Van der Waals contact surfaces

Figure 5-6 Outlines of the purine and pyrimidine bases of nucleic acids showing van der Waals contact surfaces and some of the possible directions in which hydrogen bonds may be formed. Large arrows indicate the hydrogen bonds present in the Watson-Crick base pairs. Smaller arrows indicate other hydrogen bonding possibilities. The directions of the green arrows are from a suitable hydrogen atom in the base toward an electron pair that serves as a hydrogen acceptor. This direction is opposite to that in the first edition of this book to reflect current usage.

Figure 10 Ligand profile plot for the grgi conformer of H2P- -Pr. The van der Waals contact surface is shown in the upper right figure and the atom numbering in the upper left figure. (Reprinted with permission from Ref 83. 1980 American Chemical Society)...

Figure 3 (a) Space-filling model of psoralen interacting with DNA bases for orientation 2 intercalated in the 5 -TpA site, (b) van der Waals contact surface between ligand and DNA. 

Table 5.4. Properties of CT-deleted B - HA complexes (see Fig. 5.2), showing binding energies AEb-a and intermodular bond distances i B ii and RB...A, compared with van der Waals contact distances Rft...A(vm> for heavy atoms A and B (note that optimum intermodular separations are imprecisely determined on the extremely flat potential-energy surface)...

Contacting Procedure. As shown in Figure 3, for a given values of /iA, /iB and Az, our program determines a normal translation Ax that places one or more atoms in van der Waals contact without any interpenetration as described earlier (8). The surface of the chain is defined by circumscribing a hard-sphere of the appropriate van der Waals radius Ri, around each constituent atom. In general, the final position of the two polymeric chains is characterized by the following ... 

Covalent bond distances and angles tell us how the atomic nuclei are arranged in space but they do not tell us anything about the outside surfaces of molecules. The distance from the center of an atom to the point at which it contacts an adjacent atom in a packed structure such as a crystal (Fig. 2-1) is known as the van der Waals radius. The ways in which biological molecules fit together are determined largely by the van der Waals contact radii. These, too, are listed in Table 2-1. In every case they are approximately equal to the covalent radius plus 0.08 nm. Van der Waals radii... 

Destabilizing. /3-substitution reduces conformational freedom. His and Tyr may also form hydrogen bonds with polypeptide backbone in unfolded state. Very destabilizing. Buries less hydrophobic surface area, makes less van der Waals contacts, and loses more conformational entropy on folding. 

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