Ramachandran outlier: Difference between revisions
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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>. | 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>. | ||
''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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</StructureSection> | </StructureSection> | ||
== References == | == References == | ||
<references/> | <references/> | ||
Latest revision as of 18:24, 15 July 2018
Ramachandran outlierRamachandran outlier
The Ramachandran Plot was described on 1963 by Ramachandran, G.N.; Ramakrishnan, C.; Sasisekharan, V. [1]. See Dihedral/Index for explanations. 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. However, sometimes Ramachandran outliers might play a special role in function. See for example the case of Ser-200 in the structure . Let's draw its . The following green links require that you first click the above green link to Ramachandran Plot. Notice that the residues in are colored in yellow, the residues in colored in magenta, in blue and in white. At any time you may residues. Only Gly are allowed in the lower right quarter. If we from the plot, we will find the , with phi/psi angles considered non-favourable for Serine. 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 [2].
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ReferencesReferences
- ↑ RAMACHANDRAN GN, RAMAKRISHNAN C, SASISEKHARAN V. Stereochemistry of polypeptide chain configurations. J Mol Biol. 1963 Jul;7:95-9. PMID:13990617
- ↑ 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