User:Karsten Theis/turns

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Line 331: Line 331:
<jmol>
<jmol>
<jmolButton>
<jmolButton>
-
<script>rphi2 = -60 - angle({67.C},{68.N},{68.CA},{68.C});rotate branch {68.CA} {68.N} @rphi2;rpsi2 = -30 - angle({68.N},{68.CA},{68.C},{69.N});rotate branch {68.C} {68.CA}@rpsi2;rphi3 = -90 - angle({68.C},{69.N},{69.CA},{69.C});rotate branch {69.N} {69.CA} @rphi3;rpsi3 = 0 - angle({69.N},{69.CA},{69.C},{70.N});rotate branch {69.CA} {69.C} @rpsi3; set echo top center; echo "Type I"</script>
+
<script>rphi2 = -60 - angle({67.C},{68.N},{68.CA},{68.C});rotate branch {68.CA} {68.N} @rphi2;rpsi2 = -30 - angle({68.N},{68.CA},{68.C},{69.N});rotate branch {68.C} {68.CA}@rpsi2;rphi3 = -90 - angle({68.C},{69.N},{69.CA},{69.C});rotate branch {69.N} {69.CA} @rphi3;rpsi3 = 0 - angle({69.N},{69.CA},{69.C},{70.N});rotate branch {69.CA} {69.C} @rpsi3; draw rama; set echo top center; echo "Type I; color echo white"</script>
<text>Type I</text>
<text>Type I</text>
</jmolButton>
</jmolButton>
</jmol> <jmol>
</jmol> <jmol>
<jmolButton>
<jmolButton>
-
<script>rphi2 = -57 - angle({67.C},{68.N},{68.CA},{68.C});rotate branch {68.CA} {68.N} @rphi2;rpsi2 = -47 - angle({68.N},{68.CA},{68.C},{69.N});rotate branch {68.C} {68.CA}@rpsi2;rphi3 = -57 - angle({68.C},{69.N},{69.CA},{69.C});rotate branch {69.N} {69.CA} @rphi3;rpsi3 = -47 - angle({69.N},{69.CA},{69.C},{70.N});rotate branch {69.CA} {69.C} @rpsi3; echo "alpha helix"</script>
+
<script>rphi2 = -57 - angle({67.C},{68.N},{68.CA},{68.C});rotate branch {68.CA} {68.N} @rphi2;rpsi2 = -47 - angle({68.N},{68.CA},{68.C},{69.N});rotate branch {68.C} {68.CA}@rpsi2;rphi3 = -57 - angle({68.C},{69.N},{69.CA},{69.C});rotate branch {69.N} {69.CA} @rphi3;rpsi3 = -47 - angle({69.N},{69.CA},{69.C},{70.N});rotate branch {69.CA} {69.C} @rpsi3; draw rama; echo "alpha helix"</script>
<text>(alpha helix)</text>
<text>(alpha helix)</text>
</jmolButton>
</jmolButton>
</jmol> <jmol>
</jmol> <jmol>
<jmolButton>
<jmolButton>
-
<script>rphi2 = -49 - angle({67.C},{68.N},{68.CA},{68.C});rotate branch {68.CA} {68.N} @rphi2;rpsi2 = -26 - angle({68.N},{68.CA},{68.C},{69.N});rotate branch {68.C} {68.CA}@rpsi2;rphi3 = -49 - angle({68.C},{69.N},{69.CA},{69.C});rotate branch {69.N} {69.CA} @rphi3;rpsi3 = -26 - angle({69.N},{69.CA},{69.C},{70.N});rotate branch {69.CA} {69.C} @rpsi3; echo "3-10 helix"</script>
+
<script>rphi2 = -49 - angle({67.C},{68.N},{68.CA},{68.C});rotate branch {68.CA} {68.N} @rphi2;rpsi2 = -26 - angle({68.N},{68.CA},{68.C},{69.N});rotate branch {68.C} {68.CA}@rpsi2;rphi3 = -49 - angle({68.C},{69.N},{69.CA},{69.C});rotate branch {69.N} {69.CA} @rphi3;rpsi3 = -26 - angle({69.N},{69.CA},{69.C},{70.N});rotate branch {69.CA} {69.C} @rpsi3; draw rama; echo "3-10 helix"</script>
<text>(3-10 helix)</text>
<text>(3-10 helix)</text>
</jmolButton>
</jmolButton>
</jmol> <jmol>
</jmol> <jmol>
<jmolButton>
<jmolButton>
-
<script>rphi2 = -140 - angle({67.C},{68.N},{68.CA},{68.C});rotate branch {68.CA} {68.N} @rphi2;rpsi2 = 130 - angle({68.N},{68.CA},{68.C},{69.N});rotate branch {68.C} {68.CA}@rpsi2;rphi3 = -140 - angle({68.C},{69.N},{69.CA},{69.C});rotate branch {69.N} {69.CA} @rphi3;rpsi3 = 130 - angle({69.N},{69.CA},{69.C},{70.N});rotate branch {69.CA} {69.C} @rpsi3; echo "beta strand"</script>
+
