I've written a program that will do this sort of analysis, as well as
some other analysis of PDB structures. It runs on Macs only (but could
be ported to other platforms if there is interest). Be warned that it
does not produce fancy graphical output. I use it to generate output
files which can be analyzed by other programs. For example, it can
export the contact data as a 2D array which can be imported into a
spreadsheet program.
If interested, send me some mail and I'll make it available.
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Steve A. Chervitz E-MAIL: sac at genome.stanford.edu
Department of Genetics FAX: (415)723-7016
Stanford University TEL: (415)725-8956
Stanford, CA 94305-5120 HTTP: www-genome.stanford.edu/~sac
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Ira Ropson wrote:
>> Hello,
>> Is there an easy way to construct a contact map for a protein of known
> structure in the PDB? I'd like to know and compare the nearest neighbor
> amino acids to a particular residue in a family of proteins with very
> similar structures but only 25% or so sequence identity. I could
> construct a table of interacting residues manually, by specifying a
> sphere of say 5 angstrom radius around the residue that I am probing in
> insightII or rasmol and then identifying those amino acids that are in
> that sphere. However, I can't help but think that there must be a
> better way to evaluate the entire structure at once, and that someone
> has written a program to do this for me.
>> Thanks in advance.
> Ira Ropson
>iropson at bcmic.hmc.psu.edu> If I had time for a fancy Sig file I problably wouldn't have a job.
