[gmx-users] calculate apolar contact area

Linlin Yang yanglin-89 at 163.com
Thu Nov 19 09:29:43 CET 2015


I want to calculate the apolar contacts area between a peptide and its receptor in the simulation by using g_sas, i.e.,the apolar surface area of the hydrophobic residues on the peptide that are buried by apolar surface area of the receptor.

Now I can only get the surface area of hydrophobic residues on the peptide that are buried by the receptor:
SASA1(without protein)-SASA2(with protein)=buried surface area.

But I can't distinguish how much the hydrophobic parts of receptor and the hydrophilic parts of the receptor contributes to the buried area, respectively. 

I think the buried area contributed by the hydrophobic parts of receptor, rather than by the hydrophilic parts, is the real aplar contacts area,. Because when the surface area of hydrophobic residues on the peptide are buried by hydrophilic parts of the receptor,there are no apolar contacts.

To solve the problem,I've tried to calculate the SASA of an index group comprising the peptide and the hydrophobic parts of the receptor(sidechain atoms of nonpolar residues and hydrophobic parts of other polar residues as well as all C-alpha atoms), the output SASA of the peptide is SASA3. So "SASA1(without protein)-SASA3(with hydrophobic parts of protein)" may be the apolar contacts area I need? 

But polar atoms (or the hydrophilic parts I definied) are missing in this calculation,this should affect the result ! Because some nonpolar atoms are buried by polar atoms in the receptor. So I'm confused whether there is a better way to obtain the apolar contact area.

Thank you in advance!



Thanks & With best regards!

Linlin Yang | 杨琳琳
Drug Discovery and Design Center (DDDC)
Shanghai Institute of Materia Medica (SIMM), Chinese Academy of Sciences (CAS)
Tel:+86-21-50806600  ext.1201
Address:555 Zu Chong Zhi Road, Zhang Jiang Hi-Tech Park,
             Pudong District, Shanghai, 201203, P.R. China

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