Helices in Proteins: Difference between revisions

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Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

Angel Herraez, Eric Martz, Karsten Theis, Joel L. Sussman

@@ Line 8: / Line 8: @@
    <jmolCheckbox>
      <target>jmol_3</target>
-     <scriptWhenChecked>set syncMouse on; /*set syncScript on;*/ sync * on;</scriptWhenChecked>
+     <scriptWhenChecked>script applet * @{"set syncMouse on; sync on;"};</scriptWhenChecked>
-     <scriptWhenUnchecked>sync * off;</scriptWhenUnchecked>
+     <scriptWhenUnchecked>script applet * @{"sync off;"};</scriptWhenUnchecked>
      <text>Synchronize the 3 models for rotation with your mouse.</text>
    </jmolCheckbox>
 </jmol></span>
-(For optimal results you should act with your mouse on the leftmost model)
-To re-align the 3 models, either reload this page or uncheck the synchronization and click on each of the 3 green 'Reset' links.
+To re-align the 3 models, either reload this page or click on each of the 3 green 'Reset' links.
 <table style="width:100%;">
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 <br />H bonds: N<sub>i+3</sub> &#8594; O<sub>i</sub>
 <br />φ = -49°, ψ = -26°
-<br />[[3l79]]: 514-525
+<br />from [[3l79]]: 514-525
 </td>
 <td style="vertical-align:top;text-align:center;">
@@ Line 54: / Line 53: @@
 <br />H bonds: N<sub>i+4</sub> &#8594; O<sub>i</sub>
 <br />φ = -60°, ψ = -45°
-<br />1hho chain B: 5-16
+<br />from [[1hho]] chain B: 5-16
 </td>
 <td style="vertical-align:top;text-align:center;">
@@ Line 63: / Line 62: @@
 <br />H bonds: N<sub>i+5</sub> &#8594; O<sub>i</sub>
 <br />φ = -55°, ψ = -70° (approx.)
-<br />[[2qd3]] chain A: 346-357
+<br />from [[2qd3]] chain A: 346-357
 </td>
 </tr>
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 </table>
-The alpha helix is by far the most common helix. Note that it is a right-handed helix when formed with the common L-amino acids<ref name="novotny">PMID: 15740737</ref><ref name="jourdan">PMID: 12910453</ref><ref name="moradi">PMID: 19923435</ref>. (It is left-handed when formed with D-amino acids<ref name="novotny" /><ref name="jourdan" /><ref name="moradi" />.) When viewed from either end, right-handed helices turn clockwise when followed away from you.
+Change rendering:
+<jmol>
+  <jmolButton>
+    <target>jmol_3</target>
+    <script>script applet * @{"define temp selected;select not alpha;color bluetint;select protein;wireframe only;wireframe off;select backbone;cpk 23%;wireframe 0.15;select temp;"};</script>
+    <text>backbone - ball and stick</text>
+  </jmolButton>
+  <jmolButton>
+    <target>jmol_3</target>
+    <script>script applet * @{"define temp selected;select not alpha;color bluetint;select protein;wireframe only;wireframe off;cpk 23%;wireframe 0.15;select temp;"};</script>
+    <text>backbone and sidechains - ball and stick</text>
+  </jmolButton>
+  <jmolButton>
+    <target>jmol_3</target>
+    <script>script applet * @{"define temp selected;select not alpha;color bluetint;select protein;wireframe only;wireframe off;cpk 100%;select temp;"};</script>
+    <text>spacefilling for all</text>
+  </jmolButton>
+  <jmolButton>
+    <target>jmol_3</target>
+    <script>script applet * @{"define temp selected;select protein;wireframe only;wireframe off;cartoon on;select alpha;cpk 23%;select temp;"};</script>
+    <text>reset (cartoons)</text>
+  </jmolButton>
+</jmol>
+The [[alpha helix]] is by far the most common helix. Note that it is a right-handed helix when formed with the common L-amino acids<ref name="novotny">PMID: 15740737</ref><ref name="jourdan">PMID: 12910453</ref><ref name="moradi">PMID: 19923435</ref>. (It is left-handed when formed with D-amino acids<ref name="novotny" /><ref name="jourdan" /><ref name="moradi" />.) When viewed from either end, right-handed helices turn clockwise when followed away from you.
 ==See Also==
+*[[Basics of Protein Structure]]
+*[[Alpha helix]]
+*[http://chemapps.stolaf.edu/jmol/jsmol/helix.htm JSmol helix builder]
+*[http://wiki.jmol.org/index.php/Recycling_Corner/Alpha_Helix_Generator RIBOZOME - an Alpha Helix Generator]
 *[http://en.wikipedia.org/wiki/Alpha_helix Alpha helix] at Wikipedia.
+*[http://en.wikipedia.org/wiki/310_helix 3-10 helix] at Wikipedia.
+*[http://en.wikipedia.org/wiki/Pi_helix Pi helix] at Wikipedia.
 *[[Secondary structure]]
-* [[Protein primary, secondary, tertiary and quaternary structure]] (slides for teaching)
+*[[Protein primary, secondary, tertiary and quaternary structure]] (slides for teaching)
-* [[Protein primary, secondary, tertiary and quaternary structure (Spanish)|Estructuras primaria, secundaria, terciaria y cuaternaria de las proteínas]] (en formato de presentaci&oacute;n)
+*The same in Spanish: [[Protein primary, secondary, tertiary and quaternary structure (Spanish)|Estructuras primaria, secundaria, terciaria y cuaternaria de las proteínas]] (en formato de presentaci&oacute;n)
 ==References==
 <references />