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

Previous rotamer libraries showed little significant clustering for asparagine chi(2) Or glutamine chi(3) values, but none of those studies corrected amide orientations or omitted disordered side chains. The current survey used 240 proteins at less than or equal to 1.7 Angstrom resolution with <50% homology and <30 clashes per thousand atoms (atomic overlap greater than or equal to 0.4 Angstrom). 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 greater than or equal to 40, alternate conformation, or severe clash; that selection process yielded 1,490 Asn and 863 Gin side chains. Clear clustering was observed for Asn chi(2) and Gin chi(3) (except when Gin chi(2) is trans). For Gin, 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 Gin rotamers are influenced by favorable van der Waals contacts and others by specific local H-bond patterns.