Quality control of protein models: directional atomic contact analysis

Branden & Jones state, in Nature: `Protein crystallography is an exacting trade, and the results may contain errors that are difficult to identify. It is the crystallographer's responsibility to make sure that incorrect protein structures do not reach the literature.' [Branden & Jones. (1990). Nature (London), 343, 687-689.] One of several available methods of checking structures for correctness is the evaluation of atomic contacts. From an initial hypothesis that atom-atom interactions are the primary determinant of protein folding, any protein model can be tested for proper packing by the calculation of a contact quality index. The index is a measure of the agreement between the distributions of atoms around each residue fragment in the model and equivalent distributions derived from the database of known structures solved at high resolution. The better the agreement, the higher the contact quality index. This empirical test, which is independent of X-ray data, is applied to a series of successively refined crystal structures. In all cases, the model known or expected to be better (the one with the lower R-factor) has a better contact quality index, indicating that this type of contact analysis can be used as an independent quality criterion during crystallographic refinement. Modelled proteins and predicted mutant structures can also be evaluated.