text: user12686: Suppose, the following is a diagram of a protein's polypeptide chain:
  
  What does this diagram represent?
  
  What are the letters A, E, M, W, L, N, S, etc. represent?  (I suppose these are amino acid codes. Right?)
  Which one is the c-alpha atom here?
  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:
  
  
  user6322: 
  Yes, the letters are amino acids
  It's a schematic with a whole residue as a circle —possibly from Voet and Voet.
  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) 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).
  
original_text: 12686: <p>Suppose, the following is a diagram of a protein's polypeptide chain:</p>
  <p><a href="https://i.stack.imgur.com/HWIPy.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/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.stack.imgur.com/QthLx.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/QthLx.png" alt="enter image description here" /></a></p>
   6322: <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>
  