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Messages - kanavkalra

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Below is an example:

In PDB id: 2GDI,

For instance, if we want to find out possible H-bonds between a water molecule 'HOH-373' from chain X with the surrounding atoms from the environment. The output could be as follows:

1) O2P atom of G76 chain X;   with the distance between O atom of HOH-373 and O2P atom of G76 of 2.79 Angstrom.
2) HOH 492X;  with the distance between O atom of HOH 373 and O atom of HOH492X of 2.58  Angstrom.
3) N7 of G76 X; with the distance between O of HOH 373 and N7 atom of G76X of 2.84 Angstrom.

So the above three atoms are within the H-bonding distances if we consider the distance criterion of less than 3.5 Angstrom between the donor and acceptor atoms.

RNA structures (DSSR) / Water H-Bonding with surrounding residues
« on: May 20, 2018, 09:36:50 am »
Dear Dr. Xiang-Jun Lu,
May I know if there exists any option that could help me get data for the Water H-Bonding with the surrounding residues?

Kanav Kalra

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Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.