Alpha helix: Difference between revisions
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Some amino acids are commonly found in alpha helices and others are rare. Amino acids with a side chain whose movement is largely restricted in an alpha helix (branched at beta carbon like threonine or valine) are disfavored, i.e. occur less often in alpha helices than in other secondary structure elements. Glycine, with its many possible main chain conformations, is also rarely found in helices. Knowing how likely an amino acid is to occur in an alpha helix (the so-called helix propensities), it is possible to [https://en.wikipedia.org/wiki/List_of_protein_secondary_structure_prediction_programs predict] where helices occur in a protein sequence. | Some amino acids are commonly found in alpha helices and others are rare. Amino acids with a side chain whose movement is largely restricted in an alpha helix (branched at beta carbon like threonine or valine) are disfavored, i.e. occur less often in alpha helices than in other secondary structure elements. Glycine, with its many possible main chain conformations, is also rarely found in helices. Knowing how likely an amino acid is to occur in an alpha helix (the so-called helix propensities), it is possible to [https://en.wikipedia.org/wiki/List_of_protein_secondary_structure_prediction_programs predict] where helices occur in a protein sequence. | ||
Proline is considered a helix breaker because its main chain nitrogen is not available for hydrogen bonding. Here is an example of a <scene name='77/778341/Proline/ | Proline is considered a helix breaker because its main chain nitrogen is not available for hydrogen bonding. Here is an example of a <scene name='77/778341/Proline/1'>kink in a helix</scene> (<jmol> | ||
<jmolLink> | <jmolLink> | ||
<script> select 58-61:A; structure turn; | <script> select 58-61:A; structure turn; select 50-58:A; rockets on; select 60-68; rockets on; | ||
</script> | </script> | ||
<text> | <text>show helical axes with rockets</text> | ||
</jmolLink> | </jmolLink> | ||
</jmol> ) at the position of a <scene name='77/778341/Proline/2'>proline</scene>. | </jmol> ) at the position of a <scene name='77/778341/Proline/2'>proline</scene>. | ||
