Hi!
I am stumbling over a weird thing which PyMol shows me in some structures: The attached image contains one of them. Between two residues from different chains, I'm getting a solid line, like a narrow stick. I expect a polar contact between them, but why is PyMol connecting them like that? Has anyone seen this before and can help me, what the chemical meaning is?
Kind regards,
Matthias
Bonds are drawn by proximity - if two atoms are so close that the distance falls within the bonding criterion, they are shown as connected by a bond.
see https://pymolwiki.org/index.php/Connect_cutoff
"Two atoms with VDW radii vdw1 and vdw2 are connected with a bond, if the following inequality is true:
distance
It is definitely a problem of the distance between the hydrogen and the oxygen, which according to their coordinates are so close that the distance falls below the bond-length cut-off. You do not mention how the pdb file was generated. In interpreting the X-ray structure electron density for such salt bridges, you frequently see the lysine nitrogen in a position average to the ones it would assume if forming a hydrogen bond to one or the other of the two carboxylate oxygens, resulting in a model in which the lysine apparently hydrogen bonds to both or gets too close.
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