Sc. Lovell et al., Asparagine and glutamine rotamers: B-factor cutoff and correction of amideflips yield distinct clustering, P NAS US, 96(2), 1999, pp. 400-405
Citations number
28
Categorie Soggetti
Multidisciplinary
Journal title
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
Previous rotamer libraries showed little significant clustering for asparag
ine chi(2) Or glutamine chi(3) values, but none of those studies corrected
amide orientations or omitted disordered side chains. The current survey us
ed 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 or
ientation was flipped by 180 degrees if required by H bonding or atomic cla
shes. A side chain was included only if its amide orientation was clearly d
etermined and if no atom had a B factor greater than or equal to 40, altern
ate 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-ind
ependent rotamers covering 94% of examples plus rotamers specified for stri
ctly alpha-helical, beta, and left-handed (+phi) Asn, Although the stronges
t influence on chi angles is avoidance of atomic clashes (especially with t
he NH2 hydrogens), some Asn or Gin rotamers are influenced by favorable van
der Waals contacts and others by specific local H-bond patterns.