How To
I. Select optoins in the query box
For more information on relative ASA and threshold of interface residue, see background information
II. Result Page
In case of '1a25' as a queried PDB ID, there are hits from
three different methods:
(PSIMAP, Accessible Surface Area, Voronoi Diagram)
2-1. Hits by the PSIMAP method
Each bottons are:
If you click 
:Click to visit PSIbase
which provides interaction information at SCOP Family or Superfamily level.
:Click to navigate protein structure with
Chime
:Click to navigate protein structure with
Jmol
:Click to navigate protein structure with
InterFacer
for example,
The blue and red
are different domains in '1a25' according to SCOP classification scheme.
Space filled atoms are interface atoms in the interface regions between two domains.
These atoms are within a threshold distance threshold (5 Angstrom as a default)
which has been set from the query box as you can see above.
You should have a Chime plug-in in your local computer to view the strucutre.
For more informations, read the
Instructions for viewing structures
2-2. Hits by the ASA method
If you click
from the Full View column of PDB hit table, for example, you can see
The blue colour represents protein interior
(Core) of 1a25. The red colour
represnts protein surface (Shell) of 1a25.
Space filled atoms are interface atoms between two domains of 1a25.
These atoms loose at least 1Å2solvent accessible area
when two domains aggregate with each other. When they are in free
subunit state, solvents like water are freely accessible to those atoms.
They are just buried in the protein strucutre to escape from the solvent.
That is a natural thermodynaic process.
The interface threshold (1Å2, here) can be set by the user as you can see in the query box above.
The interface threshold (1Å2, here) can be set by the user as you can see in the query box above.
2-3. Hits by the VD (Voronoi Diatram) method
in the Full View column, for example, You can see
Space filled atoms with CPK colour are interface atoms defined by
Voronoi Diagram method.