entitled as aforesaid.

                    (iii) Date of Conversion. The date on which a voluntary
conversion pursuant to Section 5(a) occurs (the "Date of Voluntary Conversion")
shall be deemed to be the date the applicable Notice of Conversion is faxed to
the Corporation or the Transfer Agent, as the case may be, provided that the
advance copy of the Notice of Conversion is faxed to the Corporation on or prior
to 6:00 p.m., New York City time, on the Date of Conversion. An automatic
conversion pursuant to Section 5(b) shall occur on the date on which such
automatic conversion is deemed to occur pursuant to Section 5(b) (the "Date of
Automatic Conversion", and together with the Date of Voluntary Conversion, the
"Date of Conversion"). The original Preferred Stock Certificates representing
the shares of Series A Preferred Stock to be converted shall be surrendered by
depositing such certificates with a common courier for either overnight or two
(2) day delivery, as soon as practicable following the Date of Voluntary
Conversion or as soon as practicable following the date such holder receives
notice of the Date of Automatic Conversion. The person or persons entitled to
receive the shares of Common Stock

                                       6

<PAGE>

                                                                     Exhibit 4.1

issuable upon such conversion shall be treated for all purposes as the record
Holder or Holders of such shares of Common Stock on the Date of Conversion.

                    (iv) No Fractional Shares on Conversion. No fractional
shares of Common Stock shall be issued upon conversion of the Series A Preferred
Stock. In lieu of any fractional share to which the Holder would otherwise be
entitled, the Corporation shall (after aggregating all shares into which shares
of Series A Preferred held by each Holder could be converted) pay cash equal to
such fraction multiplied by the market price per share of Common Stock (as
determined in a reasonable manner by the Board) at the close of business on the
Date of Conversion.

               (d) Adjustment of Conversion Price.

               (i) Adjustments of Conversion Rate Upon Issuance of Common Stock.
If at any time after the Series A Closing, the Corporation shall issue or sell,
or is, in accordance with Section 5(d)(i)(A) through (G) below, deemed to have
issued or sold, any shares of Common Stock for a consideration per share less
than the Conversion Price in effect immediately prior to the time of such issue
or sale or deemed issue or sale, then, forthwith upon such issue or sale or
deemed issue or sale, the Conversion Price shall be reduced to the net
consideration per share received or deemed received by the Corporation pursuant
to Sections 5(d)(i)(A) through (G), as applicable ("Full-Ratchet Anti-Dilution
Protection").

               (A) Issuance of Rights or Options. In case at any time the
Corporation shall in any manner grant (whether directly or by assumption in a
merger or otherwise) any warrants or other rights to subscribe for or to
purchase, or any options for the purchase of, Common Stock or any stock or
security convertible into or exchangeable for Common Stock (such warrants,
rights or options being called "Options" and such convertible or exchangeable
stock or securities being called "Convertible Securities") whether or not such
Options or the right to convert or exchange any such Convertible Securities are
immediately exercisable, and the price per share for which Common Stock is
issuable upon the exercise of such Options or upon the conversion or exchange of
such Convertible Securities (determined by dividing (i) the total amount, if
any, received or receivable by the Corporation as consideration for the granting
of such Options, plus the minimum aggregate amount of additional consideration
payable to the Corporation upon the exercise of all such Options, plus, in the
case of such Options which relate to Convertible Securities, the minimum
aggregate amount of additional consideration, if any, payable upon the issue or
sale of such Convertible Securities and upon the conversion or exchange thereof
(in all cases excluding the effect of a net issue election), by (ii) the total
maximum number of shares of Common Stock issuable upon the exercise of such
Options or upon the conversion or exchange of all such Convertible Securities
issuable upon the exercise of such Options) shall be less than the Conversion
Price in effect immediately prior to the time of the granting of such Options,
then the total maximum number of shares of Common Stock issuable upon the
exercise of such Options or upon conversion or exchange of the total

                                       7

<PAGE>

                                                                     Exhibit 4.1

maximum amount of such Convertible Securities issuable upon the exercise of such
Options shall be deemed to have been issued for such price per share as of the
date of granting of such Options and thereafter shall be deemed to be
outstanding. Except as otherwise provided in Section 5(d)(i)(C), no adjustment
of the Conversion Price shall be made upon the actual issue of such Common Stock
or of such Convertible Securities upon exercise of such Options or upon the
actual issue of such Common Stock upon conversion or exchange of such
Convertible Securities.

