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, p. 709   | 1 | 2 |

Section 22.1.4.2. The probe radius

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

22.1.4.2. The probe radius

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A series of surfaces can be described by using a probe sphere with a specified radius. Since this is to be a convenient mathematical construct in calculation, any numerical value may be chosen with no necessary relation to physical reality. Some commonly used examples are listed in Table 22.1.4.2[link].

Table 22.1.4.2| top | pdf |
Probe radii and their relation to surface definition

The values of 1.4 and, especially, 10 Å are only approximate. One could, of course, use 1.5 Å for a water radius or 15 Å for a ligand radius, depending on the specific application.

Probe radius (Å)Part of probe sphereType of surface
0 Centre (or tangent) van der Waals surface (VDWS)
1.4 Centre Solvent-accessible surface (SAS)
1.4 Tangent (one atom) Contact surface (CS, from parts of atoms)
1.4 Tangent (two or three atoms) Re-entrant surface (RS, from parts of probe)
1.4 Tangent (one, two, or three atoms) Molecular surface (MS = CS + RS)
10 Centre A ligand- or reagent-accessible surface
Tangent Minimum limit of MS (related to convex hull)
Centre Undefined

The solvent-accessible surface is intended to be a close approximation to what a water molecule as a probe might `see' (Lee & Richards, 1971[link]). However, there is no uniform agreement on what the proper water radius should be. Usually it is chosen to be about 1.4 Å.

References

Lee, B. & Richards, F. M. (1971). The interpretation of protein structures: estimation of static accessibility. J. Mol. Biol. 55, 379–400.








































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