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

Publication ,  Journal Article
Lovell, SC; Word, JM; Richardson, JS; Richardson, DC
Published in: Proc Natl Acad Sci U S A
January 19, 1999
Published version (DOI) Link to item

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 /=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.

Duke Scholars

Jane Shelby Richardson
Author Jane Shelby Richardson Biochemistry
David C. Richardson
Author David C. Richardson Biochemistry

Published In

Proc Natl Acad Sci U S A

DOI

10.1073/pnas.96.2.400

ISSN

0027-8424

Publication Date

January 19, 1999

Volume

96

Issue

2

Start / End Page

400 / 405

Location

United States

Related Subject Headings

  • Proteins
  • Protein Structure, Secondary
  • Protein Conformation
  • Molecular Conformation
  • Models, Molecular
  • Glutamine
  • Asparagine
 

Citation

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MLA
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Lovell, S. C., Word, J. M., Richardson, J. S., & Richardson, D. C. (1999). Asparagine and glutamine rotamers: B-factor cutoff and correction of amide flips yield distinct clustering. Proc Natl Acad Sci U S A, 96(2), 400–405. https://doi.org/10.1073/pnas.96.2.400
Lovell, S. C., J. M. Word, J. S. Richardson, and D. C. Richardson. “Asparagine and glutamine rotamers: B-factor cutoff and correction of amide flips yield distinct clustering.” Proc Natl Acad Sci U S A 96, no. 2 (January 19, 1999): 400–405. https://doi.org/10.1073/pnas.96.2.400.
Lovell SC, Word JM, Richardson JS, Richardson DC. Asparagine and glutamine rotamers: B-factor cutoff and correction of amide flips yield distinct clustering. Proc Natl Acad Sci U S A. 1999 Jan 19;96(2):400–5.
Lovell, S. C., et al. “Asparagine and glutamine rotamers: B-factor cutoff and correction of amide flips yield distinct clustering.” Proc Natl Acad Sci U S A, vol. 96, no. 2, Jan. 1999, pp. 400–05. Pubmed, doi:10.1073/pnas.96.2.400.
Lovell SC, Word JM, Richardson JS, Richardson DC. Asparagine and glutamine rotamers: B-factor cutoff and correction of amide flips yield distinct clustering. Proc Natl Acad Sci U S A. 1999 Jan 19;96(2):400–405.
Journal cover image

Published In

Proc Natl Acad Sci U S A

DOI

10.1073/pnas.96.2.400

ISSN

0027-8424

Publication Date

January 19, 1999

Volume

96

Issue

2

Start / End Page

400 / 405

Location

United States

Related Subject Headings

  • Proteins
  • Protein Structure, Secondary
  • Protein Conformation
  • Molecular Conformation
  • Models, Molecular
  • Glutamine
  • Asparagine