               (B) Issuance of Convertible Securities. In case the Corporation
shall in any manner issue (whether directly or by assumption in a merger or
otherwise) or sell any Convertible Securities, whether or not the rights to
exchange or convert any such Convertible Securities are immediately exercisable,
and the price per share for which Common Stock is issuable upon such conversion
or exchange (determined by dividing (i) the total amount received or receivable
by the Corporation as consideration for the issue or sale of such Convertible
Securities, plus the aggregate amount of additional consideration, if any,
payable to the Corporation upon the conversion or exchange thereof, by (ii) the
total maximum number of shares of Common Stock issuable upon the conversion or
exchange of all such Convertible Securities) shall be less than the Conversion
Price in effect immediately prior to the time of such issue or sale, then the
total maximum number of shares of Common Stock issuable upon conversion or
exchange of all such Convertible Securities shall be deemed to have been issued
for such price per share as of the date of the issue or sale of such Convertible
Securities and thereafter shall be deemed to be outstanding; provided that (a)
except as otherwise provided in Section 5(d)(i)(C), no adjustment of the
Conversion Price shall be made upon the actual issue of such Common Stock upon
conversion or exchange of such Convertible Securities and (b) if any such issue
or sale of such Convertible Securities is made upon exercise of any Options to
purchase any such Convertible Securities for which adjustments of the B
Conversion Price have been or are to be made pursuant to other provisions of
this Section 5(d)(i), no further adjustment of the Series A Conversion Price
shall be made by reason of such issue or sale.

               (C) Change in Option Price or Conversion Rate. Upon the happening
of any of the following events, namely, if (1) the purchase price or exercise
price provided for in any Option referred to in Section 5(d)(i)(A), (2) the
number of shares into which the Option is exercisable, (3) the additional
consideration, if any, payable upon the conversion or exchange of any
Convertible Securities referred to in Section 5(d)(i)(A) or (B), or (4) the rate
at which Convertible Securities referred to in Section 5(d)(i)(A) or (B) are
convertible into or exchangeable for Common Stock shall change at any time
(including, but not limited to, changes under or by reason of provisions
designed to protect against dilution), the Conversion Price in effect at the
time of such event shall forthwith be readjusted to the Conversion Price which
would have been in effect at such time had such Options or Convertible
Securities still outstanding provided for such changed purchase price,
additional consideration or conversion rate, as the case may be, at the time
initially granted, issued or sold; and on the termination or expiration of any
such Option or any such right to convert or exchange such Convertible
Securities, the Conversion Price then in effect hereunder shall forthwith be
increased to the

                                       8

<PAGE>

                                                                     Exhibit 4.1

Conversion Price which would have been in effect at the time of such termination
had such Option or Convertible Securities, to the extent outstanding immediately
prior to such termination, never been issued.

               (D) Stock Dividends. In case the Corporation shall declare a
dividend or make any other distribution upon any stock of the Corporation (other
than Common Stock or Series A Preferred Stock) payable in Common Stock, then any
Common Stock issuable in payment of such dividend or distribution shall be
deemed to have been issued or sold without consideration, unless the holders of
at least a majority of the then outstanding Series A Preferred Stock shall have
consented to such dividend or distribution.

               (E) Consideration for Stock. In case any shares of Common Stock,
Options or Convertible Securities shall be issued or sold for cash, the
consideration received therefor shall be deemed to be the amount received by the
Corporation therefor, without deduction therefrom of any expenses incurred or
any underwriting commissions or concessions paid or allowed by the Corporation
in connection therewith. In case any shares of Common Stock, Options or
Convertible Securities shall be issued or sold for a consideration other than
cash, the amount of the consideration other than cash received by the
Corporation shall be deemed to be the fair value of such consideration as
determined in good faith by the Board, without deduction of any expenses
incurred or any underwriting commissions or concessions paid or allowed by the
Corporation in connection therewith. In case any Options shall be issued in
connection with the issue and sale of other securities of the Corporation,
together comprising one integral transaction in which no specific consideration
is allocated to such Options by the parties thereto, such Options shall be
deemed to have been issued for such consideration as determined in good faith by
the Board.

