Fig 1.
Schematic illustration of a PL complex illustrating the interface (black border) and the remaining surface regions.
PL, protein-ligand.
Fig 2.
Flow chart summarizing the compilation of contacts between amino acids of the first protein (Pi1) and amino acids of the second protein (Pi2), atom contacts in PP and PL complexes, and the calculation of PR and IR.
PP, protein-protein; PL, protein-ligand; PR, polarity ratio; IR, interface atom ratio.
Fig 3.
Percentage frequencies and propensities of amino acid residues at protein interfaces of PP complexes from the ABC dataset.
(A) Percentage frequencies of amino acid residues at protein interfaces. (B) Propensities of amino acid residues at protein interfaces. PP, protein-protein; ABC, ABC dataset; homo, homodimeric PP interface; hetero, heterodimeric PP interfaces; P1, protein interface of the first protein (Pi1); P2, protein interface of the second protein (Pi2).
Fig 4.
Percentage frequencies and propensities of amino acid residues at protein interfaces of PP complexes from the PIBASE dataset.
(A) Percentage frequencies of amino acid residues at protein interfaces. (B) Propensities of amino acid residues at protein interfaces. PP, protein-protein; PIB, PIBASE dataset; homo, homodimeric PP interface; hetero, heterodimeric PP interfaces; P1, protein interface of the first protein (Pi1); P2, protein interface of the second protein (Pi2).
Fig 5.
Percentage frequencies and propensities of amino acids residues at protein interfaces of PL complexes from the ABC, PIBASE and Timbal datasets.
(A) Percentage frequencies of amino acids residues at protein interfaces. (B) Propensities of amino acids residues at protein interfaces. PL, protein-ligand; PL-ABC, PL complexes from the ABC dataset; PL-PIBASE, PL complexes from the PIBASE dataset; PL-Timbal, PL complexes from the Timbal dataset.
Fig 6.
Amino acid pairing propensities (in log2-format) for interfaces of PP complexes from the ABC dataset.
PP, protein-protein.
Fig 7.
Amino acid pairing propensities (in log2-format) for interfaces of PP complexes from the PIBASE dataset.
PP, protein-protein.
Table 1.
The average number with standard deviation of amino acid residues at the interfaces of PP complexes in the ABC and PIBASE datasets.
Table 2.
The average number with standard deviation of amino acid residues at the interfaces of PL complexes in the ABC, PIBASE and Timbal datasets.
Table 3.
The percentage frequencies of the 36 atomic contact types in PP and PL complexes.
Table 4.
Percentage frequencies (with normalized propensity values in parentheses) of apolar, polar and other atomic contacts of PP complexes from the ABC and PIBASE datasets.
Table 5.
Percentage frequencies (with normalized propensity values in parentheses) of apolar, polar and other atomic contacts of PL complexes from the ABC, PIBASE and Timbal datasets.
Table 6.
Interface atom ratio (IR) and polarity ratio (PR) (with standard deviations in parentheses) for interfaces of PP complexes from the ABC and PIBASE datasets.
Table 7.
Interface atom ratio (IR) and polarity ratio (PR) (with standard deviations in parentheses) for interfaces of PL complexes from the ABC, PIBASE and Timbal datasets.