contact map generation?

Ira Ropson iropson at bcmic.hmc.psu.edu
Tue Jan 21 11:24:29 EST 1997


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.

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