Clashes

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 StructureClashes Dictate Protein Secondary Structure

The prevalence of alpha helices and beta strands in the secondary structure of proteins results from the avoidance of clashes in the polypeptide chain, as embodied in the Ramachandran Principle. Interactive visualizations of clashes during rotations of bonds in polypeptide chains are available at Tutorial:Ramachandran principle and phi psi angles. Many other tutorials and perspectives will be found at Dihedral/Index.

Clashes vs. Model QualityClashes vs. Model Quality

The presence of too many clashes in a model calls into question its reliability. All models submitted to the Protein Data Bank (PDB) are analyzed by MolProbity, which determines a clash score, and ranks it relative to other models of the same resolution. Each PDB entry has an extensive quality report. Here are a couple of examples:

Visualization of ClashesVisualization of Clashes

• MolProbity offers visualization of clashes in
• Jmol offers visualization of clashes

See AlsoSee Also

• Tutorial:Ramachandran principle and phi psi angles
• Dihedral/Index which has links to many tutorials and resources about the Ramachandran principle, and phi and psi angles in proteins.
• Ramachandran Plot
• Quality assessment for molecular models
• Steric Effects in Wikipedia