Hi Jiri,
The surface are characterized by the probe you use to define them. Here
it's water molecule I think. In such situation : Buried Surface Area are
the surfaces */NOT/* accessible to the probe (water molec) it other word
it doesn't imply that these BSA are contact surface between your proteins.
Buried surface area = surface not accessible to the probe (because a
groove too narrow for example) + interface (between two monomers)
If you discussed about the contact between to monomer in my opinion the
surface to focus is the interface surface not the whole BSA. But it's
still possible to discuss about this point of view because interaction
between two molecules could have remote effect (far from the interface)
and for example modify the accessibility for the solvent in a different
area.
It really depend of what you are looking for : energy point of view,
surface only... and if you consider to discuss small variations the
resolution of the data and the reliability of your model may have
important influence.
Nicolas
Nicolas Foos
PhD
Structural Biology Group
European Synchrotron Radiation Facility (E.S.R.F)
71, avenue des Martyrs
CS 40220
38043 GRENOBLE Cedex 9
+33 (0)6 76 88 14 87
+33 (0)4 76 88 45 19
On 13/03/2017 21:32, chemocev marker wrote:
Hi
I am comparing some protein complex with PISA analysis. Can someone
make a note what is difference between interface area and buried
surface area. I think buried surface area also include the interface
area + the area encloses with in the protein. Does it make sense to
mentioned the interface area separately if we count the buried area??
best
Jiri
