Structure Validation by C Geometry: , and C Deviation

摘要: Geometrical validation around the C is described, with a new measure and up- dated Ramachandran plot. Deviation of ob- served atom from ideal position provides single encapsulating major structure-valida- tion information contained in bond angle distor- tions. deviation sensitive to incompatibilities between sidechain backbone caused by misfit conformations or inappropriate refinement re- straints. A , plot using density-dependent smoothing for 81,234 non-Gly, non-Pro, non- prePro residues B < 30 500 high-resolu- proteins shows sharp boundaries at critical edges clear delineation large empty areas regions that are allowed but disfavored. One such region -turn conformation near 75°,60°, counted as forbidden common struc- ture-validation programs; however, it occurs well- ordered parts good structures, overrepre- sented functional sites, strain partly compensated H-bond. Favored also defined Pro, pre- Gly (important because angles more permissive less accurately determined). Details these accurate empirical distributions poorly predicted previous theoretical calcula- tions, including left -helix, which rates favorable energy yet rarely occurs. proposed factor explaining this discrepancy crowding two-peptide NHs permits donating only New calculations Hu et al. (Pro- teins 2002 (this issue)) Ala dipeptides, mixed quantum mechanics molecular mechanics, fit our nonrepetitive data excellent detail. To run geometrical evaluations on user-uploaded file, see MOLPROBITY (http://kinemage. biochem.duke.edu) RAMPAGE (http://www-cryst. bioc.cam.ac.uk/rampage). Proteins 2003;50:437- 450.