Section 22.1.1.3.3.3. Molecular surface as the sum of the contact and re-entrant surfaces (MS = CS + RS)

Like the solvent-accessible surface, the molecular surface is also closed, but it contains a mixture of convex and concave patches, the sum of the contact and re-entrant surfaces. The ratio of these two surfaces varies with probe radius. In the limit of infinite probe radius, the molecular surface becomes convex and attains a limiting minimum value (i.e. it becomes a convex hull, similar to the one described above). The molecular surface cannot be divided up and assigned unambiguously to individual atoms.

The contact surface is not closed. Instead, it is a series of convex patches on individual atoms, simply related to the solvent-accessible surface of the same atoms. In complementary fashion, the re-entrant surface is also not closed but is a series of concave patches that is part of the probe surface where it contacts two or three atoms simultaneously. At infinite probe radius, the re-entrant areas are plane surfaces, at which point the molecular surface becomes a convex surface. The re-entrant surface cannot be divided up and assigned unambiguously to individual atoms. Note that the molecular surface is simply the union of the contact and re-entrant surfaces, so in terms of area MS = CS + RS.