PISA's interface area is 1/2 of sum BSAs for the interfacing
structures. If you go to
interface details, you also get total area of structures and their
individual BSAs.
The latter I should think would be an overinterpretation if used.
Eugene.
On Wed, May 26, 2010 at 1:45 PM, Sollepura Yogesha <[log in to unmask]> wrote:
> Dear All,
>
> I am trying to calculate BSA (Buried surface area) for a protein complex. I am using CCP4 AreaIMol.
> I used Accessible surface area module and calculate areas for " protein atoms only"
>
> I know that the buried surface area (BSA) can be calculated as: BSA = ASA(A) + ASA(B) - ASA(AB) when two proteins A and B form a complex AB
>
> So when I run areaIMol for complex AB using AB.pdb, I get
> Total area of chain A
> Total area of chain A
> Total area
> Total contact area of chain A
> Total contact area of chain A
> Total contact area
>
> So,
> How do I get my BSA?
> Do I need to split PDB in to individual chains to get Accessible surface area for each chain [ ASA(A) and ASA(B)]?
> Is the total area I got above is the ASA (AB)?
> Are there are any applications which could help get BSA
> PISA server giver ASA for each interface and total, so how could I use them to calculate BSA?
>
> Thanks in advance
> Yogi
>
|