Distinct molecular surfaces and hydrophobicity of amino acid residues in proteins

Hydrophobicity is a useful concept to rationalize the role played by amino acid residues in terms of buried or exposed conformationd with regard to th e aqueous environment in proteins. The relationship of this concept with di stinct approaches to represent the molecular surface is analyzed by computi ng reliable surface areas for three definitions namely the van der Waals, s olvent-accessible, and solvent-excluded molecular surfaces. The surface are as are obtained for all of the naturally occurring amino acids by first set ting a proper reference standard state and then calculating their values fo r a database of proteins containing a total of 4297 residues. Despite the g reat differences in these molecular sufaces, proper indexes are here define d for handling the information of interest to study the hydrophobic behavio r of amino acids provided by such surfaces.