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:
residue.areaSES/residue.areaSESgxgWarnings about calculation failures generally can be disregarded, as they refer to non-amino acid residues such as water molecules.