COMPARING THEORETICAL AND EXPERIMENTAL BACKBONE-DEPENDENT SIDE-CHAIN CONFORMATIONAL PREFERENCES FOR LINEAR, BRANCHED, AROMATIC AND POLAR RESIDUES

An Ecepp-3 conformational study based on a phi-psi, grid search with s idechain minimization was carried out on the N-acetyl N'-methyl amides of four representative amino acids: Met, Phe, Ile, and Ser, and the d istribution of X(1) backbone-dependent rotamer preferences was compare d with the similar distribution obtained from the backbone-dependent r otamer library for proteins developed by Dunbrack and Karplus (J, Mol. Biol, 230 (1993) 543), The experimental distribution is best reproduc ed theoretically in the case of the linear sidechain of Met, reasonabl y well for the bulky sidechains of the aromatic Phe and asymmetrically P-branched Ile, and only partially for the short polar sidechain of S er. In the case of the Ser dipeptide the difference is accounted for b y the missing H bonds.