Figure 3. Checking for exposed overlap.

A) Dots on the surface of PHE4 from ubiquitin (PDB id: 1UBQ). The white dots are buried, all other dots are exposed. The neighbors of this PHE, which bury most of its surface, are not shown. Atoms CZ (yellow) and CE1 (green) have exposed overlap according to the criteria used in this paper. The white dots and dark-yellow dots represent the set of dots on CZ adjacent to the plane of intersection with CE1. The dark green dots on the surface of CE1 are both exposed and adjacent to the intersection with CZ. Because both the dark-yellow set and the dark-green set are non-empty, atoms CZ and CE1 are said to have exposed overlap. B) If the adjacency condition for considering two atoms as part of the same patch were merely sphere overlap, instead of exposed overlap, then the two dimensional atoms A and B would be considered part of the same patch. Intuitively, this is mistaken, since the nitrogen (blue) and oxygen (red) atoms pictured here disrupt the patches from joining. A and B overlap, but the region where they overlap is not exposed to solvent.