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3.1 Helices

3.1.2 3.10 helix

The 3.10 helix is not a common secondary structural element in proteins. Only 3.4% of the residues are involved in 3.10 helices in the Kabsch and Sander database (1983), and nearly all those in helical segments containing 1-3 hydrogen bonds (96% less than or equal to 4 residues). Alpha helices sometimes begin or end with a single turn of a 3.10 helix (one hydrogen bond) although this accounts for <25% of residues with this classification. The average of the backbone dihedral angles were found to differ slightly from the ideal 3.10 helix (-74.0, -4.0) with values of -71.0 and -18.0 degrees, for phi and for psi, respectively. This seemingly small difference results in a larger radius (2.0 versus 1.9 Å) and a larger number of residues per helical turn (3.2 versus 3.0). The end result being a slightly better staggering of sidechains along the helical axis. Hydrogen bonds within an 3.10-helix also display a repeating pattern in which the backbone C=O of residue i hydrogen bonds to the backbone HN of residue i+3. The infrequency of this particular form of secondary structure stems from the following properties:

A good look at a geometrically pure 3.10 helix is afforded by the CPK representation shown in Figure 2 . Again notice how, like the alpha helix, all amide protons point toward the N-terminus (down) and all carbonyl oxygens point toward the C-terminus (up). Hydrogen bonds (i, i+3) are displayed as yellow line segments connecting the amide nitrogen and carbonyl oxygen pairs. The less than perfect alignment of these groups is apparent from the angle of the lines. Looking at the 3.10 helix along the helical axis from the C-terminus (top), you can see the three carbonyl oxygens of the last turn of the helix and the alignment of sidechains.

download model ideal 3.10 helix

download RasMol script

No Title - 31 MAY 96
written by Kurt D. Berndt

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