Hello friends,
I have a question.
In pymol, when we measure the distance between 2 group which form a salt bridge, to which atoms should we pay attention?
The distance between carbon in COO- and nitrogen in NH3+ is considered or we should look at the distance between H and O?
Thank you!
Commonly pdb files are lacks of H atoms and shows only heteroatoms as Nitrogen, Oxygen, etc, so may you should measure the proper distance established between N and O the classic salt bridge remembering the correct distances. I hope will be usefull.
It should be between N and O as the hydrogen atoms are not shown in PDB.
Focus on the two atoms carrying the positive (call it P) and the negative (call it N) charges, either of which may or may not contain (attached to) a hydrogen. In the case of proteins, this is very commonly (almost always) N+ and O-. The hydrogen atom, when bonded to another atom, contributes very little to bond length because it is just a proton (atomic radius = 0) especially if the atom it is bonded to is electronegative, as it will draw all electrons to itself. If there is a H between the the positive and negative groups, then it is a hydrogen-bond (by definition), not a salt bridge, strictly speaking. Note that in H-bonding, the three atoms, P...H...N must be colinear (this is important) otherwise it does not qualify as H-bonding. Also note that x-ray structures do not explicitly show the H's, but NMR structures do. HTH.
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