Tutorial

Interface definition and extraction of interfaces from the Protein Data Bank

An interface can be defined as the set of amino acids which represents a region that links two polypeptide chains in a protein structure by non-covalent interactions. Residues interacting with each other across the binding region form the interface between two chains. Interface residues are selected according to the closeness of two residues, one from each chain. We defined two types of residues in two chain interfaces: interacting and nearby. If the distance between any two atoms belonging to two residues, one from each chain, is less than the sum of their van der Waals radii plus a 0.5 Angstrom tolerance, these two residues are defined as interacting. If the distance between the alpha Carbons of a non-interacting residue and interacting residue in the same chain is a smaller than 6 Angstrom, the non-interacting residue is flagged as a nearby residue. Nearby residues are important for information relating to the architecture of the interface. The interface between chains A and B of protein 1axd (interface name:1axdAB) is shown below with nearby residues.

interface

Main Page

This is the main page of the HotPOINT. Input data is the protein structure in pdb file format and two chain identifiers (to extract the interfaces).User can utilize our prediction algorithm either by entering the four letter PDB code of a protein or uploading your own structure file that is in the PDB format with the chain identifiers. It does not work for PDB files containing only one chain. This will return an error! Hotpoint requires two chain identifiers which corresponds to a protein interface. In the output page, the names of the interface residues are tabulated with chain names, residue numbers, their relative ASA in complex, relative ASA in monomer and total pair potentials. In the last column of this table, prediction is presented as H (hot spot) or NH (non-hot spot). Predicted hot spots are highlighted with red color. The prediction results and interface residue coordinates in pdb file format are also downloadable by user.

interface

Prediction Page

HotPOINT calculates solvent accessibilities and total contact potentials online. It predicts hot spots according to the empirical model. Details of the algorithm can be found in the 'Prediction Algorithm' page on the left or in the reference Tuncbag et al. (2009) given in main page. Server interface is coded in PHP. The codes running in the background to predict hot spots are written in Python.In the output page, the names of the interface residues are tabulated with chain names, residue numbers, their relative ASA in complex, relative ASA in monomer and total pair potentials. The definition of these terms are given in 'Prediction Algorithm' page. In the last column of this table, prediction is presented as H (hot spot) or NH (non-hot spot). Predicted hot spots are highlighted with red color. 1. Coordinates of interface residues in pdb file format are downloadable by user. 2. The prediction results are also downloadable by user. 3. User can visualize overall complex, the interface residues and hot spots interactively with Jmol plugin.

interface

An example of visualization of 1axdAB interface is shown below.

interface

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