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:

the phi and psi angles of the alpha helix (lie in the center of an allowed, minimum energy region of the Ramachandran (phi, psi) map.
the dipoles of hydrogen bonding backbone atoms are in near perfect alignment.
the radius of the helix allows for favorable van der Waals interactions across the helical axis.
side chains are well staggered minimizing steric interference.

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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