P I S A
Protein Interfaces, Surfaces and Assemblies
Contents • Result Pages • List of Interfaces • Interface Details & Radar

Interface Details give extended summary of the interface, selected in the Result Tree. The following data is displayed for the two interfacing monomers:

ID Monomer ID
Class Type of monomer: Protein, RNA, DNA or Ligand.
Symmetry operation Symmetry operation (in fractional space), applied to monomers. 1st interfacing monomer is always in the original position, corrsponding to the idntity operation X,Y,Z.
Symmetry ID Symmetry ID, corresponding to symmetry operation in the previous row. The ID has form N_KLM, where N is serial number of the symmetry operation in the corresponding space symmetry group (as used by the PDB); KLM give fractional coordinates of the unit cell relative to the original cell, placed at 555.
Interface atoms Total number of atoms in the interface area for each monomer, with the percentage of the total number of atoms in brackets.
Surface atoms Total number of surface (solvent-accessible) atoms for each monomer, with the percentage of the total number of atoms in brackets.
Total atoms Total number of atoms for each monomer (100%).
Interface residues Total number of residues in the interface area for each monomer, with the percentage of the total number of residues in brackets.
Surface residues Total number of surface (solvent-accessible) residues for each monomer, with the percentage of the total number of residues in brackets.
Total residues Total number of residues for each monomer (100%).
Buried ASA Surface area, buried in the interface for each monomer (in square angstroms), with the percentage of the total surface area in brackets.
Total ASA Surface area of each monomer (in square angstroms).
Solvation energy Solvation energy of folding for each monomer (not defined for ligands), in kcal/mol.
SE gain Solvation energy gain, in kcal/mol, for each monomer. This reflects the change in monomer's solvation energy, when part of its surface loses contact with solvent due to the formation of the interface.

 

Interaction Radar gives a quick grasp of interface interaction value. This allows a user to spot interfaces that may have biological significance. The tool estimates the likelihood of the interface to be a part of biological assembly by comparing key interface properties to statistical distributions derived from the current content of the PDB. In general, the larger the are inside radar contour, the higher chances that the interface is a part of biological assembly, rather than an artefact of crystal packing.

The radar is based on 7 interface parameters. For each interface, these parameters and their values are shown in table on the right from the radar plot:

IA: Interface Area Interface Area in square angstroms
DG: Delta G Solvation energy gain upon interface formation, in kcal/mol
BE: Binding Energy Total Binding Energy of the interface, defined as solvation energy gain plus effect of hydrogen bonds, salt bridges and disulphide bonds, in kcal/mol
PV: P-value Hydrophobic P-value of the interface. The lower P-value, the more specific, or statistically surprising, the interface.
HB: Hydrogen bonds Number of hydrogen bonds formed between the interfacing monomers.
SB: Salt bridges Number of salt bridges formed between the interfacing monomers.
DS: Disulphide bonds Number of disulphide bonds formed between the interfacing monomers.

Radar beams (as indicated by parameter names, e.g. IA for Interface Area), represent probabilities that a particular value indicates a biological assemblage in the PDB, with zero probabilities placed at the beams' origin (radar center). The representation and probabilities are slightly different in Simple and Detail radar modes. These modes are swtiched in the Configuration Settings Dialog.

In Simple mode, the radar displays all 7 parameters, and the corresponding probabilities are calculated per interface type, for example, Protein-Protein, Protein-Ligand etc.

In Detail mode, the radar displays probabilities calculated for the Reference parameter, chosen in the displayed combobox:

The parameter chosen may be one of radar's parameters. Then, radar probabilities of other parameters are calculated over the subset of interfaces where reference parameter has value as in the given interface (within a margin). Choosing Interface Type for reference parameter will reproduce radar in Simple mode; Choosing Unreferenced, untyped will display probabilities calculated in disregard to the interface type.
 

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