Caption:A region of alpha-helical seocndary structure is shown with the N-terminus at the bottom and the C-terminus at the top of the figure. Each carbonyl oxygen forms a hydrogen bond with the amide hydrogen of the fourth residue further toward the C-terminus of the polypeptide chain. The hydrogen bonds are approximately parallel to the long axis of the helix. Note that all the carbonyl groups point toward the C-termius. In an ideal alpha helix, equivalent positions recur every 0.54 nm (the pitch of the helix), each amino acid residue advances the helix by 0.15 nm along the axis of the helix (the rise), and there are 3.6 amino acid residues per turn. The arrows at the ends of the helix indicate the direction from the N- to the C- terminus. In a right-handed helix the backbone turns in a clockwise direction when viewed along the axis from its N-terminus. If you imagine that the right-handed helix is a spiral staircase, you will be turning to the right as you walk down the staircase.
Notes:The orientation of the carbonyl and amide groups towards the C- and N- terminus respectively leads to a net dipole to the alpha helix. The structure derived from a polypeptide of L-amino acids (as are found in nature) result in a right-handed helix. Synthetic polypeptides made from R- amino acids lead to formation of a left-handed alpha helix. The properties of the helix are reproduced in an isomeric form.