Ramachandran plot - Revision history

Christoph at 18:52, 26 July 2012

2012-07-26T18:52:33Z

Show changes

Christoph: /* External links */

2012-05-12T08:49:17Z

‎External links

Christoph at 08:43, 12 May 2012

2012-05-12T08:43:17Z

Christoph: /* Tetrapeptide conformations and solvent effects */

2009-02-04T23:08:10Z

‎Tetrapeptide conformations and solvent effects

Christoph at 23:03, 4 February 2009

2009-02-04T23:03:59Z

Christoph at 21:02, 4 February 2009

2009-02-04T21:02:05Z

Christoph: /* Beta turns */

2009-02-04T19:52:17Z

‎Beta turns

Christoph: /* Tetrapeptide conformations and solvent effects */

2007-08-23T03:38:20Z

‎Tetrapeptide conformations and solvent effects

Christoph: /* Tetrapeptide conformations and solvent effects */

2007-08-23T03:37:25Z

‎Tetrapeptide conformations and solvent effects

Christoph: /* Beta turns */

2007-08-23T03:32:08Z

‎Beta turns

@@ Line 254: / Line 254: @@
 ==External links==
 *[http://kinemage.biochem.duke.edu/ Richardson Lab and Kinemage homepage]
 *[http://www2.warwick.ac.uk/fac/sci/moac/currentstudents/peter_cock/python/ramachandran/calculate/  Calculating Ramachandran (phi/psi) Angles] &mdash; by Peter Cock
 *[http://www2.warwick.ac.uk/fac/sci/moac/currentstudents/peter_cock/r/ramachandran/ Drawing Ramachandran (phi/psi) plots for Proteins with R] &mdash; by Peter Cock
 *[http://www.genome.ad.jp/dbget/aaindex.html AAindex] &mdash; Amino acid indices and similarity matrices
 *[[wikipedia:Ramachandran plot]]
 [[Category:Crystallography]]

← Older revision		Revision as of 08:43, 12 May 2012
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	A '''Ramachandran plot''' (also known as a '''Ramachandran Map''' or a '''Ramachandran diagram''') is a way to visualize [[wikipedia:dihedral angle\|dihedral angle]]s φ against ψ of [[amino acid]] residues in protein structure. It shows the possible conformations of φ and ψ angles for a polypeptide.		A '''Ramachandran plot''' (also known as a '''Ramachandran Map''' or a '''Ramachandran diagram''') is a way to visualize [[wikipedia:dihedral angle\|dihedral angle]]s φ against ψ of [[amino acid]] residues in protein structure. It shows the possible conformations of φ and ψ angles for a polypeptide.
		+
		+	==Structure==
		+	Below are the backbone dihedral angles φ and ψ referred to throughout this article:<br clear="all"/>
		+	[[Image:Phi-psi.jpg]]

	== Phi/Psi and Residue Type ==		== Phi/Psi and Residue Type ==

@@ Line 107: / Line 107: @@
 || -170°
 || 130°
-|| -171145.25
+|| -171,145.25
 || 5.17
 || 362.96
@@ Line 120: / Line 120: @@
 || ±180°
 || 90°
-|| -171134.25
+|| -171,134.25
 || 5.25
 || 367.01
@@ Line 133: / Line 133: @@
 || 70°
 || ±180°
-|| -171135.31
+|| -171,135.31
 || 13.30
 || 368.45
@@ Line 146: / Line 146: @@
 || 70°
 || ±180°
-|| -171120.13
+|| -171,120.13
 || 13.82
 || 357.07
@@ Line 159: / Line 159: @@
 || 70°
 || ±180°
-|| -171127.50
+|| -171,127.50
 || 13.23
 |367.36

