Ramachandran outlier

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(fixing the scripts and a better label for phi,psi of Ser)
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The [[Ramachandran Plot]] was described on 1963 by Ramachandran, G.N.; Ramakrishnan, C.; Sasisekharan, V. <ref>pmid 13990617</ref>
The [[Ramachandran Plot]] was described on 1963 by Ramachandran, G.N.; Ramakrishnan, C.; Sasisekharan, V. <ref>pmid 13990617</ref>
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Ramachandran outlier are those aminoacids with non favorable dihedral angles, and Ramachandran plot is a powerful tool for making those evident. Most of the times, Ramachandran outliers are a consequence of mistakes during the data processing.
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Ramachandran outliers are those amino acids with non favorable dihedral angles, and Ramachandran plot is a powerful tool for making those evident. Most of the times, Ramachandran outliers are a consequence of mistakes during the data processing.
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However, sometimes, Ramachandran outliers might play a special role in the structure function. See for example the case of Ser-200 in the structure <scene name='76/762493/1ea5_color_sec_struct/1'>1ea5</scene>. Let's draw the <jmol><jmolLink><script>plot ramachandran</script><text>Ramachandran Plot</text></jmolLink></jmol>.
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However, sometimes, Ramachandran outliers might play a special role in the structure function. See for example the case of Ser-200 in the structure <scene name='76/762493/1ea5_color_sec_struct/1'>1ea5</scene>. Let's draw its <jmol><jmolLink><script>plot ramachandran</script><text>Ramachandran Plot</text></jmolLink></jmol>.
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Notice that the residues in <jmol><jmolLink><script>display sheet</script><text>beta sheets</text></jmolLink></jmol> are colored in yellow, the residues in <jmol><jmolLink><script>display helix</script><text>alpha helix</text></jmolLink></jmol> colored in magenta, <jmol><jmolLink><script>display turn</script><text>beta turn</text></jmolLink></jmol> in blue and <jmol><jmolLink><script>display all; hide sheet; hide helix</script><text>others</text></jmolLink></jmol> in white. At any time you may <jmol><jmolLink><script>display all</script><text>display all</text></jmolLink></jmol> residues.
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Notice that the residues in <jmol><jmolLink><script>display sheet</script><text>beta sheets</text></jmolLink></jmol> are colored in yellow, the residues in <jmol><jmolLink><script>display helix</script><text>alpha helix</text></jmolLink></jmol> colored in magenta, <jmol><jmolLink><script>display turn</script><text>beta turn</text></jmolLink></jmol> in blue and <jmol><jmolLink><script>display all; hide sheet,helix,turn;</script><text>others</text></jmolLink></jmol> in white. At any time you may <jmol><jmolLink><script>display all</script><text>display all</text></jmolLink></jmol> residues.
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Only Gly are allowed in the lower right-hand side quarter. If we <jmol><jmolLink><script>display all; hide Gly</script><text>hide Gly</text></jmolLink></jmol> from the plot, will find the <jmol><jmolLink><script>select [SER]200:A;color selectionHalos green;selectionHalos on;label "%phi %psi"</script><text>Ser 200</text></jmolLink></jmol>.
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Only Gly are allowed in the lower right-hand side quarter. If we <jmol><jmolLink><script>display all; hide Gly</script><text>hide Gly</text></jmolLink></jmol> from the plot, will find the <jmol><jmolLink><script>select [SER]200:A;color selectionHalos green;selectionHalos on; label "\u03C6 = %5.1[phi]\uB0|\u03C8 = %5.1[psi]\uB0";</script><text>Ser 200</text></jmolLink></jmol>.

Revision as of 10:58, 15 August 2017

Ramachandran outlier

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References

  1. ↑ RAMACHANDRAN GN, RAMAKRISHNAN C, SASISEKHARAN V. Stereochemistry of polypeptide chain configurations. J Mol Biol. 1963 Jul;7:95-9. PMID:13990617

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Jaime Prilusky, Eric Martz, Angel Herraez

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