Dihedral/Dihedral angles in proteins

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
(adjusting position of the legend; text highlights)
(a simpler interface)
Line 22: Line 22:
:In all these, "C" means the carboxylic carbon, forming the amide or peptide bond with the N. Peptide bonds are displayed in black.
: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.-->
+
 +
First, select one of the angles:
 +
<big>
<jmol>
<jmol>
-
<jmolButton>
+
<jmolRadioGroup>
-
<text>Prepare ϕ</text>
+
<item>
-
<script>zap; set echo middle center; echo please wait...; refresh; script /wiki/images/c/ce/Phi-rot_uni.spt; e_legend; select all;labels off;</script>
+
<script>zap; set echo middle center; echo please wait...; refresh; script /wiki/images/c/ce/Phi-rot_uni.spt</script>
-
</jmolButton>
+
<text>ϕ</text>
 +
</item>
 +
<item>
 +
<script>zap; set echo middle center; echo please wait...; refresh; script /wiki/images/2/22/Psi-rot_uni.spt; e_legend; select all;labels off;</script>
 +
<text>ψ</text>
 +
</item>
 +
</jmolRadioGroup>
</jmol>
</jmol>
-
animation, and then:
+
</big>
-
<jmol>
+
-
<jmolButton>
+
-
<text>play/pause</text>
+
-
<script>if(_animating) {frame pause} else {frame play}</script>
+
-
</jmolButton>
+
-
</jmol>
+
-
<jmol>
+
After the model has loaded,
-
<jmolButton>
+
-
<text>Prepare ψ</text>
+
-
<script>zap; set echo middle center; echo please wait...; refresh; script /wiki/images/2/22/Psi-rot_uni.spt; e_legend; select all;labels off;</script>
+
-
</jmolButton>
+
-
</jmol>
+
-
animation, and then:
+
<jmol>
<jmol>
<jmolButton>
<jmolButton>

Revision as of 18:50, 8 September 2016

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"
Personal tools