Asparagine and glutamine rotamers: B-factor cutoff and correction of amide flips yield distinct clustering.

Abstract

Previous rotamer libraries showed little significant clustering for asparagine chi2 or glutamine chi3 values, but none of those studies corrected amide orientations or omitted disordered side chains. The current survey used 240 proteins at </=1.7 A resolution with <50% homology and <30 clashes per thousand atoms (atomic overlap >/=0.4 A). All H atoms were added and optimized, and amide orientation was flipped by 180 degrees if required by H bonding or atomic clashes. A side chain was included only if its amide orientation was clearly determined and if no atom had a B factor >/=40, alternate conformation, or severe clash; that selection process yielded 1,490 Asn and 863 Gln side chains. Clear clustering was observed for Asn chi2 and Gln chi3 (except when Gln chi2 is trans). For Gln, five major and four minor rotamers cover 87% of examples. For Asn, there are seven backbone-independent rotamers covering 94% of examples plus rotamers specified for strictly alpha-helical, beta, and left-handed (+phi) Asn. Although the strongest influence on chi angles is avoidance of atomic clashes (especially with the NH2 hydrogens), some Asn or Gln rotamers are influenced by favorable van der Waals contacts and others by specific local H-bond patterns.