<p>Glycine has a single hydrogen atom as its side chain:</p>

<p><a href="https://i.sstatic.net/BKoQT.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/BKoQT.png" alt="Glycine from Wikipedia"></a></p>

<p>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.</p>

<p>But which of the two hydrogens is the side chain?</p>

<p>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:</p>

<p><a href="https://i.sstatic.net/YZjyB.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/YZjyB.png" alt="L-alanine"></a></p>

<p><sub>The images are taken from WikiMedia Commons:
<a href="https://commons.wikimedia.org/wiki/File:Glycine-3D-balls.png" rel="nofollow noreferrer">glycine</a>
and <a href="https://commons.wikimedia.org/wiki/File:L-alanine-3D-balls.png" rel="nofollow noreferrer">L-alanine</a>.</sub></p>

CC BY-SA 4.0
2018-06-04T17:58:56.013Z
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?
Jonathon Byrd
CC BY-SA 4.0
2018-06-05T08:13:48.583Z
@JonathonByrd yes, I'd think so
marcin
CC BY-SA 4.0
2018-06-04T17:26:05.910Z
2018-06-04T17:26:05.910Z
marcin
<p>I have a dataset of pdb-format protein structure decoys/models generated by tertiary structure prediction programs. Many of these are missing hydrogen atoms.</p>

<p>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.</p>

<p>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.</p>

<proteins><protein-structure><pdb><3d-structure>
Determining position of side chain hydrogen in glycine residues from coordinates of backbone atoms
# Determining position of side chain hydrogen in glycine residues from coordinates of backbone atoms

(Asked by: username_0 on 2018-06-04)

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.

**Tags:** proteins, protein-structure, pdb, 3d-structure

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## 1 answers

### Answer by username_1 on 2018-06-04. Score: 3 | Accepted answer

Glycine has a single hydrogen atom as its side chain:

[![Glycine from Wikipedia](https://i.sstatic.net/BKoQT.png)](https://i.sstatic.net/BKoQT.png)

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](https://i.sstatic.net/YZjyB.png)](https://i.sstatic.net/YZjyB.png)

The images are taken from WikiMedia Commons:
[glycine](https://commons.wikimedia.org/wiki/File:Glycine-3D-balls.png)
and [L-alanine](https://commons.wikimedia.org/wiki/File:L-alanine-3D-balls.png).

> **Comments:**
> **username_0**: 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?  
> **username_1**: @JonathonByrd yes, I'd think so  

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