The solvent exposure
of an amino acid
in a protein
measures to what extent theamino acid is accessible to the solvent
) 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.
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.
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.... Read More