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RNA structures (DSSR) / Re: Water H-Bonding with surrounding residues
« on: May 20, 2018, 05:23:54 pm »
Hi,
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.
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.