@@ Line 173: / Line 173: @@
 #A type I &beta;-turn conformation with &phi;<sub>1</sub> = -100° and &psi;<sub>1</sub> = -20° for Ala<sub>1</sub> residue where the 14-membered H-bond is absent. The Gly<sub>4</sub> residue was fixed at the same energetically favourable conformation as in 3 above.
-"A tetrapeptide can be classified into one of the above types if all four angles fall within 30° of the 'ideal' angles given in the table.<ref name=Wilmot1988>Wilmot CM, Thornton JM (1988). Analysis and prediction of the different types of beta-turn in proteins. ''J Mol Biol, 203:221-32''.</ref> Beta turns not fulfilling the requirements for one of the above turns are classified as 'other'. Many unclassifiable turns represent distortions of the the conventional turn types, lying just outside the standard limits. Therefore, the same authors showed that it is possible to increase the number of classifiable turns by allowing one of the four angles to deviate by as much as 45°.<ref name=Wilmot1990>Wilmot CM, Thornton JM (1990). Beta-turns and their distortions: a proposed new nomenclature. ''Protein Eng, 3:479-93''.</ref>"&mdash;Peter N. Robinson<ref name=Robinson>[http://www.charite.de/ch/medgen/compgen/ramachandran/ Ramachandran: A Java Program For Drawing Ramachandran Plots] (accessed: 2006-11-04)</ref>
+"A tetrapeptide can be classified into one of the above types if all four angles fall within 30° of the 'ideal' angles given in the table.<ref name=Wilmot1988>Wilmot CM, Thornton JM (1988). Analysis and prediction of the different types of beta-turn in proteins. ''J Mol Biol, 203:221-32''.</ref> Beta turns not fulfilling the requirements for one of the above turns are classified as 'other'. Many unclassifiable turns represent distortions of the the conventional turn types, lying just outside the standard limits. Therefore, the same authors showed that it is possible to increase the number of classifiable turns by allowing one of the four angles to deviate by as much as 45°.<ref name="Wilmot1990">Wilmot CM, Thornton JM (1990). "Beta-turns and their distortions: a proposed new nomenclature". ''Protein Eng, 3:479-93''.</ref>"&mdash;Peter N. Robinson<ref name="Robinson">[http://www.charite.de/ch/medgen/compgen/ramachandran/ Ramachandran: A Java Program For Drawing Ramachandran Plots] (accessed: 2006-11-04)</ref>
 ==Gamma turns==
@@ Line 180: / Line 208: @@
 {| align="center" style="border: 1px solid #999; background-color:#FFFFFF"
 |-
-! colspan="3" bgcolor="#EFEFEF" | '''Table 3: Gamma turn angles'''
+! colspan="3" bgcolor="#EFEFEF" | '''Table 4: Gamma turn angles'''
 |-align="center" style="color:#ffffff;background-color:#1188ee;"
 !Turn type

@@ Line 23: / Line 23: @@
 == This week's unusual Ramachandran plots ==
 Every week, Kleywegt and Jones (after updating their local copy of the PDB) check the Ramachandran plots of all protein chains. All chains that have 20 or more residues, and of which at least 10% are outliers are listed in this file: http://xray.bmc.uu.se/gerard/rama/ramathisweek.txt (Note that this list may include NMR and theoretical models.)
 == Beta turns ==
@@ Line 158: / Line 174: @@
 "A tetrapeptide can be classified into one of the above types if all four angles fall within 30° of the 'ideal' angles given in the table.<ref name=Wilmot1988>Wilmot CM, Thornton JM (1988). Analysis and prediction of the different types of beta-turn in proteins. ''J Mol Biol, 203:221-32''.</ref> Beta turns not fulfilling the requirements for one of the above turns are classified as 'other'. Many unclassifiable turns represent distortions of the the conventional turn types, lying just outside the standard limits. Therefore, the same authors showed that it is possible to increase the number of classifiable turns by allowing one of the four angles to deviate by as much as 45°.<ref name=Wilmot1990>Wilmot CM, Thornton JM (1990). Beta-turns and their distortions: a proposed new nomenclature. ''Protein Eng, 3:479-93''.</ref>"&mdash;Peter N. Robinson<ref name=Robinson>[http://www.charite.de/ch/medgen/compgen/ramachandran/ Ramachandran: A Java Program For Drawing Ramachandran Plots] (accessed: 2006-11-04)</ref>
 ==Calculation of ''E''<sub>solute</sub>==

