Solvent exposure

The solvent exposure of an amino acid in a protein measures to what extent the amino acid is accessible to the solvent (usually water) surrounding the protein. Generally speaking, hydrophobic amino acids will be buried inside the protein and thus shielded from the solvent, while hydrophilic amino acids will be close to the surface and thus exposed to the solvent. However, like with many biological rules exceptions are common and hydrophilic residues are frequently found to be buried in the native structure and vice versa.

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Solvent exposure can be numerically described by several measures, the most popular measures being accessible surface area and relative accessible surface area. Other measures are for example:

• Contact number: number of amino acid neighbors within a sphere around the amino acid.
• Residue depth: distance of the amino acid to the molecular surface.
• Half sphere exposure: number of amino acid neighbors within two half spheres around the amino acid.

References

Lee B, Richards F. (1971) The interpretation of protein structures: estimation of static accessibility. J. Mol. Biol. 55:379-400

Greer J, Bush B. (1978) Macromolecular shape and surface maps by solvent exclusion. Proc. Natl. Acad. Sci. USA 75:303-307.

Connolly M. (1983) Solvent-accessible surfaces of proteins and nucleic acids. Science 221:709-713

Chakravarty S, Varadarajan R. (1999) Residue depth: a novel parameter for the analysis of protein structure and stability. Structure Fold. Des. 7:723-732.

Pintar A, Carugo O, Pongor S. (2003) Atom depth in protein structure and function. Trends Biochem. Sci. 28:593-597.

Hamelryck T. (2005) An amino acid has two sides: A new 2D measure provides a different view of solvent exposure. Proteins Struct. Func. Bioinf. 59:38-48.