The relationship between protein accessible surface area and number of native contacts in its structure
Bogatyreva, N.S.; Ivankov, D.N.
Molekuliarnaia Biologiia 42(6): 1048-1055
2008
ISSN/ISBN: 0026-8984 PMID: 19140326 Document Number: 622250
The degree of folding for a protein is usually characterized by either solvent-accessible surface area or by number of formed native contacts. It is clearly that these two values must be coupled with each other, since the decrease in solvent-accessible surface area must be accompanied with the corresponding increase in the number of native contacts. In this study we show that this relationship does exist and is excellent (correlation coefficient is higher than 99%), which can be used for accurate and fast estimate of accessible surface area by means of number of native contacts. Among commonly used methods for native contacts calculation thebest correlation is observed for atom-atom scheme, if hydrogen atoms are taken into account and cutoff value for the distance between atoms' centers is 8 angstroms. The latter means that for hiding protein interior from water two layers of surface atoms are necessary.