Local preferences of the charged amino acids in the SC hot spots.

<p>Local preferences of the charged amino acids in the SC hot spots.</p

Observed SC Pair occurrences.

<p>The values in a given row are the occurrences of the residue <i>a</i> in contact with the residues <i>b_i</i>, cited on columns. Thus, there are twenty rows <i>a_i</i> and twenty column <i>b_i,</i> - <i>i</i>- covering the 20 different amino acids. Due to the counting procedure the table is read row-wise (material and methods).</p

SC and BB hot spot geometrical pair tendencies.

<p>Legend as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0094745#pone-0094745-t009" target="_blank">table 9</a>. L, M and S stand for long, medium and short side chains. × stands for L, M and S.</p

SC and BB hot spot pair chemical tendencies.

<p>The number of pairs with a ratio SC pair frequency to BB pair frequency above 1.0±0.2 indicates the SC pair tendency. The number of pairs with a ratio below 0.8±0.2 indicates the BB pair tendency (table based on <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0094745#pone-0094745-g002" target="_blank">Fig. 2C</a>). The second column, total, indicates the pair combinatory of the chemical pair property mentioned in the first column. Fhi, Ch and P stand for hydrophobic, charged and polar residues. X stands for fhi, ch and P.</p

Comparison of the 210 frequencies of the BB and SC hot spot pairs.

<p>The frequencies of the SC hot spots pairs are plotted against those of the BB hot spots pairs, both in log scale. Pairs with identical BB and SC frequencies are on the diagonal. Pairs more frequent in SC are found above the diagonal whereas pairs more frequent in BB are found below the diagonal.</p

Ratio of f_ab/(f_a.f_b) for the SC hot spot pairs.

<p>Ratio of f_ab/(f_a.f_b) for the SC hot spot pairs.</p

Illustration of the Gemini procedure on a trivial example.

<p>A. Interatomic distances between chain 1 and chain 2. On each chain, atoms are indicated by small filled circles labeled with letters. For clarity, only a few of the interatomic distances are indicated by dotted lines. B. Closest atoms. For every atom of S₁, Gemini chooses the closest atoms on S₂ (left picture) and for every atom of S₂, Gemini chooses the closest atoms on S₁ (right picture). The closest atoms are encircled. C. Mutually closest atoms. Gemini selects the atoms mutually the closest. The amino acids to which the mutually closest atoms belong are indicated by big filled circles. R stands for residue and the subscript is the position of the amino acid on the sequence. D. Gemini graph of amino acids in interaction. The distances between amino acids in contact are now arbitrary fixed to the same value because the information on the “real” interatomic distances is now lost. The pair of residues R99 and R25 is a single pair of amino acids (<i>k</i> = 1, that is one link connecting two residues). The residue R96 is a multiple contact amino acid because it is involved in two single pairs one with R29 and the other with R27, respectively.</p

The p53 intermolecular β-strand network.

<p>A. Atomic structure of the p53 tetramerization domain (PDB 1SAK). The picture is generated with Rasmol, the four chains are shown in different colored ribbons. The G334 residue is indicated in spacefill. B. Gemini graph of the WT p53 tetramerization domain. The intermolecular β-strands composed of the residues 324 to 334, are highlighted by the yellow and purple arrows. The vertical arrows point to the residue 334. The links and hot spot contacts of G334 are shown by dotted red lines and red circles, respectively. C. Gemini graph of the G334V mutant. The hot spots whose links are affected by the mutation are underlined in red. The changes are not limited to residues in direct contact with G334 or to residues of the intermolecular β-strands.</p

Chemical properties of the intermolecular β-strands and of the whole chains (%).

<p>Chemical properties of the intermolecular β-strands and of the whole chains (%).</p

Number of contacts of the hot spots.

<p>A. The degree distributions of the BB and SC hot spots are plotted on a semi-log scale. The degree distribution <i>P(k)</i> of the SC hot spots decreases exponentially (R² = 0.99). B. Linear correlation between the number of atoms of a SC hot spot and its tendency to have more than one contact. The ratio of the frequency of an amino acid in multiple contacts to its frequency in single contact is plotted against the number of its side chain atoms. C. Probability of a SC hot spot to have <i>k</i> contacts. The probabilities for a SC hot spot to have <i>k</i>>3 (♦) or <i>k</i> = 1 (○) are plotted against the number of atoms of its respective amino acid. The horizontal line indicates the probability at which every amino acid has the same probability to have <i>k</i> contacts (0.05 = 1/20). The vertical line indicates a number of atoms equals to 14.</p