               (F) Record Date. In case the Corporation shall take a record of
the holders of its Common Stock for the purpose of entitling them (i) to receive
a dividend or other distribution payable in Common Stock, Options or Convertible
Securities or (ii) to subscribe for or purchase Common Stock, Options or
Convertible Securities, then such record date shall be deemed to be the date of
the issue or sale of the shares of Common Stock deemed to have been issued or
sold upon the declaration of such dividend or the making of such other
distribution or the date of the granting of such right of subscription or
purchase, as the case may be.

               (G) Treasury Shares. The number of shares of Common Stock
outstanding at any given time shall not include shares owned or held by or for
the account of the Corporation, and the disposition of any such shares shall be
considered an issue or sale of Common Stock for the purpose of this Section
5(d)(i).

               (ii) Certain Issues of Common Stock Excepted. Anything herein to
the contrary notwithstanding, the Corporation shall not be required to make any
adjustment of the

                                       9

<PAGE>

                                                                     Exhibit 4.1

Conversion Price in the case of the issuance or sale from and after the date of
filing of this Certificate of Designation of Anti-Dilution Excluded Securities
(as defined below).

               (iii) Adjustments for Subdivisions, Common Stock Dividends,
Combinations or Consolidations of Common Stock. If the outstanding shares of
Common Stock shall be subdivided or increased, by stock split, stock dividend or
otherwise, into a greater number of shares of Common Stock, the Conversion Price
shall concurrently with the effectiveness of such subdivision or payment of such
stock dividend, be proportionately decreased. If the outstanding shares of
Common Stock shall be combined or consolidated, by reclassification or
otherwise, into a lesser number of shares of Common Stock, the Conversion Price
shall, concurrently with the effectiveness of such combination or consolidation,
be proportionately increased.

               (iv) Adjustments for Reclassification, Exchange and Substitution.
If the Common Stock issuable upon conversion of the Series A Preferred Stock
shall be changed into the same or a different number of shares of any other
class or classes of stock, whether by capital reorganization, reclassification
or otherwise (other than a subdivision or combination of shares provided for
above), the Conversion Price shall, concurrently with the effectiveness of such
reorganization or reclassification, be proportionately adjusted such that the
Series A Preferred Stock shall be convertible into, in lieu of the number of
shares of Common Stock which the holders would otherwise have been entitled to
receive, a number of shares of such other class or classes of stock equivalent
to the number of shares of Common Stock that would have been subject to receipt
by the holders upon conversion of the Series A Preferred Stock immediately
before that change.

               (v) Adjustments for Merger, Sale, Lease or Conveyance. In case of
any consolidation with or merger of the Corporation with or into another
corporation, or in case of any sale, lease or conveyance to another Corporation
of the assets of the Corporation as an entirety or substantially as an entirety,
which is not treated as a liquidation, dissolution or winding up pursuant to
Section 4(d) above, the Series A Preferred Stock shall after the date of such
consolidation, merger, sale, lease or conveyance be convertible into the number
of shares of stock or other securities or property (including cash) to which the
Common Stock issuable (at the time of such consolidation, merger, sale, lease or
conveyance) upon conversion of the Series A Preferred Stock would have been
entitled upon such consolidation, merger, sale, lease or conveyance; and in any
such case, if necessary, the provisions set forth herein with respect to the
rights and interests thereafter of the holders of the Series A Preferred Stock
shall be appropriately adjusted so as to be applicable, as nearly as may
reasonably be, to any shares of stock or other securities or property thereafter
deliverable on the conversion of the shares of Series A Preferred Stock.

               (vi) Fractional Shares. If any adjustment under this Section 5(d)
would create a fractional share of Common Stock or a right to acquire a
fractional share of Common

                                       10

<PAGE>

                                                                     Exhibit 4.1

Stock, such fractional share shall be rounded to the nearest whole number of
shares with one-half share being rounded up.

          Section 6. Voting Rights. Except to the extent otherwise expressly
provided by law or in Section 7, the Series A Preferred Stock shall vote
together with all other classes and series of voting stock of the Corporation as
a single class on all actions to be taken by the stockholders of the
Corporation. Each share of Series A Preferred Stock shall entitle the Holder
thereof to that number of votes on each such action as is equal to the number of
shares of Common Stock (excluding fractions of a share) into which it is
convertible pursuant to Section 5 on all matters to be voted on by the
stockholders of the Corporation and shall vote along with the holders of Common
Stock as a single class.

