Alpha helix: Difference between revisions

(One intermediate revision by the same user not shown)

Line 8:

<text>side chains</text>

</jmolLink></jmol> pointing away from the helical axis. (Stereo: <jmol><jmolLink>

<script> stereo 5

<script> stereo -5

</script>

Line 54:

</jmol>) at the position of a <scene name='77/778341/Proline/5'>proline</scene>.

Prolines are often found near the beginning or end of an alpha helix, as in this example of <scene name='77/778341/Proline_cap/1'>the helix in crambin</scene> (this is an ultra high resolution structure where hydrogen atoms - white - are resolved and some atoms are shown in multiple positions). At the <scene name='77/778341/Proline_cap_detail/4'>C-terminal end</scene> of the helix, there is a proline that interrupts the regular pattern of n to n+4 hydrogen bonds. Instead, the helix ends with an n to n+3 hydrogen bond (one turn of a so-called 3-10 helix, see [[Helices in Proteins]]). The subsequent proline is in the center of a turn, followed by a glycine (which is part of an n to n+3 hydrogen bond also typical for turns).

Prolines are often found near the beginning or end of an alpha helix, as in this example of <scene name='77/778341/Proline_cap/1'>the helix in crambin</scene> (this is an ultra high resolution structure where hydrogen atoms - white - are resolved and some atoms are shown in multiple positions). At the <scene name='77/778341/Proline_cap_detail/5'>C-terminal end</scene> of the helix, there is a proline that interrupts the regular pattern of n to n+4 hydrogen bonds. Instead, the helix ends with an n to n+3 hydrogen bond (one turn of a so-called 3-10 helix, see [[Helices in Proteins]]). The subsequent proline is in the center of a turn, followed by a glycine (which is part of an n to n+3 hydrogen bond also typical for turns).

The beginnings and ends of helices are called N-caps and C-caps, respectively, and they have interesting [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2143812/ sequence and structural patterns] involving main chain or side chain hydrogen bonding.

Alpha helix: Difference between revisions

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@@ Line 8: / Line 8: @@
    <text>side chains</text>
 </jmolLink></jmol> pointing away from the helical axis. (Stereo: <jmol><jmolLink>
-<script>  stereo 5
+<script>  stereo -5
    </script>
    <text>ON</text>
@@ Line 54: / Line 54: @@
 </jmol>) at the position of a <scene name='77/778341/Proline/5'>proline</scene>.
-Prolines are often found near the beginning or end of an alpha helix, as in this example of <scene name='77/778341/Proline_cap/1'>the helix in crambin</scene> (this is an ultra high resolution structure where hydrogen atoms - white - are resolved and some atoms are shown in multiple positions). At the <scene name='77/778341/Proline_cap_detail/4'>C-terminal end</scene> of the helix, there is a proline that interrupts the regular pattern of n to n+4 hydrogen bonds.  Instead, the helix ends with an n to n+3 hydrogen bond (one turn of a so-called 3-10 helix, see [[Helices in Proteins]]). The subsequent proline is in the center of a turn, followed by a glycine (which is part of an n to n+3 hydrogen bond also typical for turns).
+Prolines are often found near the beginning or end of an alpha helix, as in this example of <scene name='77/778341/Proline_cap/1'>the helix in crambin</scene> (this is an ultra high resolution structure where hydrogen atoms - white - are resolved and some atoms are shown in multiple positions). At the <scene name='77/778341/Proline_cap_detail/5'>C-terminal end</scene> of the helix, there is a proline that interrupts the regular pattern of n to n+4 hydrogen bonds.  Instead, the helix ends with an n to n+3 hydrogen bond (one turn of a so-called 3-10 helix, see [[Helices in Proteins]]). The subsequent proline is in the center of a turn, followed by a glycine (which is part of an n to n+3 hydrogen bond also typical for turns).
 The beginnings and ends of helices are called N-caps and C-caps, respectively, and they have interesting [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2143812/ sequence and structural patterns] involving main chain or side chain hydrogen bonding.