h***@bioc.uzh.ch
2017-07-08 15:51:30 UTC
Dear Ashwani Kumar
To get the interface area between two molecular entities, you calculate the accessible surface of the complex and that of the separated entities, the difference between the two is twice the interface area. Any tool that allows you to calculate a solvent accessible surface area can be used for this, including the get_area command in Pymol. I personally like to use the program NACCESS, as it also gives me the per-atom and per-residue contributions, divided into hydrophobic and hydrophilic, main-chain and side chain contributions, or the rosetta interface analysis tool if I am interested in the energetics of the interface.
The PISA analysis is most relevant for assessing the probability of an interface observed in the crystal being biologically relevant. As to the distance, there is no general definition: VdW and hydrogen bonding contacts determine how close the two entities can approach each other. In assessing e.g. docked complexes, the center-of-gravity - center-of-gravity distance may help to sort different solutions as to how close the two entities get to each other (in PyMOL, you calculate the center of gravity using the appropriate center of mass script - it returns the coordinates of the cog as well as a pseudo atom indicating the position.
Annemarie Honegger
Message: 1
Date: Sat, 8 Jul 2017 02:12:05 +0530
From: Ashwani Kumar <***@gmail.com>
To: pymol-***@lists.sourceforge.net
Subject: [PyMOL] interface surface Area and distances in two dimeres
Message-ID:
<CAG=kqZRdKTnRakBu5V2Qp5p3kcfkyQ=***@mail.gmail.com>
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Dear All
I would like know interface surface area between two dimers and distances
like if protein has 4 monomer (A, B,C,D chains ) in ASU.
chainA an D are forming biological unit as dimer similarly chain B&C also
.
I would like know interface area between dimer ( chainAD) and Chain BC.
I have trired PISA of CCP4 and PDBe PISA.
it calculate the interface surface area between dimer of chain AD or chain
BC etc.
i have also find the interface Residues two chains in pymol.
Kindly help please
Regards
Ashwani Kumar
SRF - ICMR
Structural Biology lab
NCCS PUNE
To get the interface area between two molecular entities, you calculate the accessible surface of the complex and that of the separated entities, the difference between the two is twice the interface area. Any tool that allows you to calculate a solvent accessible surface area can be used for this, including the get_area command in Pymol. I personally like to use the program NACCESS, as it also gives me the per-atom and per-residue contributions, divided into hydrophobic and hydrophilic, main-chain and side chain contributions, or the rosetta interface analysis tool if I am interested in the energetics of the interface.
The PISA analysis is most relevant for assessing the probability of an interface observed in the crystal being biologically relevant. As to the distance, there is no general definition: VdW and hydrogen bonding contacts determine how close the two entities can approach each other. In assessing e.g. docked complexes, the center-of-gravity - center-of-gravity distance may help to sort different solutions as to how close the two entities get to each other (in PyMOL, you calculate the center of gravity using the appropriate center of mass script - it returns the coordinates of the cog as well as a pseudo atom indicating the position.
Annemarie Honegger
Message: 1
Date: Sat, 8 Jul 2017 02:12:05 +0530
From: Ashwani Kumar <***@gmail.com>
To: pymol-***@lists.sourceforge.net
Subject: [PyMOL] interface surface Area and distances in two dimeres
Message-ID:
<CAG=kqZRdKTnRakBu5V2Qp5p3kcfkyQ=***@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
Dear All
I would like know interface surface area between two dimers and distances
like if protein has 4 monomer (A, B,C,D chains ) in ASU.
chainA an D are forming biological unit as dimer similarly chain B&C also
.
I would like know interface area between dimer ( chainAD) and Chain BC.
I have trired PISA of CCP4 and PDBe PISA.
it calculate the interface surface area between dimer of chain AD or chain
BC etc.
i have also find the interface Residues two chains in pymol.
Kindly help please
Regards
Ashwani Kumar
SRF - ICMR
Structural Biology lab
NCCS PUNE