PISA and Accessible and Buried Surface Area
The 'View' 'Interface' option, using JMol, from the 'Interface Details' page, gives a excellent indication of the meaning of these terms.
The non-interfacing atoms which are solvent accessible, are coloured light blue and dark blue for the two molecules respectively.
Inaccessible atoms are coloured grey. These are more easily seen if you zoom into the display. (mouse wheel forward).
It is apparent from this display that the solvent molecules would not fit into the holes where the grey atoms are.
Interfacing atoms, (atoms which are part of interfacing residues), those atoms which are exposed to the other molecule and not the solvent,
and may be involved in bonding across the interface, are coloured
red and green respectively. Note: not all the atoms in an interfacing residue will be involving in interface formation or contact.
Some may be exposed to the solvent and some may be inaccessible.
This can be confirmed by hovering the mouse over a particular atom, when information about residue number and atom name is displayed.
This is confirmed by inspection of the detailed table at the bottom of the 'Details' view.
Accessible surface area calculations are based on finite element analysis
(numerical analysis calculation) as a full exact analysis using integrals is
"quite complex" even for something like water. A water probe of 1.4A in
diameter is rolled over the surface of the protein and the sum of all sampled
points in contact with this probe represents the surface area normalised by the
precision of the element analysis.
A second approximation is that the calculation uses enhanced radii to
approximate the position of hydrogen atoms. This is clearly a significant
aproximation as hydrogen atom positions are not isotropic around the parent
atom, so increasing the radius of an atom to take account of the hydrogen create
Finally - the calculation of the ASA of the interface is calculated as follows:
(all numbers are A^2)
If T is the total accessible surface area of the combined molecular components
A:B where ":" is the interface between A and B, then you can see this total
excludes the interface area.
If TA and TB are the surface area of each molecular component A and B :-
When A is in contact with B then the burried area of this contact of A MUST be
the same as the area on B - since they are the same mutual contact.
Therefore the missing area for A:B due to : is the same on A and B in isolation
- so the measure of contact ":" missing in the A:B complex is counted twice -
once in TA and once in TB
Interface Area : = (TA + TB - T) / 2.0
So if TA = 1000, TB = 2000, T = 2500
interface area = ((1000 + 2000) - 2500) / 2.0 = 250