We are now looking along the axis of a 12 residue alpha-helix with all the side chains omitted. Notice the small hole in the center. The three amide nitrogens at this end of the helix lack H-bonding partners within the helix.

  Sideview. The green dots are where side chains are attached to the alpha carbon.

  The beta-carbons (green) of the side chains point out from cylinder of the helix.

  Same magnification but now we are looking at the complete helix.