@@ Line 28: / Line 28: @@
 The standard criteria for defining a beta turn are that a beta turn comprises four amino acid residues, whereby the distance between the first and the last alpha carbon is less than 7 Ångströms and the central two residues are not helical. Eight conventional turn types (I,I',II,II',VIa, VIb, VIII, and other) are defined according to the phi (&phi;) and psi (&psi;) torsion angles of the second and third residues.
-<div style="float:left; margin:0px 20px 20px 0px;">
+<div style="float:center; margin:0px 20px 20px 0px;">
 {| align="center" style="border: 1px solid #999; background-color:#FFFFFF"
 |-
@@ Line 55: / Line 55: @@
 <div align="center">Source: Wilmot, ''et al.''<ref name=Wilmot1988>Wilmot CM, Thornton JM (1988). Analysis and prediction of the different types of beta-turn in proteins. ''J Mol Biol, 203:221-32''.</ref></div>
 </div>
 ===Tetrapeptide conformations and solvent effects===
 ''Note: The following section is for the tetrapeptide, HCO-L-Ala-L-Pro-Gly-Gly-OMe.''
@@ Line 63: / Line 64: @@
 The Table 2 uses [[wikipedia:CNDO/2|CNDO/2]] molecular orbital total energies in kcal/mole, molecular dipole moments in [[wikipedia:Debye|Debyes]], and expose molecular surface areas in Å<sup>2</sup>.
-<div style="float:left; margin:0px 20px 20px 0px;">
+<div style="float:center; margin:0px 20px 20px 0px;">
 {| align="center" style="border: 1px solid #999; background-color:#FFFFFF"
 |-
@@ Line 148: / Line 149: @@
 <div align="center">Source: Renugopalakrishnan, ''et al.''<ref name="Renugopalakrishnan1981">Renugopalakrishnan V, Khaled MA, Rapaka RS, Urry DW (1981). The tetrapeptide, HCO-L-Ala-L-Pro-Gly-Gly-OMe: conformations and solvent effects. ''Biomolecular Structure, Conformation, Function, and Evolution - Volume 2''. Pergamon Press - Oxford.</ref></div>
 </div>
 where,
 #Prefered ''in vacuo'' conformation of HCO-APGG-OMe with a type II &beta;-turn between Ala<sub>1</sub> C=O and Gly<sub>4</sub> NH and a 14-membered H-bonded ring between Gly<sub>4</sub> C=O and Ala<sub>1</sub> NH.

@@ Line 58: / Line 58: @@
 ''Note: The following section is for the tetrapeptide, HCO-L-Ala-L-Pro-Gly-Gly-OMe.''
 <br clear="all"/>
-   &phi;<sub>1</sub>     &phi;<sub>1</sub>         &phi;<sub>2</sub>    &phi;<sub>2</sub>         &phi;<sub>3</sub>    &phi;<sub>3</sub>         &phi;<sub>4</sub>     &phi;<sub>4</sub>
+          &phi;<sub>1</sub>     &phi;<sub>1</sub>         &phi;<sub>2</sub>    &phi;<sub>2</sub>         &phi;<sub>3</sub>    &phi;<sub>3</sub>         &phi;<sub>4</sub>     &phi;<sub>4</sub>
-  N----Ca----C'----N----Ca----C'----N----Ca----C'----N----Ca----C'----O----CH3
+  HCO----N----Ca----C'----N----Ca----C'----N----Ca----C'----N----Ca----C'----O----CH3
-      Ala<sub>1</sub>             Pro<sub>2</sub>             Gly<sub>3</sub>             Gly<sub>4</sub>
+             Ala<sub>1</sub>             Pro<sub>2</sub>             Gly<sub>3</sub>             Gly<sub>4</sub>
 The Table 2 uses [[wikipedia:CNDO/2|CNDO/2]] molecular orbital total energies in kcal/mole, molecular dipole moments in [[wikipedia:Debye|Debyes]], and expose molecular surface areas in Å<sup>2</sup>.