PSdbView presents the information graphically, I don't know if
there is a way to get the table printed and David Deerfield.
Requires JAVA capable viewer.
http://www.psc.edu/~geigel/PSdb/PSdb.html
That info will also be in Steven Bryant's thresding database - under
research projects on the NCBI web site.
iropson at bcmic.hmc.psu.edu (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.
