Helices in Proteins: Difference between revisions
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fixing the sync (currently, it only works well when driven from the leftmost JSmol) SUCCESS! |
m basic link at the top of list; add mention of Spanish |
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</jmol></span> | </jmol></span> | ||
To re-align the 3 models, either reload this page or | To re-align the 3 models, either reload this page or click on each of the 3 green 'Reset' links. | ||
<table style="width:100%;"> | <table style="width:100%;"> | ||
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<br />H bonds: N<sub>i+3</sub> → O<sub>i</sub> | <br />H bonds: N<sub>i+3</sub> → O<sub>i</sub> | ||
<br />φ = -49°, ψ = -26° | <br />φ = -49°, ψ = -26° | ||
<br />[[3l79]]: 514-525 | <br />from [[3l79]]: 514-525 | ||
</td> | </td> | ||
<td style="vertical-align:top;text-align:center;"> | <td style="vertical-align:top;text-align:center;"> | ||
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<br />H bonds: N<sub>i+4</sub> → O<sub>i</sub> | <br />H bonds: N<sub>i+4</sub> → O<sub>i</sub> | ||
<br />φ = -60°, ψ = -45° | <br />φ = -60°, ψ = -45° | ||
<br />1hho chain B: 5-16 | <br />from [[1hho]] chain B: 5-16 | ||
</td> | </td> | ||
<td style="vertical-align:top;text-align:center;"> | <td style="vertical-align:top;text-align:center;"> | ||
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<br />H bonds: N<sub>i+5</sub> → O<sub>i</sub> | <br />H bonds: N<sub>i+5</sub> → O<sub>i</sub> | ||
<br />φ = -55°, ψ = -70° (approx.) | <br />φ = -55°, ψ = -70° (approx.) | ||
<br />[[2qd3]] chain A: 346-357 | <br />from [[2qd3]] chain A: 346-357 | ||
</td> | </td> | ||
</tr> | </tr> | ||
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</table> | </table> | ||
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== | ==See Also== | ||
*[[Basics of Protein Structure]] | |||
*[[Alpha helix]] | *[[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/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]] | *[[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 presentación) | *The same in Spanish: [[Protein primary, secondary, tertiary and quaternary structure (Spanish)|Estructuras primaria, secundaria, terciaria y cuaternaria de las proteínas]] (en formato de presentación) | ||
==References== | ==References== | ||
<references /> | <references /> | ||