<p>There are three options:</p>
<ol>
<li>it's a badly phrased Ramachandran plot question</li>
<li>it's a question aimed at the describing the properties of different SS</li>
<li>it's a trick question</li>
</ol>
<p>φ &amp; ψ can be used to classify SS (cf. Ramachandran plot), these are however proper dihedrals, so require 4 atoms, which you lack.</p>
<p>The sequential Cαs in a strand are increasingly distant by 3–4Å, while in a helix there's a periodicity every 3–4 residues. The images you were given are likely to remind you that between two strands in a sheet the Cαs are ~5Å away from the other strand, but the order is different —the indices will increase together in parallel strands, but not in anti-parallel strands.</p>
<p>A C-alpha trace has the issue that the residues are often not known (<code>UNK</code> is technically represented as homoalanine, but is an unknown) and the resolution is &gt; 4Å. Any SS allocation will be highly inaccurate making it a trick question.</p>

CC BY-SA 4.0
2022-03-23T14:05:09.963Z
2022-03-23T14:05:09.963Z
Matteo Ferla
<p>We are working on an algorithm to assign proteins only on the basis of alpha-carbons.</p>
<p>My teacher told me to draw a diagram to represent hydrogen bonds only on the basis of alpha-carbons.</p>
<p>I showed him the following picture:</p>
<p><a href="https://i.sstatic.net/bHeUA.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/bHeUA.png" alt="enter image description here" /></a></p>
<p>He said this picture doesn't count, as this diagram shows all the atoms.</p>
<p>I couldn't figure out how to do this without showing oxygen, non-alpha-carbon, and nitrogen atoms.</p>
<p>How can I draw a diagram of hydrogen bonds only on the basis of C-alpha backbone?</p>

<protein-structure><homework>
How can I draw a diagram of hydrogen bonds only on the basis of C-alpha backbone?
# How can I draw a diagram of hydrogen bonds only on the basis of C-alpha backbone?

(Asked by: username_0 on 2022-03-22)

We are working on an algorithm to assign proteins only on the basis of alpha-carbons.

My teacher told me to draw a diagram to represent hydrogen bonds only on the basis of alpha-carbons.

I showed him the following picture:

[![enter image description here](https://i.sstatic.net/bHeUA.png)](https://i.sstatic.net/bHeUA.png)

He said this picture doesn't count, as this diagram shows all the atoms.

I couldn't figure out how to do this without showing oxygen, non-alpha-carbon, and nitrogen atoms.

How can I draw a diagram of hydrogen bonds only on the basis of C-alpha backbone?

**Tags:** protein-structure, homework

---

## 1 answers

### Answer by username_1 on 2022-03-23. Score: 2 | Accepted answer

There are three options:

1. it's a badly phrased Ramachandran plot question
2. it's a question aimed at the describing the properties of different SS
3. it's a trick question

φ & ψ can be used to classify SS (cf. Ramachandran plot), these are however proper dihedrals, so require 4 atoms, which you lack.

The sequential Cαs in a strand are increasingly distant by 3–4Å, while in a helix there's a periodicity every 3–4 residues. The images you were given are likely to remind you that between two strands in a sheet the Cαs are ~5Å away from the other strand, but the order is different —the indices will increase together in parallel strands, but not in anti-parallel strands.

A C-alpha trace has the issue that the residues are often not known (`UNK` is technically represented as homoalanine, but is an unknown) and the resolution is > 4Å. Any SS allocation will be highly inaccurate making it a trick question.


---

