What does the following diagram represent?

Question

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

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:

Answer 1

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) 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).