Previous analyses of protein structures have focused primarily on their secondary structures, three-dimensional folds, and binding or active sites while their molecular surfaces have received much less attention due possibly to the lack of accurate and robust programs for their computation. Using SES A we have computed and analyzed the molecular surfaces of three mutually exclusive sets, G, S and M, of protein crystal structures. G and S include only non-membrane proteins with the latter having only monomers while M has only membrane proteins. The analyses show that the average areas for three SES patch types each follows a power law with respect to the number of atoms n in a structure. Specifically, SAS area per atom micro s decreases while probe area per atom micro p increases with n. Most interestingly, the fitted power laws for micro s intersect, respectively, with those for micro p at, n = 956, n = 934 and n = 1, 024 for G, S and M. They correspond approximately to 58, 60 and 68 amino acid residues. Together they provide an explanation for protein structural integrity and stability in general and the transition in particular from peptides typically with random conformations in solution to proteins usually with a dominant conformation. We have also analyzed the molecular surfaces of the AlphaFold predicted models for twenty seven proteomes. The analyses show that the micro s for thirteen prokaryotic proteomes are similar to those for the experimentally-derived structures while the micro s for fourteen eukaryotic proteomes differ largely from them. The differences may have significant implications in theory in that there exist genuine differences between prokaryotic and eukaryotic proteomes, and in application in that the current AlphaFold models for eukaryotic proteomes are not adequate for, say, structure-based drug design.
