Alpha helix: Difference between revisions
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In an alpha helix, the main chain arranges in a <scene name='77/778341/Ribbon/1'>right-handed helix</scene> with the side chains (green) pointing away from the helical axis. The alpha helix is stabilized by <scene name='77/778341/Hbonds/2'>hydrogen bonds</scene> from amino acid n to n+4. There are <scene name='77/778341/Wheel/1'>3.6 residues per turn</scene>. If you <jmol> | In an alpha helix, the main chain arranges in a <scene name='77/778341/Ribbon/1'>right-handed helix</scene> with the side chains (green) pointing away from the helical axis. The alpha helix is stabilized by <scene name='77/778341/Hbonds/2'>hydrogen bonds</scene> from amino acid n to n+4. There are <scene name='77/778341/Wheel/1'>3.6 residues per turn</scene>. If you <jmol> | ||
<jmolLink> | <jmolLink> | ||
<script> select visible; var a = [ | <script> select visible; var a = [20%, 30%, 50%, 80%, 100%]; for(var i IN a) {spacefill @i; delay 0.4;} | ||
</script> | </script> | ||
<text>increase the sphere radii</text> | <text>increase the sphere radii</text> | ||
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[The previous scenes were inspired by a beautiful set of figures in Stryer's biochemistry textbook (https://www.ncbi.nlm.nih.gov/books/NBK22580/figure/A322/?report=objectonly).] | [The previous scenes were inspired by a beautiful set of figures in Stryer's biochemistry textbook (https://www.ncbi.nlm.nih.gov/books/NBK22580/figure/A322/?report=objectonly).] | ||
Apart from the characteristic hydrogen bonding patters, the other identifying feature of alpha helices are the main chain torsion angles phi and psi. If you plot phi against psi for each residue (so-called Ramachandran plot), you find that the phi/psi combination found in alpha helices fall into one of the three "allowed" (i.e. observed) areas for non-glycine residues. For a more detailed explanation, see [[Ramachandran Plot]] or http://www.cryst.bbk.ac.uk/PPS95/course/3_geometry/rama.html. | Apart from the characteristic hydrogen bonding patters, the other identifying feature of alpha helices are the main chain torsion angles <jmol> | ||
<jmolLink> | |||
<script> select visible; draw rama | |||
</script> | |||
<text>phi and psi</text> | |||
</jmolLink> | |||
</jmol>. If you plot phi against psi for each residue (so-called Ramachandran plot), you find that the phi/psi combination found in alpha helices fall into one of the three "allowed" (i.e. observed) areas for non-glycine residues. For a more detailed explanation, see [[Ramachandran Plot]] or http://www.cryst.bbk.ac.uk/PPS95/course/3_geometry/rama.html. | |||
'''Which amino acids are found in alpha helices?''' | '''Which amino acids are found in alpha helices?''' | ||