Van der Waals Radii

Q:
I am writing about your article, The Packing Density in Proteins: Standard Radii and Volumes, published by JMB on 1999. In the article, in particular in table 2, you list a series of radii associated to each atom according to the number of hydrogens it has attached and a number you call the “valence”. However, valences of carbon are 2 and 4, and the list shows a valence 3 carbon; also valences for nitorgen are 3 and 5, and the tible shows a valence 4 one. Could you please explain what you mean by the term “valence” exactly? In particular, I am interested in knowing the type of heavy atoms you can find in glutamine and alanine residues, and their radii.

A:
Here, the term “valence” is perhaps best described in Table 1 (instead of Table 2). What is meant by the “n-term” (here, used synonymously with valence) is usually a geometric descriptor designating the orientation of other atomic species around that atom (for example, n=4 usually means that the atom builds a tetrahedron, whereas n=3 usually means that the atom is trigonal planar). Strictly speaking, and perhaps more accurately, n just designates the total number of atoms bound to a central atom. So, in your example of carbon’s n=3 in Table 2, these are carbon atoms which are connected to 3 other atoms (an example of C3H0 may be the carbonyl carbon in a protein backbone, and C3H1 may be a carbon atom in a phenyl group of PHE). In your example of nitrogen’s n=4, the N4H3 may represent the epsilon-amino group in LYS, since it is bound to 4 other atoms (one carbon and 3 hydrogen atoms).

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