          Section 7. Protective Provisions.

                    So long as at least 50% of the shares of Series A Preferred
Stock issued at the Series A Closing remain outstanding (as adjusted for any
stock splits, stock dividends, combinations, recapitalizations involving equity
of the Corporation, reclassifications of other similar events involving a change
with respect to the Series A Preferred Stock) or, if the Corporation has failed
to comply with its obligations to redeem the shares of Series A Preferred Stock
in accordance with Section 11, so long as any shares of Series A Preferred Stock
issued at the Series A Closing remain outstanding, the Corporation shall not,
without first obtaining the written consent of the Holders of at least a
majority of the then outstanding shares of Series A Preferred Stock:

                    (a) merge or consolidate with one or more corporations or
sell all or substantially all of the capital stock or assets of the Corporation;

                    (b) make an acquisition or series of related acquisitions
for consideration aggregating more than $10,000,000 in value;

                    (c) alter or amend the Charter or the Corporation's bylaws
so as to affect adversely the voting powers, preferences or other rights of the
Holders of the Series A Preferred Stock;

                    (d) issue any Senior Securities or any Parity Securities or
securities that are convertible into Senior Securities or Parity Securities;

                    (e) pay any dividends or distributions on the capital stock
of the Corporation, except for dividends paid on the Series A Preferred Stock as
contemplated in this Certificate of Designation;

                                       11

<PAGE>

                                                                     Exhibit 4.1

                    (f) voluntarily liquidate or dissolve, recapitalize or
reorganize the Corporation;

                    (g) borrow funds (in one or a series of related borrowings)
in an amount more than $1,000,000 other than revolving lines of credit provided
by lenders based upon the Corporation's accounts receivable;

                    (h) redeem or purchase any of the capital stock of the
Corporation, except repurchases of employee Common Stock upon termination of
employment pursuant to employment agreements in effect at the time of the Series
A Closing;

                    (i) increase or decrease the number of members of the Board;
or

                    (j) elect, appoint or remove the Chief Executive Officer,
Chief Financial Officer, President or Chief Operating Officer of the
Corporation.

          Section 8. Status of Converted Stock. In the event any shares of
Series A Preferred Stock shall be converted pursuant to Section 5 hereof, the
shares so converted shall be canceled, shall return to the status of authorized
but unissued Preferred Stock of no designated series, and shall not be issuable
by the Corporation as Series A Preferred Stock.

          Section 9. Preemptive Rights. Each Holder of Series A Preferred Stock
or debt or equity of the Corporation that is convertible into shares of Series A
Preferred Stock shall be entitled to purchase its pro rata share (calculated by
multiplying the number of securities issued in such equity offering including
those issued pursuant this Section 9 by a fraction, the numerator of which is
the number of shares of Common Stock held by such holder on a Fully Diluted
Basis and the denominator of which is the number of shares of Common Stock held
by all such holders of securities of the Corporation on a Fully Diluted Basis)
of any future private equity offering by the Corporation, except for the
Preemptive Rights Excluded Securities.

          Section 10. Reservation of Stock. The Corporation shall at all times
reserve and keep available out of its authorized but unissued shares of Common
Stock and Series A Preferred Stock: (a) solely for the purpose of effecting the
conversion of shares of Series A Preferred Stock issued or issuable to the
Holders, such number of shares of Common Stock as shall from time to time be
sufficient to effect the conversion of all outstanding shares of Series A
Preferred Stock and rights to acquire shares of Series A Preferred Stock, (b)
solely for the purpose of effecting the exercise of all of the Warrants, such
number of shares of Common Stock as shall from time to time be sufficient to
effect the exercise of all of the outstanding Warrants and (c) solely for the
purpose of effecting the conversion of the Notes, such number of shares of
Series A Preferred Stock and Common Stock as shall from time to time be
sufficient to effect the conversion of all outstanding Notes; and if at any time
the number of authorized but unissued shares of Common Stock or Series A
Preferred Stock shall not be sufficient to effect the

                                       12

<PAGE>

                                                                     Exhibit 4.1

conversion of all then outstanding shares of Series A Preferred Stock and rights
to acquire shares of Series A Preferred Stock, the exercise of the Warrants and
the conversion of the Notes issued or issuable to the Holders, in addition to
such other remedies as shall be available to the Holder of Series A Preferred
Stock or such rights, the Corporation shall take such corporate action as may,
in the opinion of its counsel, be necessary to increase its authorized but
unissued shares of Common Stock and Series A Preferred Stock, as applicable, to
such number as shall be sufficient for such purposes, including, without
limitation, using best efforts to obtain stockholder approval of any necessary
amendment to the Charter.

