Alpha-Helix Geometry Part. 1
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The figure below shows the three main chain torsion angles of a polypeptide. These are phi, psi and omega.
The planarity of the peptide bond restricts omega to 180 degrees in very nearly all of the main chain peptide bonds. In rare cases omega = 0 degrees for a cis peptide bond which, as stated above, usually involves proline.
If you have MAGE installed here is a kinemage you can manipulate to gain a better appreciation of these angles (and chi1). This is highly recommended according to Dr Mills.
Pauling and Corey twisted models of polypeptides around to find ways of getting the backbone into regular conformations which would agree with alpha-keratin fibre diffraction data. The most simple and elegant arrangement is a right-handed spiral conformation known as the 'alpha-helix'.
If you have RasMol installed, here's a coordinate file for a helix you can examine. (Click here for a chemical MIME-stamped file from the Birkbeck server).
The figure below shows how a right-handed helix differs from a left-handed one. An easy way to remember this is to hold both your hands in front of you with your thumbs pointing up and your fingers curled towards you. For each hand the thumbs indicate the direction of translation and the fingers indicate the direction of rotation.
j.cooper 2/1/95
Index to Course Material
Index to Section 3
Geometry Index
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Last updated 4th Mar '96