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I have a dataset of pdb-format protein structure decoys/models generated by tertiary structure prediction programs. Many of these are missing hydrogen atoms.

Specifically, I'd like to determine the rough location of side-chain hydrogens in glycine residues, given the CA, C, N, and O coordinates. Is this possible? I don't need too much precision - I just need the general direction relative to the rest of the residue. More specifically, I want a vector originating at the CA that points roughly in the direction of the side chain.

I've looked at software for generating hydrogen atoms from pdb structures, however, I need to know which ones are glycine side chains, and was wondering if there might be a simpler way to predict hydrogen locations given coordinates of backbone atoms.

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Glycine has a single hydrogen atom as its side chain:

Glycine from Wikipedia

All the six bond angles with the CA atom in the middle are about 109° (C-CA-N, C-CA-HA3, C-CA-HA2, N-CA-HA3, N-CA-HA2 and HA3-CA-HA2 using the CCD naming convention). This defines the rough direction of the hydrogen atoms.

But which of the two hydrogens is the side chain?

If it is a left-handed protein, I'd assume that it's the hydrogen pointing toward the screen, similarly to the side chain in L-alanine:

L-alanine

The images are taken from WikiMedia Commons: glycine and L-alanine.

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  • $\begingroup$ Thank you! So, for clarification, if I find the two vectors where bond angles N-CA-HA and C-CA-HA are about 109 degrees, and choose the one corresponding to a left-handed protein (assuming my structures are left-handed), I will likely have a reasonable estimate for the direction vector I'm looking for? $\endgroup$ – Jonathon Byrd Jun 4 '18 at 17:58
  • $\begingroup$ @JonathonByrd yes, I'd think so $\endgroup$ – marcin Jun 5 '18 at 8:13

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