[ccp4bb] domain contact surface
Dear all, I am trying to calculate the domain-domain contact surface from one chain. I see AREAIMOL to only tell you the accessible surface area/residue. Could any other software/webserve could specify residues in the contact surface and calculate the total contact area? Thanks J.
Re: [ccp4bb] domain contact surface
You would have to cheat a little bit, and relabel the second domain chain id to something different. Or you can split the pdb file into two. That would still be necessary for using the EBI PISA server at http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html as I have just been doing. In my case I wanted the interface between multi- chain domains, so I had to pretend they were one chain each. It works alright. Pierre Dr. Pierre Rizkallah, Senior Lecturer in Structural Biology, WHRI, School of Medicine, Cardiff University, Heath Park, CF14 4XN email: rizkall...@cf.ac.uk phone + 44 29 2074 2248 >>> Jane Bailey 19/02/10 3:44 PM >>> Dear all, I am trying to calculate the domain-domain contact surface from one chain. I see AREAIMOL to only tell you the accessible surface area/residue. Could any other software/webserve could specify residues in the contact surface and calculate the total contact area? Thanks J.
Re: [ccp4bb] domain contact surface
Ed Pozharski wrote: http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html Try PISA server - it will identify contacts and report total buried surface area per contact. On Fri, 2010-02-19 at 16:42 +0100, Jane Bailey wrote: Dear all, I am trying to calculate the domain-domain contact surface from one chain. I see AREAIMOL to only tell you the accessible surface area/residue. Could any other software/webserve could specify residues in the contact surface and calculate the total contact area? Thanks J. Dear all, Thanks very much for the answers. I managed to get the interface from PISA by assign two chain IDs onto two domains, as suggested by Pierre and Amy. It gave the interface Solvent-accessible area of each domain: 274.2, 312.2, but not the BSA. However I saw it gave the BSA of individual residue from the interface. Do people get the total interface BSA by adding them up? best Jane
Re: [ccp4bb] domain contact surface
Hello Again, The buried surface area is twice the interface area, because the interface is counted twice when working out the solvent accessible area which disappeared upon interfacing, once on molecule 1 and once on molecule 2. This is a matter of definition. While I prefer to quote the interface area, quite a number of people prefer the buried surface area. Either one should be alright, as long as you say clearly which one you are reporting. Pierre Dr. Pierre Rizkallah, Senior Lecturer in Structural Biology, WHRI, School of Medicine, Cardiff University, Heath Park, CF14 4XN email: rizkall...@cf.ac.uk phone + 44 29 2074 2248 >>> Jane Bailey 19/02/10 4:57 PM >>> Ed Pozharski wrote: > http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html > > Try PISA server - it will identify contacts and report total buried > surface area per contact. > > On Fri, 2010-02-19 at 16:42 +0100, Jane Bailey wrote: > >> Dear all, >> >> I am trying to calculate the domain-domain contact surface from one >> chain. I see AREAIMOL to only tell you the accessible surface >> area/residue. Could any other software/webserve could specify residues >> in the contact surface and calculate the total contact area? >> >> Thanks >> >> J. >> > > > Dear all, Thanks very much for the answers. I managed to get the interface from PISA by assign two chain IDs onto two domains, as suggested by Pierre and Amy. It gave the interface Solvent-accessible area of each domain: 274.2, 312.2, but not the BSA. However I saw it gave the BSA of individual residue from the interface. Do people get the total interface BSA by adding them up? best Jane
Re: [ccp4bb] domain contact surface
Dear Jane, If you rename one of domains with a different chain ID (in the PDB) you can submit the structure to PISA (http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html) and it will do the job. Regards Rafa === Rafael Fernández Leiro Departamento de Biología Celular y Molecular Facultad de Ciencias Universidade da Coruña Campus de A Zapateira s/n E-15071 La Coruña (Spain) Phone: +34 981 167 000 / 2136 (Lab.) +34 666 003 613(Home) === El 19/02/2010, a las 16:42, Jane Bailey escribió: > Dear all, > > I am trying to calculate the domain-domain contact surface from one chain. I > see AREAIMOL to only tell you the accessible surface area/residue. Could any > other software/webserve could specify residues in the contact surface and > calculate the total contact area? > > Thanks > > J.
