Quantifying the accessible surface area of protein residues in their local environment

Abstract

The quantification of the packing of residues in proteins and docking of ligands to macromolecules is important in understanding protein stability and drug design. The number of atoms in contact (within a distance of 4.5 Å) can be used to describe the local environment of a residue. As this number increases, the accessible surface area (ASA) of the residue decreases exponentially and the variation can be described in terms of an exponential equation of the form y = a₁exp(-x/a₂), each residue having its own set of parameters a₁ and a₂, which also depend on whether the whole residue or just the side chain is considered. Hydrophobic and hydrophilic residues can be distinguished on the basis of both the average number of surrounding atoms and the variation of ASA. For a given number of partner atoms, a comparison of the observed ASA with the expected value obtained from the equation provides a method of assessing the goodness of packing of the residue in a protein structure or its importance in the binding of a ligand. The equation provides a method to estimate the ASA of a protein molecule and the average relative accessibilities of different residues, the latter being inversely correlated with hydrophobicity values.