Rotamers: to be or not to be? An analysis of amino acid side-chain conformations in globular proteins.

Originally, rotamers were defined as side-chain torsion (chi-angle) combinations corresponding to the local minima of potential energy (van-der-Waals and torsion terms) for the side-chain of a terminally blocked amino acid. If at least one chi-angle differed by more than 20 degrees from that of a rotamer, the side-chain was considered as deviant both from energetic (increase in potential energy of no less than 1 to 2 kcal/mol) and geometric (precision of atom positioning is worse than 0.5 A) aspects. In this work the distribution of side-chain conformations in protein crystal structures is analysed. Large deviations from rotameric chi-values occur systematically and cannot be attributed merely to errors in crystal structure determination. The "rotamericity" (the fraction of residues within +/- 20 degrees of the chi-angles of a rotamer) not only remains substantially below 100% (70 to 95% for various amino acids) with improving crystallographic resolution but actually decreases for 8 out of 17 amino acid types after a critical resolution limit is crossed. This effect has been observed for external as well as for internal residues. The set of amino acid side-chain conformations in globular proteins cannot be considered as normally distributed around some rotamer points. Outliers occur systematically. The rotamericity of an amino acid depends essentially on the different environments the amino acid meets in real protein structures. Factors such as the backbone torsion angles of the residue itself, the secondary structure and tertiary contacts influence the rotamericity. The deviations in regions of regular main-chain structure from the average g-:t:g+ relationship in the chi 1-angle become much more evident if, in addition to the typical secondary structure assignments, the actual backbone torsion angles of the residue are taken into account. In alpha-helices the t:g+ distribution in the chi 1-angle correlates with physical properties describing volume, extension and flexibility of the side-chain. In beta-strands the factors influencing the t:g+ distribution in the chi 1-angle are the polarity and hydrophobicity of the side-chain. Nevertheless, a considerable number of residues do not comply with the statistical preferences observed for the side-chain conformation. Large deviations from the rotamer values are observed especially in cases when normally advantageous chi 1-values are not allowed and adjustments in chi 2 become necessary to accommodate the side-chain.(ABSTRACT TRUNCATED AT 400 WORDS)