Atom cont

Lo Conte, L., Chothia, C and Janin, J. (1999) The atomic structure of protein-protein recognition sites../. Mol. Biol. 285,2177-2198. 

Fig. 13.3. (cont.) and (13.7). The wavefunctions are calculated using the empirical fit PES of Sorbie and Murrell (1975). The arrows indicate qualitatively the route of the evolving time-dependent wavepacket in the excited state. The dashed contours in (a) and (b) represent the A-state PES. Right-hand side The corresponding absorption spectra as functions of the energy in the excited electronic state. E = 0 corresponds to three ground-state atoms, H + O + H. Within this normalization the lowest eigenvalue of H20(A) is -9.500 eV. 

Fig. 14.4. (cont.) respect to exchange of the two hydrogen atoms. The dashed contours in the top panel represent the PES in the excited electronic state. In contrast to Figure 13.3 we show here the wavefunction rather than its modulus square ... 

In addition to angle strain and torsional trdin. stertr Mrain is yet a third factor that cont ributes to the over l strain energy of cycloalkanes. As in gauche butane (Senonbonded atom in o molecule repel ua other if they approach tcK> closely and attoropt to occupy the same... 

FIGURE 9.6 (cont d). The fully contoured electron-density map. Carbon atoms represented by filled circles, nitrogen and oxygen atoms by open circles. Contour interval 1 electron/A, zero contour dotted. 

FIGURE 9.17 (cont d). Examples of deformation density maps, (b) Dynamic deformation-density map in which motion of the atoms has not been corrected for. ... 

FIGURE 11.6 (cont d). (c) View onto a benzene molecule in the crystal structure, showing the intermolecular interactions listed in (b). Carbon and hydrogen atoms drawn with filled circles are those in one asymmetric unit. Positions of all other atoms are generated from these by application of the symmetry operations of the space group. 

FIGURE 12.28 (cont d). Stereoviews of a portion of an a helix in crambin (Ref 91). (b) View perpendicular to the helix axis, and (c) view down the helix axis Hydrogen atoms are not shown. Carbon atoms, open circles nitrogen atoms, filled circles oxygen atoms, stippled circles. 

FIGURE 12.42 (cont d). (b) Arrangement of atoms in base pairs in nucleic acids. 

FIGURE 16.4 (cont d). Portions of an output file from the Protein Data Bank, (b) The end of the amino-acid sequence, the presence of metal ions, and orthogonal coordinates of each atom together with its displacement factor. Courtesy the Protein Data Bank. 

The Voronoi calculation can be performed on protein atoms buried at interfaces as well as inside proteins. However, the procedure has a serious limitation a Voronoi polyhedron can be drawn around an atom only if it is completely surrounded by other atoms. At interfaces, only about one-third of the atoms that contribute to the interface area B have zero accessible surface area. These atoms are located mostly at the center of the interface, which biases the F/Fq ratio in an opposite way to the gap index, which is biased toward the periphery. However, high-resolution X-ray structures usually report positions for immobilized water molecules, which are abundant at interfaces (see Section II,D). These molecules may also be used to close the polyhedra, making the evaluation of Voronoi volumes possible for atoms which are surrounded by both protein atoms and immobilized water molecules (Fig. 4). On average, there are as many such interface atoms as there are completely buried atoms. Thus, a Voronoi calculation taking into account the crystallographic water molecules applies to two-thirds of the interface atoms on average instead of only one-third and up to 90% in specific cases (Lo Conte et al., 1999). 

In the 75 protein-protein complexes of Lo Conte et al. (1999), 96% of the interfaces have V/Vq in the range 0.97-1.06. Thus, the packing of atoms buried at protein-protein interfaces is very similar to that of the protein interior. In 36 complexes with X-ray structures at a resolution of 2.5 A and better, the V/Vq ratios calculated in the presence of water molecules were distributed over a narrow range of 0.97-1.03 (Fig. 5, top). Therefore, their interfaces are packed like the protein core, except that water, which is almost entirely excluded from the protein core, makes an important contribution to the packing at protein-protein interfaces. There is one exception to this rule in the sample analyzed by Lo Conte et al. (1999) the complex between cytochrome peroxidase and cytochrome c [PDB code, Iccp (Pelletier and Kraut, 1992)]. Its interface is small and has only a few buried atoms and a large volume ratio (1.07). In contrast, the 19 protease-inhibitor and the 19 antigen-antibody complexes of this sample have mean V/Vq ratios of 1.00 and 1.01, respectively. Thus, unlike 5c and the gap index, the volume ratio indicates that these two types of interfaces are close-packed and shows no difference in their packing density, at least for their buried atoms. 

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