Dear Vamsi, I do not think there is a definite answer. This is a somewhat philosophical rather than technical question... it depends what you are going to do with the resulting list of residues. You could try different values and see whether the resulting set of residues agrees with your intuition. If I remember correctly, there are some alanine scanning papers that indicate even residues that are in contact are not always important for binding energy. These were experiments done on protein-protein systems, however. Perhaps there are some published papers that discuss these issues for substrates -- if anybody has an opinion on this topic or can suggest references, please speak up! However, if you have a protein-ligand complex structure, why not just use the "Find Contacts/Clashes" tool instead of dealing with solvent- accessible surface areas? That is what I would use. "Find Contacts/Clashes" documentation: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findclash...
Also, the "distances, H-bonds, contacts" section of this tutorial includes an example of finding residues that interact with a ligand: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ squalene.html> Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Sep 30, 2009, at 3:33 AM, vamsi krishna wrote:
Dear all, I am using chimera to calculate solvent accessibility of residues , may i ask you what cutoff is appropriate to identify surface residues significant for substrate binding .
Thank you vamsi