<script>rphi2 = -140 - angle({67.C},{68.N},{68.CA},{68.C});rotate branch {68.CA} {68.N} @rphi2;rpsi2 = 130 - angle({68.N},{68.CA},{68.C},{69.N});rotate branch {68.C} {68.CA}@rpsi2;rphi3 = -140 - angle({68.C},{69.N},{69.CA},{69.C});rotate branch {69.N} {69.CA} @rphi3;rpsi3 = 130 - angle({69.N},{69.CA},{69.C},{70.N});rotate branch {69.CA} {69.C} @rpsi3; draw rama; echo "beta strand"</script>
<text>(beta strand)</text>
<text>(beta strand)</text>
</jmolButton>
</jmolButton>
</jmol> <jmol>
</jmol> <jmol>
<jmolButton>
<jmolButton>
-
<script>rphi2 = 60 - angle({67.C},{68.N},{68.CA},{68.C});rotate branch {68.CA} {68.N} @rphi2;rpsi2 = 30 - angle({68.N},{68.CA},{68.C},{69.N});rotate branch {68.C} {68.CA}@rpsi2;rphi3 = 90 - angle({68.C},{69.N},{69.CA},{69.C});rotate branch {69.N} {69.CA} @rphi3;rpsi3 = 0 - angle({69.N},{69.CA},{69.C},{70.N});rotate branch {69.CA} {69.C} @rpsi3; echo "Type I prime"</script>
+
<script>rphi2 = 60 - angle({67.C},{68.N},{68.CA},{68.C});rotate branch {68.CA} {68.N} @rphi2;rpsi2 = 30 - angle({68.N},{68.CA},{68.C},{69.N});rotate branch {68.C} {68.CA}@rpsi2;rphi3 = 90 - angle({68.C},{69.N},{69.CA},{69.C});rotate branch {69.N} {69.CA} @rphi3;rpsi3 = 0 - angle({69.N},{69.CA},{69.C},{70.N});rotate branch {69.CA} {69.C} @rpsi3; draw rama; echo "Type I prime"</script>
<text>Type I prime</text>
<text>Type I prime</text>
</jmolButton>
</jmolButton>
</jmol> <jmol>
</jmol> <jmol>
<jmolButton>
<jmolButton>
-
<script>rphi2 = -60 - angle({67.C},{68.N},{68.CA},{68.C});rotate branch {68.CA} {68.N} @rphi2;rpsi2 = 120 - angle({68.N},{68.CA},{68.C},{69.N});rotate branch {68.C} {68.CA}@rpsi2;rphi3 = 80 - angle({68.C},{69.N},{69.CA},{69.C});rotate branch {69.N} {69.CA} @rphi3;rpsi3 = 0 - angle({69.N},{69.CA},{69.C},{70.N});rotate branch {69.CA} {69.C} @rpsi3; echo "Type II"</script>
+
<script>rphi2 = -60 - angle({67.C},{68.N},{68.CA},{68.C});rotate branch {68.CA} {68.N} @rphi2;rpsi2 = 120 - angle({68.N},{68.CA},{68.C},{69.N});rotate branch {68.C} {68.CA}@rpsi2;rphi3 = 80 - angle({68.C},{69.N},{69.CA},{69.C});rotate branch {69.N} {69.CA} @rphi3;rpsi3 = 0 - angle({69.N},{69.CA},{69.C},{70.N});rotate branch {69.CA} {69.C} @rpsi3; draw rama; echo "Type II"</script>
<text>Type II</text>
<text>Type II</text>
</jmolButton>
</jmolButton>
Line 373: Line 373:
</jmol> <jmol>
</jmol> <jmol>
<jmolButton>
<jmolButton>
-
<script>plot ramachandran; delay 5; model 1</script>
+
<script>save state ~one;
 +
plot ramachandran; delay 5; restore state ~one</script>
<text>rama</text>
<text>rama</text>
</jmolButton>
</jmolButton>

Revision as of 02:15, 12 February 2025

A beta turn is a secondary structure element consisting of four consecutive amino acids (or three consecutive peptide planes). The geometry of turns correspond to a change in the direction of the polypeptide backbone, with a short distance between the first and fourth alpha carbon.

Turns in 3D

                                                             Phi  2    3

                                                             Psi  2    3    

Drag the structure with the mouse to rotate

References

  1. de Brevern AG. A Perspective on the (Rise and Fall of) Protein β-Turns. Int J Mol Sci. 2022 Oct 14;23(20):12314. PMID:36293166 doi:10.3390/ijms232012314
  2. Wilmot CM, Thornton JM. Analysis and prediction of the different types of beta-turn in proteins. J Mol Biol. 1988 Sep 5;203(1):221-32. PMID:3184187 doi:10.1016/0022-2836(88)90103-9

Proteopedia Page Contributors and Editors (what is this?)

Karsten Theis

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