Re: [ccp4bb] surface area
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
[ccp4bb] surface area
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
[ccp4bb] surface area calcualtion
Hello all can any one suggest any server or tool which can calculate the burried surface area between the domains of the same monomer? PISA calculates the interfacial surace area between the monomer or oligomer. Can areamol calculate it? Thanks in advance Thomas
Re: [ccp4bb] surface area calcualtion
Thomas, The Areaimol program within the CCP4 suite should do what you're looking for: http://www.ccp4.ac.uk/html/areaimol.html Although its a calculation of surface accessability, you can delete sections of your protein to get at the buried area between two sections of your protein. Cheers, Jim On Fri, Mar 20, 2009 at 2:48 PM, Jhon Thomas jhon1.tho...@gmail.com wrote: Hello all can any one suggest any server or tool which can calculate the burried surface area between the domains of the same monomer? PISA calculates the interfacial surace area between the monomer or oligomer. Can areamol calculate it? Thanks in advance Thomas -- Jim Fairman Graduate Research Assistant Department of Biochemistry, Cellular, and Molecular Biology (BCMB) University of Tennessee -- Knoxville 216-368-3337 jfair...@utk.edu james.fair...@case.edu
