[Chimera-users] Solvent Accessibility of Amino Acids

Elaine Meng meng at cgl.ucsf.edu
Fri Jun 24 09:31:09 PDT 2016


Hi Eric,
Not “a tool” per se, but when you show a molecular surface, the surface areas (both solvent-accessible surface SAS and solvent-excluded surface SES) per atom and per residue are automatically computed and available as attributes named areaSAS and areaSES.  You can do all kinds of things with these attributes, like select all the residues with surface areas above or below some cutoff (for subsequent coloring or other actions), or simply write out the values to a file.  Note the surface that is actually displayed is the SES.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/representation.html#surfaces>
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/defineattrib.html#attribdef>

However, the surface area values are are not automatically normalized into % or fractional accessibility relative to that same residue type in a completely exposed or unfolded state, they are just the “raw” square-angstrom areas.  Fortunately in 2014 another group calculated SES for the standard amino acids in Gly-X-Gly tripeptides using the Chimera parameters (VDW radii etc.) and these are suitable for normalization using Chimera’s “Attribute Calculator” tool.  The normalization values and detailed instructions for calculating relative exposure (normalized SESA) here:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/surfnorm.html>

To summarize: provided that a molecular surface can be calculated for some protein structure, you immediately have per-residue areas available, both SASA and SESA.  You can also calculate a normalized SESA per residue.

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 Jun 24, 2016, at 12:53 AM, Eric Berg <edberg at ucsc.edu> wrote:

> Hello,
> I've been spending some time trying to determine solvent accessibility for certain regions of protein complexes. I need something that is precise enough to determine the solvent accessibility of individual amino acids within a selected region (or the entire complex). There are a few tools online, but so far I haven't found something that does this.
> 
> Does Chimera currently have a tool for measuring solvent accessibility of individual amino acids?
> Eric Berg




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