Dihedral/Dihedral angles in proteins
From Proteopedia
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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>). Both are '''''dihedral angles''''', meaning an angle formed between two planes (as compared to regular angles, formed between two lines or bonds). | 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. | + | They are also called '''''torsion angles''''', meaning the torsion or rotation around a bond. |
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| - | phi (ϕ) is | + | '''phi (ϕ)''' is the angle between 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 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> | * 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 | + | Therefore ϕ means rotation around the N—C<sup>α</sup> bond. |
| - | psi (ψ) is | + | '''psi (ψ)''' is the angle between 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 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> | * 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> | + | Therefore ψ means rotation around the C<sup>α</sup>—C bond. |
:Note that planes 2 and 3 coincide. | :Note that planes 2 and 3 coincide. | ||
| - | :In all these, "C" means the carboxylic carbon, forming the amide or peptide bond | + | :In all these, "C" means the carboxylic carbon, forming the amide or peptide bond with the N. Peptide bonds are displayed in black. |
| - | You can run animations that continuously rotate the model changing one of the angles: | + | 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.--> | ||
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</jmol> | </jmol> | ||
| - | <span style="color:#F000F0;">''' | + | '''Clashes''': <span style="color:#F000F0;">'''magenta cylinders'''</span> are displayed where neighbour atoms collide (hence there is an unfavourable conformation for those particular ϕ, ψ values). |
</div> | </div> | ||
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<uploadedFileContents>1iy4_34-36.pdb</uploadedFileContents> | <uploadedFileContents>1iy4_34-36.pdb</uploadedFileContents> | ||
<pspeed>8</pspeed> | <pspeed>8</pspeed> | ||
| - | <script>script /wiki/images/0/0c/Phi-Psi_uni.spt; function e_legend() { draw id "d_N" fixed diameter 2 [ | + | <script>script /wiki/images/0/0c/Phi-Psi_uni.spt; function e_legend() { draw id "d_N" fixed diameter 2 [88 95%] color @{{_N}.color};set echo id "e_N" [90 94%];echo N;color echo @{{_N}.color}; draw id "d_CA" fixed diameter 2 [88 90%] color [x70AB70];set echo id "e_CA" [90 89%];echo "C\u03B1";color echo [x70AB70]; draw id "d_CO" fixed diameter 2 [88 85%] color [xBF9090];set echo id "e_CO" [90 84%];echo "C=O";color echo [xBF9090]; draw id "d_O" fixed diameter 2 [88 80%] color @{{_O}.color};set echo id "e_O" [90 79%];echo "O";color echo @{{_O}.color}; draw id "d_C" fixed diameter 2 [88 75%] color @{{35.CB}.color};set echo id "e_C" [90 74%];echo "C";color echo @{{35.CB}.color}; } e_legend; select all;labels off;</script> |
</jmolApplet> | </jmolApplet> | ||
</jmol> | </jmol> | ||
Revision as of 12:00, 16 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: Clashes: magenta cylinders are displayed where neighbour atoms collide (hence there is an unfavourable conformation for those particular ϕ, ψ values). |
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