Multi-protein complexes and interface residue overlap.

The subunits of multi-protein complexes bind together simultaneously and therefore these subunit proteins are not competing to bind to the same interface. For each subunit S in the complex, we test all pairs of its binding partners for sharing binding residues on the surface of S. Each binding pair then has n = 0, 1, 2 etc. overlapping residues. Whereas most binding pairs do not share interface residues, clearly there is some overlap. If one accounts for specific atoms in an interface rather than residues, the overlap decreases but is still present. For the proteasome, there are still 22% and 7% of interface pairs that share atoms (at 4 Å and 3.5 Å cutoffs, respectively).