          Section 11. Redemption Rights. The record Holders of the Series A
Preferred Stock shall have redemption rights as follows:

                    (a) The Series A Preferred Stock shall be subject to
redemption, at the option of the holders of a majority of the then outstanding
shares of Series A Preferred Stock at any time after the fourth anniversary of
the Series A Closing, in four equal quarterly installments, with the first
installment being made within sixty (60) days of the date of exercise of such
option and the last installment on the date that is 9 months thereafter, in
whole or in part, at a per share redemption price equal to the Series A Original
Issue Price (as adjusted for any stock splits, stock dividends, combinations,
recapitalizations involving equity securities of the Corporation,
reclassifications of other similar events involving a change with respect to the
Series A Preferred Stock or the Common Stock) per share plus any accrued but
unpaid dividends, payable in immediately available funds.

                    (b) If the funds legally available to the Corporation for
the payment of the redemption price of the Series A Preferred Stock are not
sufficient to redeem all of the shares of the Series A Preferred Stock required
to be redeemed on any date, such funds shall be used to redeem the number of
shares of Series A Preferred Stock which may be redeemed from such amount on a
pro rata basis. If, at the end of each calendar quarter, thereafter (or more
often than quarterly at the option of the Corporation), additional funds become
available for the redemption of additional shares of Series A Preferred Stock
required to be so redeemed, the Corporation shall immediately use such funds to
redeem shares of Series A Preferred Stock until such time as all of the shares
of Series A Preferred Stock required to be redeemed pursuant to this Section 11
have been redeemed.

                    (c) If, on the dates established for redemption pursuant to
Section 11(a), all of the shares of Series A Preferred Stock to be redeemed on
each such date are not redeemed in full, all rights in respect of such shares of
Series A Preferred Stock that have not been redeemed, including the right to
receive the applicable redemption price, plus accrued and unpaid dividends,
shall continue to be outstanding as evidenced by the certificates representing
such shares. The exercise by the Holders of the option to redeem any shares of
Series A Preferred Stock which were not redeemed on the dates established for
redemption pursuant to Section 11(a), may be rescinded by such Holders at any
time following the date established for

                                       13

<PAGE>

                                                                     Exhibit 4.1

such redemption by written notice to the Corporation. All shares of Series A
Preferred Stock redeemed pursuant to Section 11(a) shall be retired and shall be
restored to the status of authorized and unissued shares of Preferred Stock,
without designation as to series or class and may thereafter be reissued,
subject to compliance with the terms hereof, as shares of any series of
Preferred Stock other than shares of Series A Preferred Stock.

                    (d) If the Corporation does not, or is unable to, redeem the
Series A Preferred Stock as required by this Section 11, the Holders shall have
the right, but not the obligation, to pursue all remedies available to them at
law or in equity and shall have the right to designate additional members to the
Board such that the directors designated by such Holders constitute a majority
of the members of the Board if the Corporation is unable to effect any such
quarterly redemption installment for a period of nine (9) consecutive months
after such installment was required to be paid pursuant to Section 11(a) hereof;
provided, that if any such installment remains unpaid for a period of nine (9)
consecutive months after such installment was required to be paid, such Holders
shall be entitled to such increased Board representation unless all such
installments that are then past due are paid. Such additional members of the
Board shall be designated and elected in accordance with the provisions of
Section 2.1 of the Stockholders' Voting Agreement.

          Section 12. Definitions. As used in this Certificate, the following
capitalized terms have the following meanings.

