Protein surface analysis. Part 1: Hydrophobicity densities

An image-oriented modality to functionally describe protein surfaces is presented, in terms of the hydrophobicity distribution on protein surface. Distributions of charges and mutual electrical potentials can also be considered in a similar way. The discrete hydrophobicities of the atoms that form a surface atom neighborhood are replaced by an approximately equivalent hydrophobicity density distribution, computed in a standardized octagonal pattern around each atom. The resemblance of two surface atom neighborhoods belonging to the same or two distinct proteins is defined as the sum of the products of the hydrophobicity densities of the corresponding patches (the pattern´s central circles and angular sectors having the same position). The similitude and the interaction of a pair of atom neighborhoods are defined on this basis, as the resemblance for parallel, respectively, anti-parallel orientations of the normals on the molecule(s) surfaces in the points where the central atoms are located.