Dihedral/Dihedral angles in proteins
From Proteopedia
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| - | ==Dihedral angles in proteins: Phi and Psi== | ||
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The model displayed on the right is a tripeptide (Trp<sub>34</sub>–Glu<sub>35</sub>–Ser<sub>36</sub> within the protein lysozyme). | The model displayed on the right is a tripeptide (Trp<sub>34</sub>–Glu<sub>35</sub>–Ser<sub>36</sub> within the protein lysozyme). | ||
| - | This page illustrates the meaning of phi (ϕ) and psi (ψ) angles, both around the alpha carbon of the central residue (Glu<sub>35</sub>). | + | This page illustrates the meaning of '''phi (ϕ)''' and '''psi (ψ)''' angles, both around the alpha carbon of the central residue (Glu<sub>35</sub>). Both are '''''dihedral angles''''', meaning an angle formed between two planes (as compared to regular angles, formed between two lines or bonds). |
| + | They are also called ''torsion angles'', meaning the torsion or rotation around a bond. | ||
| + | <!-- | ||
| + | Note that each alpha carbon (residue ''i'') belongs to two peptide planes (with residues ''i−1'' and ''i+1'' respectively). | ||
| + | --> | ||
| - | phi (ϕ) is the angle between the planes displayed as <span style="background-color:thistle; padding:0 1.5ex; margin-right:0.5ex; font-size:0.7em;"></span><span style="font-size:0.7em; color:#555;">(1)</span> and <span style="background-color:plum; padding:0 1.5ex; margin-right:0.5ex; font-size:0.7em;"></span><span style="font-size:0.7em; color:#555;">(2)</span> | ||
| - | + | phi (ϕ) is defined by these two planes: | |
| + | * plane defined by C<sub>i−1</sub>, N<sub>i</sub> and C<sup>α</sup><sub>i</sub><br>displayed as <span style="background-color:thistle; padding:0 1.5ex; margin-right:0.5ex; font-size:0.7em;"></span><span style="font-size:0.7em; color:#555;">(1)</span> | ||
| + | * plane defined by N<sub>i</sub>, C<sup>α</sup><sub>i</sub> and C<sub>i</sub><br>displayed as <span style="background-color:plum; padding:0 1.5ex; margin-right:0.5ex; font-size:0.7em;"></span><span style="font-size:0.7em; color:#555;">(2)</span> | ||
| + | Therefore ϕ means rotation around the N-C<sup>α</sup> bond. | ||
| - | (planes 2 and 3 coincide) | ||
| + | psi (ψ) is defined by these two planes: | ||
| + | * plane defined by N<sub>i</sub>, C<sup>α</sup><sub>i</sub> and C<sub>i</sub><br>displayed as <span style="background-color:moccasin; padding:0 1.5ex; margin-right:0.5ex; font-size:0.7em;"></span><span style="font-size:0.7em; color:#555;">(3)</span> | ||
| + | * plane defined by C<sup>α</sup><sub>i</sub>, C<sub>i</sub> and N<sub>i+1</sub><br>displayed as <span style="background-color:sandybrown; padding:0 1.5ex; margin-right:0.5ex; font-size:0.7em;"></span><span style="font-size:0.7em; color:#555;">(4)</span> | ||
| + | Therefore ψ means rotation around the C<sup>α</sup>-C bond. | ||
| - | You can run animations that continuously rotate the model changing one of the angles | + | :Note that planes 2 and 3 coincide. |
| + | :In all these, "C" means the carboxylic carbon, forming the amide or peptide bond | ||
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| + | You can run animations that continuously rotate the model changing one of the angles: | ||
<!--, or use the slider or controls to manually progress through different values of the angles.--> | <!--, or use the slider or controls to manually progress through different values of the angles.--> | ||
| - | Bright magenta cylinders are displayed where neighbour atoms collide (hence there is an unfavourable conformation for those particular ϕ, ψ values). | ||
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| + | Bright magenta cylinders are displayed where neighbour atoms collide (hence there is an unfavourable conformation for those particular ϕ, ψ values). | ||
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Revision as of 08:47, 15 July 2016
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The model displayed on the right is a tripeptide (Trp34–Glu35–Ser36 within the protein lysozyme). This page illustrates the meaning of phi (ϕ) and psi (ψ) angles, both around the alpha carbon of the central residue (Glu35). Both are dihedral angles, meaning an angle formed between two planes (as compared to regular angles, formed between two lines or bonds). They are also called torsion angles, meaning the torsion or rotation around a bond.
Therefore ϕ means rotation around the N-Cα bond.
Therefore ψ means rotation around the Cα-C bond.
You can run animations that continuously rotate the model changing one of the angles: animation, and then: animation, and then: Bright magenta cylinders are displayed where neighbour atoms collide (hence there is an unfavourable conformation for those particular ϕ, ψ values). |
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