Analytical approximation to the accessible surface area of proteins.
We propose an analytical substitute to the geometrical construction that is commonly used in calculating the protein surface area that is accessible to the solvent. A statistical approach leads to an expression of accessible surface areas as a function of distances between pairs of atoms or of residues in the protein structure, assuming only that these atoms or residues are randomly distributed in space but not penetrating each other. This function gives good estimates of the accessible surface area and of the area buried in subunit contacts for a number of proteins. Its evaluation is very fast, and the function can be differentiated, which opens the way to new applications of accessibility measurements in the study of proteins. As an example, we show that the presence of domains is easily detected by an automatic procedure based on surface areas only.
Service de Biochimie Cellulaire, Institut Pasteur 28, rue du Docteur Roux, 75724 Paris 15, France.
S J
SJ
Wodak
J
J
Janin