Structure validation by Calpha geometry: phi,psi and Cbeta deviation.
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).
Lovell
Simon C
SC
Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom.
Davis
Ian W
IW
Arendall
W Bryan
WB
de Bakker
Paul I W
PI
Word
J Michael
JM
Prisant
Michael G
MG
Richardson
Jane S
JS
Richardson
David C
DC
D000596:Amino Acids / Q000737:chemistry*; D002244:Carbon / Q000737:chemistry; D005998:Glycine / Q000737:chemistry; D021621:Imaging, Three-Dimensional; D020407:Internet; D008958:Models, Molecular; D015394:Molecular Structure; D011392:Proline / Q000737:chemistry; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*
D000596:Amino Acids; D011506:Proteins; D002244:Carbon; D011392:Proline; D005998:Glycine