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3.1 Helices

3.1.1 alpha helix

The alpha helix is the most abundant helical conformation found in globular proteins accounting for 32-38% of all residues (Kabsch & Sander, 1983; Creighton, 1993). The average length of an alpha helix is 10 residues as taken from surveys of this structural database. The average dihedral angles phi and psi (-64 +/- 7, -41 +/- 7) also obtained from these surveys are found to differ slightly from the geometrically pure alpha helix (-57.8, -47.0). The abundance of this particular form of secondary structure stems from the following properties:

A good look at a geometrically pure alpha helix is afforded by the CPK representation shown in Figure 2 . Notice how all amide protons point toward the N-terminus (down) and all carbonyl oxygens point toward the C-terminus (up). The repeating nature of the phi, psi pairs ensure this orientation. Hydrogen bonds within an alpha-helix also display repeating pattern in which the backbone C=O of residue i hydrogen bonds to the backbone HN of residue i+4.

Looking at the helix along the helical axis from the C-terminus (top), you can see the four carbonyl oxygens of the last turn of the helix and the dispersion of sidechains. Residues in positions (i, i+3) and (i, i+4) are positioned in such a way as to force interaction of their sidechains. This can have a stabilizing effect if the residues are of opposite charge or are both hydrophobic (see "stereochemical" ). Interaction between aromatic rings (Phe) at position (i) and His at position (i+4) appears to have a stabilizing effect on the helical conformation of the C-peptide of ribonuclease in solution (Armstrong et al., 1993).

download model ideal alpha helix

download RasMol script

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

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