International
Tables for
Crystallography
Volume F
Crystallography of biological macromolecules
Edited by E. Arnold, D. M. Himmel and M. G. Rossmann

International Tables for Crystallography (2012). Vol. F, ch. 22.1, pp. 707-708   | 1 | 2 |

Section 22.1.3.3.3. Molecular surface as the sum of the contact and re-entrant surfaces (MS = CS + RS)

M. Gersteina* and F. M. Richardsa

aDepartment of Molecular Biophysics & Biochemistry, 266 Whitney Avenue, Yale University, PO Box 208114, New Haven, CT 06520, USA
Correspondence e-mail:  Mark.Gerstein@yale.edu

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

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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.








































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