Clashes: Difference between revisions
From Proteopedia
Jump to navigationJump to search
Eric Martz (talk | contribs) No edit summary |
Eric Martz (talk | contribs) No edit summary |
||
| Line 1: | Line 1: | ||
''Clashes'' in protein models, also called ''steric clashes'', occur when two non-bonded atoms are impossibly close to each other. This happens when the van der Waals radii of the atoms overlap; that is, when two atoms are occupying the same space. Clashes typically occur in lower resolution models due to the difficulties of obeying all chemical constraints while optimizing the fit of the model to the experimental data. Clashes are more common in X-ray crystallographic models with resolutions of 3.0 Å or worse, or in cryo-EM models. (NMR models generally lack clashes because they are forced to obey chemical constraints.) | ''Clashes'' in protein models, also called ''steric clashes'', occur when two non-bonded atoms are impossibly close to each other. This happens when the van der Waals radii of the atoms overlap; that is, when two atoms are occupying the same space. Clashes typically occur in lower resolution models due to the difficulties of obeying all chemical constraints while optimizing the fit of the model to the experimental data. Clashes are more common in X-ray crystallographic models with resolutions of 3.0 Å or worse, or in cryo-EM models. (NMR models generally lack clashes because they are forced to obey chemical constraints.) | ||
==Clashes Dictate Protein Secondary Structure== | |||
The prevalence of alpha helices and beta strands in proteins results from the avoidance of clashes in the polypeptide chain, as embodied in the Ramachandran Principle. Interactive visualization of clashes during rotations of bonds in a polypeptide chain is available at [[Tutorial:Ramachandran principle and phi psi angles]]. | |||
==Clashes vs. Model Quality== | ==Clashes vs. Model Quality== | ||
