The indistinguishability of epitopes from protein surface is explained by the distinct binding preferences of each of the six antigen-binding loops.

General protein-protein interfaces are known to be enriched, compared with other surface patches, with amino acids that can form stabilizing interactions. However, several studies reported that there are hardly any differences between the amino acid composition of B-cell epitopes and that of antigen surface residues. If the amino acid composition of epitopes is indistinguishable from other surface patches, how do antibodies (Abs) identify epitopes? Here, we analyze the antigen binding regions (ABRs, roughly corresponding to the complementarity determining regions) and the epitopes in a non-redundant set of all known Ab-antigen complexes. We find that the ABRs differ significantly from each other in their amino acid composition and length. Analysis of the energetic contribution of each ABR to antigen binding reveals that, while H3 often plays a key role in antigen binding, in many antibodies other ABRs are more important. Moreover, each ABR has a distinct propensity to bind different amino acids on the antigen. The combined binding preferences of the ABRs yield a total preference to amino acids with a composition that is virtually identical to that of surface residues. These results suggest that antibodies evolved to recognize protein surfaces. They may help in improving Ab engineering and B-cell epitope prediction.