Ramachandran outlier

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==Ramachandran outlier==
==Ramachandran outlier==
<StructureSection load='' size='340' side='right' caption='' scene='76/762493/1ea5_color_sec_struct/3'>
<StructureSection load='' size='340' side='right' caption='' scene='76/762493/1ea5_color_sec_struct/3'>
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The [[Ramachandran Plot]] was described on 1963 by Ramachandran, G.N.; Ramakrishnan, C.; Sasisekharan, V. <ref>pmid 13990617</ref>
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The [[Ramachandran Plot]] was described on 1963 by Ramachandran, G.N.; Ramakrishnan, C.; Sasisekharan, V. <ref>pmid 13990617</ref>. See [[Dihedral/Index]] for explanations.
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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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Ramachandran outliers are those amino acids with non-favorable dihedral angles, and the Ramachandran plot is a powerful tool for making those evident. Most of the time, 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/3'>1ea5</scene>. Let's draw its <jmol><jmolLink><script>calculate structure;select protein;cartoon only;color structure;plot ramachandran</script><text>Ramachandran Plot</text></jmolLink></jmol>.
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However, sometimes Ramachandran outliers might play a special role in function. See for example the case of Ser-200 in the structure <scene name='76/762493/1ea5_color_sec_struct/3'>1ea5</scene>. Let's draw its <jmol><jmolLink><script>calculate structure;select protein;cartoon only;color structure;plot ramachandran</script><text>Ramachandran Plot</text></jmolLink></jmol>.
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''The following green links require that you '''first''' click the above green link to Ramachandran Plot.''
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.
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 "\u03C6 =\u20%5.1[phi]\uB0|\u03C8 =\u20%5.1[psi]\uB0";set labelOffset 10 0;</script><text>Ser 200</text></jmolLink></jmol>, with angle values considered non favourable for a Serine .
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Only Gly are allowed in the lower right quarter. If we <jmol><jmolLink><script>display all; hide Gly</script><text>hide Gly</text></jmolLink></jmol> from the plot, we will find the <jmol><jmolLink><script>select [SER]200:A;color selectionHalos green;selectionHalos on;label "\u03C6 =\u20%5.1[phi]\uB0|\u03C8 =\u20%5.1[psi]\uB0";set labelOffset 10 0;</script><text>Ser 200</text></jmolLink></jmol>, with phi/psi angles considered non-favourable for Serine.
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However, in this case a misplaced residue (Ser 200) seems to play an important role in the function of this structure, leading to the alpha/beta fold <ref>pmid 1409539</ref>
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However, in this case, a Ramachandran-misplaced residue (Ser 200) seems to play an important role in the function of this structure, a member of the alpha/beta hydrolase fold <ref>pmid 1409539</ref>.
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</StructureSection>
</StructureSection>
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== References ==
== References ==
<references/>
<references/>

Current revision

Ramachandran outlier

Drag the structure with the mouse to rotate

References

  1. ↑ RAMACHANDRAN GN, RAMAKRISHNAN C, SASISEKHARAN V. Stereochemistry of polypeptide chain configurations. J Mol Biol. 1963 Jul;7:95-9. PMID:13990617
  2. ↑ Ollis DL, Cheah E, Cygler M, Dijkstra B, Frolow F, Franken SM, Harel M, Remington SJ, Silman I, Schrag J, et al.. The alpha/beta hydrolase fold. Protein Eng. 1992 Apr;5(3):197-211. PMID:1409539

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