Relative Exposure of Amino Acids

The relative exposure of an amino acid indicates its degree of burial in a structure. Relative exposure can be calculated by normalizing the surface area of the residue in the structure by the surface area of the same type of residue in some reference state. Although raw (non-normalized) surface areas could be used to classify residues as buried or exposed, normalization reduces the bias toward classifying smaller residues as more buried and larger as more exposed.

Chimera displays solvent-excluded molecular surfaces composed of probe contact, toroidal, and reentrant surface. These differ from solvent-accessible surfaces, which are traced out by the probe center. The surfaces and their analytical areas are computed by the MSMS package. When a molecular surface is generated in Chimera, total areas are given in the Reply Log, and solvent-excluded and solvent-accessible surface areas per residue are assigned as attributes named areaSES and areaSAS, respectively. Normalized surface areas are not calculated automatically, but one approach is given below.

Gly-X-Gly tripeptides in which X is the residue type of interest are often used as the reference state. Solvent-excluded surface areas of the 20 standard amino acids in Gly-X-Gly tripeptides have been kindly supplied by the Murgita group as supplementary data for:

Transient protein-protein interface prediction: datasets, features, algorithms, and the RAD-T predictor. Bendell CJ, Liu S, Aumentado-Armstrong T, Istrate B, Cernek PT, Khan S, Picioreanu S, Zhao M, Murgita RA. BMC Bioinformatics. 2014 Mar 24;15:82.

Importantly, these areas were calculated in Chimera using the default radii for atoms and surface probe (confirmed by communication with the authors). The values have been reformatted into a file for attribute assignment in Chimera: areaSESgxg.txt

To calculate normalized areas for amino acid residues in a protein structure:

Open the structure in Chimera and generate a molecular surface using the default atomic and probe radii (surface command or Actions... Surface... show in the menu). This automatically creates the residue attribute areaSES, solvent-excluded surface areas in the structure. If needed, use split or surfcat to make the surface enclose the desired set(s) of atoms, for example, each protein chain individually rather than all of the chains collectively.
From this page, save the file areaSESgxg.txt as plain text.
Start Define Attribute (in menu under Tools... Structure Analysis) and browse to open areaSESgxg.txt. This creates the residue attribute areaSESgxg, solvent-excluded surface areas in the Gly-X-Gly context.
Start Attribute Calculator (in menu under Tools... Structure Analysis) and define a new attribute for residues, for example named relSESA, according to the formula:
residue.areaSES/residue.areaSESgxg
Warnings about calculation failures generally can be disregarded, as they refer to non-amino acid residues such as water molecules.

As with any other attribute, values of the new residue attribute (relSESA in this example) can be shown with color, used in selection and command-line atom specification, and saved to a file. See also: measure buriedArea

Notes

less applicable to terminal residues and residues with missing atoms
applies only to standard amino acids (not MSE, etc.)
Dock Prep could be used beforehand to repair truncated sidechains and mutate MSE to MET, but turning off (unchecking) hydrogen addition and other options is recommended for purposes of surface area calculation
normalized areas may exceed 1.0 because the areas in the Gly-X-Gly reference state are not the maximum possible areas
depending on the definition of the reference state, there may be other equally valid sets of normalization denominators
other reasonable measures of burial may not use surface areas at all

UCSF Computer Graphics Laboratory / June 2014