Hi Ira, I don't know of any table of maximal solvent accessible surface areas for each residue type when bounded by glycines. Maybe someone on the Chimera mailing list will know. A Chimera Python script could run through the PDB and accumulate per-residue surface area statistics. One trouble with that would be that surface calculation fails in Chimera in some percentage of cases (~5%) due to numerical problems. Tom
Hi Tom,
Love the software. Do you have a table for calculating the maximum available surface area for amino acids eg.(Gly-Xxx-Gly) so that I can get a relative percentage exposed surface area from the calculations? Do you know how to find one in the literature? Has anyone written a program that describes the possible surface exposure for a residue in a particular secondary structure and/or a particular sequence? This maximal value would certainly be different depending on the local sequence and structure. For example, a residue in the middle of a helix would have to be shielded from the solvent by the i+4 and i-4 residues, and the size of those residues would matter.
Thanks, Ira
On 12/10/10 2:41 PM, Tom Goddard wrote:
Hi Sumitro,
I made a Chimera video tutorial showing how to determine which residues are on the surface.
http://www.cgl.ucsf.edu/chimera/videodoc/surfaceresidues/index.html
Tom
Hi Ira, There is such a table in the Getarea online manual (about halfway down this page): <http://curie.utmb.edu/area_man.html>
From that page, 'The "random coil" value of a residue X is the average solvent-accessible surface area of X in the tripeptide Gly-X-Gly in an ensemble of 30 random conformations.'
Be aware, however, that various programs use different atomic radii and that those values will affect the surface areas. Chimera likely uses different radii than Getarea, but I believe both programs use reasonable values and that it may still be useful to normalize by the Getarea random coil values as long as you are aware of these issues. At least the default probe radius in Chimera and Getarea is the same, 1.4 Angstroms. It is unclear if Getarea uses the same random coil values even if you specify a different probe radius. Also be careful about solvent-excluded surface (which is what Chimera displays) versus solvent-accessible surface. Chimera gives both kinds of areas, whereas the Getarea random coil values are SAS. The SAS is farther out from the atomic centers and the values range much larger. I hope this helps, 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 Dec 13, 2010, at 6:08 PM, Tom Goddard wrote:
Hi Ira, I don't know of any table of maximal solvent accessible surface areas for each residue type when bounded by glycines. Maybe someone on the Chimera mailing list will know. A Chimera Python script could run through the PDB and accumulate per-residue surface area statistics. One trouble with that would be that surface calculation fails in Chimera in some percentage of cases (~5%) due to numerical problems. Tom
Hi Tom, Love the software. Do you have a table for calculating the maximum available surface area for amino acids eg.(Gly-Xxx-Gly) so that I can get a relative percentage exposed surface area from the calculations? Do you know how to find one in the literature? Has anyone written a program that describes the possible surface exposure for a residue in a particular secondary structure and/or a particular sequence? This maximal value would certainly be different depending on the local sequence and structure. For example, a residue in the middle of a helix would have to be shielded from the solvent by the i+4 and i-4 residues, and the size of those residues would matter. Thanks, Ira
participants (2)
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Elaine Meng -
Tom Goddard