Is there an excuse for the non-conformist? Notes on the calculated energies, atom–atom contacts and natural abundance of the different conformers of alanine in proteins

The calculated energies of alanine model conformers correlate with the natural abundance of alanine conformers in proteins. However, the observed conformational distribution of alaine in proteins cannot be described solely on the basis of quantum chemical calculations of the corresponding diamide. We suggest that amino acid residue conformation in a folded protein is the result of multiple factors, among which the relative energy of the residue is one of the most important ones. In this study, we investigate the possible role of a second factor, namely atom–atom contacts. We found that natural conformer abundance correlates well with the atom–atom contacts of the respective conformers. Additionally, contacts can also be responsible for the deviations form the conformer distribution expected on the basis of the calculated energies. However, the observed correlations are much more robust for surface than for internal residues in proteins, suggesting that residue conformation is influenced by other interactions to a greater extent in the core of proteins.