Your best bet is PDB format. Google it up, it gives coordinates and such for each aa.
Date: Sun, 07 Jun 2009 06:57:35 +0100
From: Sujita Purushothaman <sujita from skhot.net>
Subject: [Bio-software] Data Structure for protein
To: bio-soft from net.bio.net
Message-ID: <4A2B56CF.10102 from skhot.net>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
I'm writing a program which has to hold information about the 3d
structure of a protein, and make modifications to the coordinates. I was
wondering if anyone can comment on suitable data structures that can be
used for this, pros and cons?
Thanks in advance!