Dihedral/Index
From Proteopedia
(Difference between revisions)
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** Simplified 3D models in JSmol that can be rotated with your mouse, and set to various dihedral angles: [http://biomodel.uah.es/model5/prot/diedros_en.htm in English] and [http://biomodel.uah.es/model5/prot/diedros.htm Spanish]. | ** Simplified 3D models in JSmol that can be rotated with your mouse, and set to various dihedral angles: [http://biomodel.uah.es/model5/prot/diedros_en.htm in English] and [http://biomodel.uah.es/model5/prot/diedros.htm Spanish]. | ||
</td></tr><tr><td> | </td></tr><tr><td> | ||
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[[Image:Phi-rotation-EM.gif|right]] | [[Image:Phi-rotation-EM.gif|right]] | ||
** Animated explanation identifying the 4 atoms for phi in a polypeptide, and rotating it clockwise (positive angles) and counter-clockwise (negative angles): | ** Animated explanation identifying the 4 atoms for phi in a polypeptide, and rotating it clockwise (positive angles) and counter-clockwise (negative angles): | ||
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*** As a YouTube video [https://tinyurl.com/RamachandranPrincipleYoutube in English]. (Dihedral at 1:52 - 3:10) | *** As a YouTube video [https://tinyurl.com/RamachandranPrincipleYoutube in English]. (Dihedral at 1:52 - 3:10) | ||
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[[Image:Dihedral-AH.gif|right]] | [[Image:Dihedral-AH.gif|right]] | ||
* '''[[Dihedral/Dihedral_angles_in_proteins|Dihedral angles in proteins]]''': an interactive display of phi and psi dihedral angles using a model of a tripeptide. | * '''[[Dihedral/Dihedral_angles_in_proteins|Dihedral angles in proteins]]''': an interactive display of phi and psi dihedral angles using a model of a tripeptide. | ||
** A regular page in Proteopedia. | ** A regular page in Proteopedia. | ||
** Simple presentation, featuring a 3D model with planes, clashes and animations. | ** Simple presentation, featuring a 3D model with planes, clashes and animations. | ||
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* '''[[Phi and Psi Angles]]''': a more detailed, guided explanation of determination and display of angles in the 3D model. | * '''[[Phi and Psi Angles]]''': a more detailed, guided explanation of determination and display of angles in the 3D model. | ||
** A regular page in Proteopedia. | ** A regular page in Proteopedia. | ||
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| + | [[Image:Ramachandran-jsmol.png|right|180px]] | ||
* '''The [[Ramachandran Plot]]''' | * '''The [[Ramachandran Plot]]''' | ||
** A regular page in Proteopedia. Featured in an article in Biochemistry and Molecular Biology Education, 2010. | ** A regular page in Proteopedia. Featured in an article in Biochemistry and Molecular Biology Education, 2010. | ||
** Extensive description with instructions on ''how to display the Ramachandran plot for any protein structure''. | ** Extensive description with instructions on ''how to display the Ramachandran plot for any protein structure''. | ||
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* '''[[Tutorial:Ramachandran_Plot_Inspection|Ramachandran Plot Inspection]]''' | * '''[[Tutorial:Ramachandran_Plot_Inspection|Ramachandran Plot Inspection]]''' | ||
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** Interactive Ramachandran plot with many controls and details, connecting the Ramachandran plot with the display on the 3D model. Includes planes, clashes and animations. | ** Interactive Ramachandran plot with many controls and details, connecting the Ramachandran plot with the display on the 3D model. Includes planes, clashes and animations. | ||
** You can display phi and psi for ''any pair of amino acids in any protein structure''. | ** You can display phi and psi for ''any pair of amino acids in any protein structure''. | ||
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[[Image:Dihedral-angles-anim.gif|right]] | [[Image:Dihedral-angles-anim.gif|right]] | ||
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*** [[Dihedral/Ramachandran_Principle_Quiz|quiz in English]] | *** [[Dihedral/Ramachandran_Principle_Quiz|quiz in English]] | ||
*** [[Dihedral/Ramachandran_Principle_Quiz (Spanish)|quiz in Spanish]] | *** [[Dihedral/Ramachandran_Principle_Quiz (Spanish)|quiz in Spanish]] | ||
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* [http://clfs690.alivetek.org/CLFS690/amino/animballjmol.htm Another animation] of phi and psi angles connected to a Ramachandran plot (by David Jollie) | * [http://clfs690.alivetek.org/CLFS690/amino/animballjmol.htm Another animation] of phi and psi angles connected to a Ramachandran plot (by David Jollie) | ||
* [[Ramachandran outlier]] showcases a special case where a residue is not conforming to the favored values in the Ramachandran plot. | * [[Ramachandran outlier]] showcases a special case where a residue is not conforming to the favored values in the Ramachandran plot. | ||
| + | </td></tr></table> | ||
Revision as of 21:38, 14 July 2018
Dihedral angles in proteins and the Ramachandran plot
This in an index page pointing to several resources on these topics.
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