3.1 Helices

3.1.3 pi-helix

The pi helix is an extremely rare secondary structural element in proteins. Hydrogen bonds within an pi-helix display a repeating pattern in which the backbone C=O of residue i hydrogen bonds to the backbone HN of residue i+5. Like the 3.10 helix, one turn of pi helix is sometimes found at the ends of regular alpha helices but pi helices longer than a few i, i+5 hydrogen bonds are not found. The infrequency of this particular form of secondary structure stems from the following properties:

the phi and psi angles of the pure pi helix (-57.1, -69.7) lie at the very edge of an allowed, minimum energy region of the Ramachandran (phi, psi) map.
the pi helix requires that the angle tau (N-CA-C') be larger (114.9) than the standard tetrahedral angle of 109.5 degrees.
the large radius of the pi helix means the polypeptide backbone is no longer in van der Waals contact across the helical axis forming an axial hole too small for solvent water to fill.
side chains are more staggered than the ideal 3.10 helix but not as well as the alpha helix.

A good look at a geometrically pure pi helix is afforded by the CPK representation shown in Figure 2 . Again notice how, like the alpha and 3.10 helices, all amide protons point toward the N-terminus (down) and all carbonyl oxygens point toward the C-terminus (up). Looking at the pi helix down the helical axis from the C-terminus (top), you can see the four carbonyl oxygens of the last turn of the pi helix and the spread of the sidechains.

download model pi helix

download RasMol script

No Title - 31 MAY 96

written by Kurt D. Berndt

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