Laboratoire d'Enzymologie et Biochimie Structurales CNRS 91198-Gif-sur-Yvette, France
At least three types of protein-protein interactions can be identified in X-ray structures as deposited in the PDB: (a) crystal contacts; (b) contacts between subunits of oligomeric proteins; (c) contacts between components of protein- protein complexes. Whereas there is a conceptual difference between interactions of types (b) and (c) that preexist crystallization and those of type (b) that may be considered as crystal artefacts, the distinction between the three types is not always obvious: a subunit contact may also be a crystal contact; the status of contacts generated by non-crystallographic symmetry is often uncertain. Moreover, the distinction can be made only on the basis of biochemical data that are often absent or undecisive. In general, the necessary information is not present in the PDB file.
A survey of protein-protein interaction in the PDB is never- theless useful, even though it cannot be exhaustive. We examined 30 protein-protein complexes and 152 crystal forms where the asymmetric unit contains a single copy of a monomeric protein. The first sample represents type (c) interactions; in the second, contacts generated by lattice translations and screw rotations are representative of type (a) interactions. The two can be compared to subunit contacts of type (b) examined in earlier studies. Obvious differences are the dominance of point group symmetry in the latter, and the extent of the interaction as measured by the interface area which increases from type (a) to type (c) and type (b).