Atom Depth as a Descriptor of the Protein Interior

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Atom Depth as a Descriptor of the Protein Interior Alessandro Pintar, Oliviero Carugo, Sándor Pongor Biophysical Journal Volume 84, Issue 4, Pages 2553-2561 (April 2003) DOI: 10.1016/S0006-3495(03)75060-7 Copyright © 2003 The Biophysical Society Terms and Conditions

Figure 1 (a) Plot of mean residue dpx (dpxr, Å), (b) occluded surface packing value (OSP), and (c) residue solvent accessibility (rsa, %) versus residue number for the C-terminal bromodomain of human TAFII250 (PDB: 1EQF; residues 1500–1625). In the dpxr plot, important residues are labeled with their amino acid one-letter code and residue number; the same residues are labeled with an asterisk in the OSP and rsa plots. (d) Plot of mean residue dpx (dpxr, Å) versus OSP and rsa (%). Biophysical Journal 2003 84, 2553-2561DOI: (10.1016/S0006-3495(03)75060-7) Copyright © 2003 The Biophysical Society Terms and Conditions

Figure 2 Plot of the number of observations (number of atoms, %) in each dpx interval (a, Δ=1.00Å; b, Δ=0.50Å; c, Δ=0.25Å; d, Δ=0.10Å) for the double bromodomain module of human TAFII250 (PDB: 1EQF). In b, c, and d, the peak corresponding to solvent-accessible atoms (dpx=0) is out of scale for clarity. Biophysical Journal 2003 84, 2553-2561DOI: (10.1016/S0006-3495(03)75060-7) Copyright © 2003 The Biophysical Society Terms and Conditions

Figure 3 Plot of the maximum (dpxmax, circles) and average (dpxave, diamonds) value of dpx versus chain length for a set of 136 single-chain proteins for which the crystal structure has been determined at a resolution ≤2.0Å. Biophysical Journal 2003 84, 2553-2561DOI: (10.1016/S0006-3495(03)75060-7) Copyright © 2003 The Biophysical Society Terms and Conditions

Figure 4 Plot of the mean residue depth (dpxr, Å) for each amino acid type (one-letter code), calculated from a set of 136 protein structures (see text for details). Top, overall; bottom, by secondary structure assignment (square, strand; circle; helix; triangle: turn, diamond, coil). Standard deviation values are also shown. Biophysical Journal 2003 84, 2553-2561DOI: (10.1016/S0006-3495(03)75060-7) Copyright © 2003 The Biophysical Society Terms and Conditions

Figure 5 Plot of the maximum (dpxmax, circles) and average (dpxave, squares) values for representative structures of the four-helix bundle topology (a, mainly α-proteins, CATH code: 1.20.120; 17 homologous superfamilies) and the jelly rolls topology (b, mainly β-proteins, CATH code: 2.60.120; 17 homologous superfamilies) plotted versus chain length (number of residues). Biophysical Journal 2003 84, 2553-2561DOI: (10.1016/S0006-3495(03)75060-7) Copyright © 2003 The Biophysical Society Terms and Conditions

Figure 6 (a) Mean residue depth (dpxr, Å, filled diamonds) and residue-solvent accessibility (rsa, Å2, empty diamonds) calculated for 3CHY and plotted versus sequence entropy (S) calculated for 98 structural neighbors of 3CHY. (b) Mean residue depth (dpxr, Å, lower line) and sequence entropy (S, upper line) plotted versus residue number. In a, also a linear fit of dpxr is shown. In b, line breaks represent positions at which less than two-thirds of residues could be aligned. Biophysical Journal 2003 84, 2553-2561DOI: (10.1016/S0006-3495(03)75060-7) Copyright © 2003 The Biophysical Society Terms and Conditions