<ol>
<li>Yes, the letters are amino acids</li>
<li>It's a schematic with a whole residue as a circle —possibly from Voet and Voet.</li>
<li>Residue <code>i</code> is the one in focus, the reference. <code>i-1</code> is the preceding residue. Have a gander at <a href="http://en.wikipedia.org/wiki/Turn_(biochemistry)" rel="nofollow noreferrer">en.wikipedia.org/wiki/Turn_(biochemistry)</a> where this type of relative notation is important.</li>
</ol>
<p>The diagram shows how secondary structure (helices, sheets etc.) affect the distance between the residues. In a helix a residue 3 positions down will be close, but not in a sheet.</p>
<p>However, for assignment of secondary structure it may be easier to look at the φ and ψ angles:</p>
<ul>
<li>α helix: phi=-57.8, psi=-47.0</li>
<li>π helix: phi=-57.1, psi=-69.7</li>
<li>3.10 helix: phi=-74.0, psi=-4.0</li>
<li>β sheet: phi=-139, psi=+135</li>
</ul>
<p>Although these have a range and you can get π bulges within α helices —important for conformation switching for pore opening (capsaicin binding to TRPV1 is a classic example).</p>

CC BY-SA 4.0
2021-08-31T12:57:42.630Z
2021-08-31T12:57:42.630Z
Matteo Ferla
<p>Suppose, the following is a diagram of a protein's polypeptide chain:</p>
<p><a href="https://i.sstatic.net/HWIPy.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/HWIPy.png" alt="enter image description here" /></a></p>
<p>What does this diagram represent?</p>
<ol>
<li>What are the letters A, E, M, W, L, N, S, etc. represent?  (I suppose these are amino acid codes. Right?)</li>
<li>Which one is the c-alpha atom here?</li>
<li>What are the sequence numbers <code>i-2</code>, <code>i-1</code>, <code>i</code>, <code>i+1</code>, <code>i+2</code>, etc. represent? Why there are negative and positive increments from <code>i</code>?</li>
</ol>
<p>The following is a related diagram:</p>
<p><a href="https://i.sstatic.net/QthLx.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/QthLx.png" alt="enter image description here" /></a></p>

CC BY-SA 4.0
2021-08-22T06:50:35.207Z
1. Yes, 2. it's a schematic with a whole residue was a circle —from Voet and Voet IIRC. 3. Residue `i` is the one in focus, the reference. i-1 is the preceding residue. Have a gander at https://en.m.wikipedia.org/wiki/Turn_(biochemistry) where this type of relative notation is important.
Matteo Ferla
CC BY-SA 4.0
2021-08-24T02:31:28.757Z
is this from a school or university assignment?
user3479780
CC BY-SA 4.0
2021-08-24T02:35:13.937Z
@user3479780, this is not an assignment. this is a personal study for data analysis.
user366312
<proteins><protein-structure>
What does the following diagram represent?
# What does the following diagram represent?

(Asked by: username_0 on 2021-08-22)

Suppose, the following is a diagram of a protein's polypeptide chain:

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

What does this diagram represent?

1. What are the letters A, E, M, W, L, N, S, etc. represent? (I suppose these are amino acid codes. Right?)
2. Which one is the c-alpha atom here?
3. What are the sequence numbers `i-2`, `i-1`, `i`, `i+1`, `i+2`, etc. represent? Why there are negative and positive increments from `i`?

The following is a related diagram:

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

**Tags:** proteins, protein-structure
> **Comments:**
> **username_1**: 1. Yes, 2. it's a schematic with a whole residue was a circle —from Voet and Voet IIRC. 3. Residue `i` is the one in focus, the reference. i-1 is the preceding residue. Have a gander at https://en.m.wikipedia.org/wiki/Turn_(biochemistry) where this type of relative notation is important.  
> **username_2**: is this from a school or university assignment?  
> **username_0**: @user3479780, this is not an assignment. this is a personal study for data analysis.  

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## 1 answers

### Answer by username_1 on 2021-08-31. Score: 2 | Accepted answer

1. Yes, the letters are amino acids
2. It's a schematic with a whole residue as a circle —possibly from Voet and Voet.
3. Residue `i` is the one in focus, the reference. `i-1` is the preceding residue. Have a gander at [en.wikipedia.org/wiki/Turn\_(biochemistry)](http://en.wikipedia.org/wiki/Turn_(biochemistry)) where this type of relative notation is important.

The diagram shows how secondary structure (helices, sheets etc.) affect the distance between the residues. In a helix a residue 3 positions down will be close, but not in a sheet.

However, for assignment of secondary structure it may be easier to look at the φ and ψ angles:

* α helix: phi=-57.8, psi=-47.0
* π helix: phi=-57.1, psi=-69.7
* 3.10 helix: phi=-74.0, psi=-4.0
* β sheet: phi=-139, psi=+135

Although these have a range and you can get π bulges within α helices —important for conformation switching for pore opening (capsaicin binding to TRPV1 is a classic example).


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