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Structure validation by Calpha geometry: phi,psi and Cbeta deviation.

Publication ,  Journal Article
Lovell, SC; Davis, IW; Arendall, WB; de Bakker, PIW; Word, JM; Prisant, MG; Richardson, JS; Richardson, DC
Published in: Proteins
February 15, 2003

Geometrical validation around the Calpha is described, with a new Cbeta measure and updated Ramachandran plot. Deviation of the observed Cbeta atom from ideal position provides a single measure encapsulating the major structure-validation information contained in bond angle distortions. Cbeta deviation is sensitive to incompatibilities between sidechain and backbone caused by misfit conformations or inappropriate refinement restraints. A new phi,psi plot using density-dependent smoothing for 81,234 non-Gly, non-Pro, and non-prePro residues with B < 30 from 500 high-resolution proteins shows sharp boundaries at critical edges and clear delineation between large empty areas and regions that are allowed but disfavored. One such region is the gamma-turn conformation near +75 degrees,-60 degrees, counted as forbidden by common structure-validation programs; however, it occurs in well-ordered parts of good structures, it is overrepresented near functional sites, and strain is partly compensated by the gamma-turn H-bond. Favored and allowed phi,psi regions are also defined for Pro, pre-Pro, and Gly (important because Gly phi,psi angles are more permissive but less accurately determined). Details of these accurate empirical distributions are poorly predicted by previous theoretical calculations, including a region left of alpha-helix, which rates as favorable in energy yet rarely occurs. A proposed factor explaining this discrepancy is that crowding of the two-peptide NHs permits donating only a single H-bond. New calculations by Hu et al. [Proteins 2002 (this issue)] for Ala and Gly dipeptides, using mixed quantum mechanics and molecular mechanics, fit our nonrepetitive data in excellent detail. To run our geometrical evaluations on a user-uploaded file, see MOLPROBITY (http://kinemage.biochem.duke.edu) or RAMPAGE (http://www-cryst.bioc.cam.ac.uk/rampage).

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Published In

Proteins

DOI

EISSN

1097-0134

Publication Date

February 15, 2003

Volume

50

Issue

3

Start / End Page

437 / 450

Location

United States

Related Subject Headings

  • Proteins
  • Protein Conformation
  • Proline
  • Molecular Structure
  • Models, Molecular
  • Internet
  • Imaging, Three-Dimensional
  • Glycine
  • Carbon
  • Bioinformatics
 

Citation

APA
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Lovell, S. C., Davis, I. W., Arendall, W. B., de Bakker, P. I. W., Word, J. M., Prisant, M. G., … Richardson, D. C. (2003). Structure validation by Calpha geometry: phi,psi and Cbeta deviation. Proteins, 50(3), 437–450. https://doi.org/10.1002/prot.10286
Lovell, Simon C., Ian W. Davis, W Bryan Arendall, Paul I. W. de Bakker, J Michael Word, Michael G. Prisant, Jane S. Richardson, and David C. Richardson. “Structure validation by Calpha geometry: phi,psi and Cbeta deviation.Proteins 50, no. 3 (February 15, 2003): 437–50. https://doi.org/10.1002/prot.10286.
Lovell SC, Davis IW, Arendall WB, de Bakker PIW, Word JM, Prisant MG, et al. Structure validation by Calpha geometry: phi,psi and Cbeta deviation. Proteins. 2003 Feb 15;50(3):437–50.
Lovell, Simon C., et al. “Structure validation by Calpha geometry: phi,psi and Cbeta deviation.Proteins, vol. 50, no. 3, Feb. 2003, pp. 437–50. Pubmed, doi:10.1002/prot.10286.
Lovell SC, Davis IW, Arendall WB, de Bakker PIW, Word JM, Prisant MG, Richardson JS, Richardson DC. Structure validation by Calpha geometry: phi,psi and Cbeta deviation. Proteins. 2003 Feb 15;50(3):437–450.
Journal cover image

Published In

Proteins

DOI

EISSN

1097-0134

Publication Date

February 15, 2003

Volume

50

Issue

3

Start / End Page

437 / 450

Location

United States

Related Subject Headings

  • Proteins
  • Protein Conformation
  • Proline
  • Molecular Structure
  • Models, Molecular
  • Internet
  • Imaging, Three-Dimensional
  • Glycine
  • Carbon
  • Bioinformatics