Relative accessible surface area or relative solvent accessibility (RSA) of a protein residue is a measure of residue solvent exposure. It can be calculated by formula:
To measure the relative solvent accessibility of the residue side-chain only, one usually takes MaxASA values that have been obtained from Gly-X-Gly tripeptides, where X is the residue of interest. Several MaxASA scales have been published[1][2][3]
and are commonly used (see Table).
In this table, the more recently published MaxASA values (from Tien et al. 2013[1]) are systematically larger than the older values (from Miller et al. 1987[2] or Rose et al. 1985[3]). This discrepancy can be traced back to the conformation in which the Gly-X-Gly tripeptides are evaluated to calculate MaxASA. The earlier works used the extended conformation, with backbone angles of and .[2][3] However, Tien et al. 2013[1] demonstrated that tripeptides in extended conformation fall among the least-exposed conformations. The largest ASA values are consistently observed in alpha helices, with backbone angles around and . Tien et al. 2013 recommend to use their theoretical MaxASA values (2nd column in Table), as they were obtained from a systematic enumeration of all possible conformations and likely represent a true upper bound to observable ASA.[1]
ASA and hence RSA values are generally calculated from a protein structure, for example with the software DSSP.[4] However, there is also an extensive literature attempting to predict RSA values from sequence data, using machine-learning approaches.[5][6]
Prediction tools
Experimentally predicting RSA is an expensive and time-consuming task. In recent decades, several computational methods have been introduced for RSA prediction.[7][8][9]
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Miller, S.; Janin, J.; Lesk, A. M.; Chothia, C. (1987). "Interior and surface of monomeric proteins". J. Mol. Biol. 196 (3): 641–656. doi:10.1016/0022-2836(87)90038-6. PMID3681970.
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Kabsch, W.; Sander, C. (1983). "Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features". Biopolymers. 22 (12): 2577–2637. doi:10.1002/bip.360221211. PMID6667333. S2CID29185760.