Determining position of side chain hydrogen in glycine residues from coordinates of backbone atoms

Question

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.

Answer 1

Glycine has a single hydrogen atom as its side chain:

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:

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