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Alpha helix secondary structure

The peptide backbone twists forming a helix with the amino acid sidechains protruding outwards.

(to simplify, H atoms are not shown)

The helix can be seen better if we draw just a line that joins the alpha carbons.

Let's show again the bonds in the backbone, still with hidden sidechains: .

(move the molecule and you will perceive the helical shape)

The helix is stabilized by hydrogen bonds (••••••) between the carbonyl groups and the nitrogens in the peptide bonds.


Axial view (from the end).
Observe that the helix turns to the right (it is right-handed), as the thread in a screw.

Show sidechains.

Each amino acid in its own color:
Ser- Glu- Ala-Ala- Ile- Asn- Arg- Gln- Ile- Asn- Leu- Glu- Leu- Tyr- Ala

In models for large proteins, the portions with alpha helix conformation are usually rendered in a simplified “cartoon” form as a spiral ribbon , or as a cylinder .