          "Anti-Dilution Excluded Securities" mean any of the following
securities: (1) securities issued to employees, consultants, officers or
directors of the Corporation or options to purchase Common Stock granted by the
Corporation to employees, consultants, officers, or directors of the Corporation
pursuant to any option plan, agreement or other arrangement duly adopted by the
Corporation and approved by the compensation committee of the Board; (2)
securities issued on exercise of the Warrants; (3) securities issued on
conversion of the Notes; (4) the Series A Preferred Stock and any Common Stock
issued upon conversion of the Series A Preferred Stock; (5) for the avoidance of
doubt, securities issued on the conversion of any Convertible Securities or the
exercise of any Options, in each case, outstanding on the date of the filing
hereof; (6) for the avoidance of doubt, securities issued in connection with a
stock split, stock dividend, combination, reorganization, recapitalization or
other similar event for which adjustment is made in accordance with Section
5(d)(iii) or (iv); and (7) securities issued to financial institutions in
connection with commercial credit transactions, equipment credit financings or
similar credit transactions approved by the Board, including each member of the
Board which may be designated by a Pequot Majority in Interest pursuant to
Section 2.1(a)(ii) of the Stockholders' Voting Agreement.

          "Fully Diluted Basis" means when used in reference to the number of
shares of Common Stock held by a person or entity at any time, a number of
shares of Common Stock equal to the sum of (x) the number of issued and
outstanding shares of Common Stock then held

                                       14

<PAGE>

                                                                     Exhibit 4.1

by or such person or entity, plus (y) the total number of shares of Common Stock
issuable upon the exercise, conversion or exchange of all Convertible Securities
[and Options] issued and outstanding at such time that are then held by such
person or entity.

          "Note Purchase Agreement" means that certain Subordinated Note and
Series A Convertible Preferred Stock Purchase Agreement, dated July 18, 2003,
between the Corporation and the purchasers named therein.

          "Pequot Majority in Interest" shall have the meaning ascribed to it in
the Stockholders' Voting Agreement.

          "Preemptive Rights Excluded Securities" mean an of the following
securities: (1) securities issued to employees, consultants, officers or
directors of the Corporation or options to purchase Common Stock granted by the
Corporation to employees, consultants, officers, or directors of the Corporation
pursuant to any option plan, agreement or other arrangement duly adopted by the
Corporation and approved by the compensation committee of the Board; (2)
securities issued on exercise of the Warrants; (3) securities issued on
conversion of the Notes; (4) the Series A Preferred Stock and any Common Stock
issued on conversion of the Series A Preferred Stock; (5) for the avoidance of
doubt, securities issued on the conversion of any Convertible Securities or the
exercise of any Options, in each case, outstanding on the date of the filing
hereof; (6) for the avoidance of doubt, securities sold by the Corporation in
any public offering; (7) for the avoidance of doubt, securities issued in
connection with a stock split, stock dividend, combination, reorganization,
recapitalization or other similar event for which adjustment is made in
accordance with Section 5(d)(iii), (iv) or (v); (8) securities issued to
financial institutions in connection with commercial credit transactions,
equipment credit financings or similar credit transactions approved by the Board
including each member of the Board designated by a Pequot Majority in Interest
pursuant to Section 2.1(a)(ii) of the Stockholders' Voting Agreement, and the
issuance of Common Stock upon the conversion or exercise of any such securities
constituting Convertible Securities or Options; and (9) the issuance of
securities of the Corporation issued for consideration other than cash pursuant
to a merger, consolidation, acquisition or similar business combination by the
Corporation approved by the Board.

          "Senior Indebtedness" means the indebtedness of the Corporation under
that certain Credit Agreement dated November 2, 2001, as amended, by and between
the Corporation and Bank of America, N.A. and any other Senior Indebtedness as
such term is defined in the Note Purchase Agreement.

          "Stockholders' Voting Agreement" means that certain Stockholders'
Voting Agreement effective on or about the date hereof by and among the
Corporation and certain stockholders of the Corporation listed on the signature
pages thereto.

                                       15

<PAGE>

                                                                     Exhibit 4.1

                          Signature on following page.

                                       16

<PAGE>

          IN WITNESS WHEREOF, the Corporation has caused this Certificate to be
duly executed on its behalf by its President this     day of          , 2003.
                                                  ---        ---------

                                         ANALEX CORPORATION


                                         By:
                                            ------------------------------------
                                              Name:  Sterling E. Phillips, Jr.
                                              Title: President