Protein Shell::Core::Face Comparison Server

INTERPARE   The Protein Interfaceome Database

2. Accessible Surface Area [click to see conceptual animation]



The Accessible Surface Area (ASA) method detects protein regions that are buried to be excluded from a solvent when forming a multimer or a complex. If more than two subunits interact or aggregate with each other, they lose some area that could be accessible by a solvent in the state of free subunit or domain.

In the InterPare method, we define residues as interface residues if they lost more than 1A^°2 solvent accessible surface area (ASA) on aggregation or complexation (Jones et al., 1996, 1997, 2000). The ASA of protein molecules was calculated using a program called NACCESS (Hubbard S., http://wolf.bms.umist.ac.uk/naccess) which is an implementation of the algorithm developed by Lee and Richards (Lee et al., 1971). It calculates the absolute ASA and the relevant ASA in terms of total residues, side chains, polar atoms, and non-polar atoms.

Relative accessibilities are calculated for each amino acid in the protein by expressing the summed residue accessible surface as a percentage of that observed in an ALA-X-ALA tri-peptide (Hubbard et al., 1991).
Surface residues are defined as those residues that had a relative ASA of more than 5% (Miller et al., 1987).
Interior residues are defined as those residues that have a relative ASA of less than 5%.
The default van der Waals radii of atoms were taken from Chothia (Chothia, 1976). We used water of 1.40 van der Waals radii as a solvent.




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