Dihedral/Dihedral angles in proteins

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m (Dihedral angles in proteins moved to Dihedral/Dihedral angles in proteins: relocating to aggregate several resources as sub-pages)
 
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{{Theoretical_model}}
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<table>
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==Dihedral angles in proteins: Phi and Psi==
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<tr>
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<StructureSection load='1iy4_34-36.pdb' size='400' side='right' caption='a tripeptide' scene='61/611457/Initial_display/1'>
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<td>
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The model on the right is a tripeptide (Trp<sub>34</sub>&ndash;Glu<sub>35</sub>&ndash;Ser<sub>36</sub> within the protein lysozyme).
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<div style="height:500px; overflow:auto; padding-right:1ex;">
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This page illustrates the meaning of phi (&#x03D5;) and psi (&#x03C8;) angles, both around the alpha carbon of the central residue (Glu<sub>35</sub>).
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The model displayed on the right is a tripeptide (Trp<sub>34</sub>&ndash;Glu<sub>35</sub>&ndash;Ser<sub>36</sub> within the protein lysozyme).
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This page illustrates the meaning of '''phi (&#x03D5;)''' and '''psi (&#x03C8;)''' 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).
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They are also called '''''torsion angles''''', meaning the torsion or rotation around a 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.
 
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Bright magenta cylinders are displayed where neighbour atoms collide (hence there is an unfavourable conformation for those ϕ, ψ values).
 
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The scene does not work well:
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'''phi (&#x03D5;)''' is the angle between these two planes:
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<scene name='61/611457/Phi_rotation/2'>Animate changes in the phi angle</scene>.
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* plane defined by C<sub>i&minus;1</sub>, N<sub>i</sub> and C<sup>&alpha;</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>
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* plane defined by N<sub>i</sub>, C<sup>&alpha;</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>
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Therefore ϕ means rotation around the N—C<sup>&alpha;</sup> bond.
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</StructureSection>
 
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'''psi (&#x03C8;)''' is the angle between these two planes:
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* plane defined by N<sub>i</sub>, C<sup>&alpha;</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>
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* plane defined by C<sup>&alpha;</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>
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Therefore ψ means rotation around the C<sup>&alpha;</sup>—C bond.
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Let's try with a tag:
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:Note that planes 2 and 3 coincide.
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:In all these, "C" means the carboxylic carbon, forming the amide or peptide bond with the N. Peptide bonds are displayed in black.
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You can run '''animations''' that continuously rotate the model changing one of the angles.
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First, select one of the angles:
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<big>
<jmol>
<jmol>
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<jmolApplet>
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<jmolRadioGroup>
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<float>right</float>
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<item>
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<size>400</size>
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<script>zap; set echo middle center; echo please wait...; refresh; script /wiki/images/c/ce/Phi-rot_uni.spt; set measurements 0.25;</script>
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<color>white</color>
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<text>ϕ</text>
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<uploadedFileContents>1iy4_34-36.pdb</uploadedFileContents>
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</item>
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<pspeed>2</pspeed>
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<item>
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</jmolApplet>
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<script>zap; set echo middle center; echo please wait...; refresh; script /wiki/images/2/22/Psi-rot_uni.spt; set measurements 0.25; e_legend; select all;labels off;</script>
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<text>ψ</text>
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</item>
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</jmolRadioGroup>
</jmol>
</jmol>
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</big>
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After the model has loaded,
<jmol>
<jmol>
<jmolButton>
<jmolButton>
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<script>script wiki/images/c/ce/Phi-rot_uni.spt;
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<text>play/pause</text>
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</script>
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<script>if(_animating) {frame pause} else {frame play}</script>
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<text>animation of rotation</text>
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</jmolButton>
</jmolButton>
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</jmol>
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</jmol>
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== References ==
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'''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).
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<references/>
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</div>
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</td>
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<td>
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<jmol>
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<jmolApplet>
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<size>500</size>
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<color>white</color>
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<uploadedFileContents>1iy4_34-36.pdb</uploadedFileContents>
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<pspeed>8</pspeed>
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<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>
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</jmolApplet>
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</jmol>
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</td>
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</tr>
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</table>

Current revision

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.


phi (ϕ) is the angle between these two planes:

  • plane defined by Ci−1, Ni and Cαi
    displayed as (1)
  • plane defined by Ni, Cαi and Ci
    displayed as (2)

Therefore ϕ means rotation around the N—Cα bond.


psi (ψ) is the angle between these two planes:

  • plane defined by Ni, Cαi and Ci
    displayed as (3)
  • plane defined by Cαi, Ci and Ni+1
    displayed as (4)

Therefore ψ means rotation around the Cα—C bond.

Note that planes 2 and 3 coincide.
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.

First, select one of the angles:

After the model has loaded,

Clashes: magenta cylinders are displayed where neighbour atoms collide (hence there is an unfavourable conformation for those particular ϕ, ψ values).

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

Angel Herraez

Retrieved from "http://52.214.119.220/wiki/index.php/Dihedral/Dihedral_angles_in_proteins"
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