Solvent exposure
Solvent exposure occurs when a
Some common solvents include
In biology, the solvent exposure of an
Solvent exposure can be numerically described by several measures, the most popular measures being
- 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.