Ramachandran Plot: Difference between revisions
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== Plot regions limited by steric hindrance == | == Plot regions limited by steric hindrance == | ||
<table width='400' align='right' cellpadding='5'><tr><td rowspan='2'> </td><td bgcolor='#eeeeee'><applet load='1MBO' size='390' frame='true' align='right' scene ='Ramachandran_Plots/Tripeptide_disallowed/1' caption='' /></td></tr><tr><td bgcolor='#eeeeee'><center>'''Tripeptides Illustrating the Presence or Absence of Steric Hindrance'''<scene name='Ramachandran_Plots/Tripeptide_disallowed/1'> (Initial scene)</scene></center></td></tr></table> | <table width='400' align='right' cellpadding='5'><tr><td rowspan='2'> </td><td bgcolor='#eeeeee'><applet load='1MBO' size='390' frame='true' align='right' scene ='Ramachandran_Plots/Tripeptide_disallowed/1' caption='' /></td></tr><tr><td bgcolor='#eeeeee'><center>'''Tripeptides Illustrating the Presence or Absence of Steric Hindrance'''<scene name='Ramachandran_Plots/Tripeptide_disallowed/1'> (Initial scene)</scene></center></td></tr></table> | ||
Most combinations of ψ and φ are sterically forbidden, as illustrated in the tripeptide, Glu-Ser-Ala. With Ser having values of ψ = -116<sup>o</sup> and φ = 55<sup>o</sup> the Ser side chain is in contact with the Ala, colored blue. In plots of native peptides the data points will form clusters in the several areas in which steric hindrance does not occur. These regions are illustrated in the Figure on the left. The core regions (blue in the Figure) contain the most favorable combinations of ψ and φ and contain the greatest number of points.[[Image:Ramaplot.png|thumb|left|Figure: Ramachandran Plot showing two core regions (blue) and four allowed regions (green).]] Plots of some proteins contain a small third core region in the upper right quadrant. The allowed regions (green in the Figure) can be located around the core regions or can be unassociated with a core region, but they contain fewer data points than the core regions. The generous regions (not shown in the Figure)extend beyond the allowed regions. The remaining areas are the disallowed regions. Observe that the data point -116<sup>o</sup>, 55<sup>o</sup> for Ser of the above tripeptide would fall in the lower right quadrant which contains only a disallowed region. If the Ser in the tripeptide has ψ and φ values of -47<sup>o</sup> and -57<sup>o</sup> which are in the core region in the lower left, the <scene name='Ramachandran_Plots/Tripeptide_allowed/1'>Ser side chain</scene> is rotated away from the Ala and is not in contact with the Ala. Most, if not all, of the points in the above plots for α-helix and β-sheet are in one of the core areas.<p> | Most combinations of ψ and φ are sterically forbidden, as illustrated in the tripeptide, '''<font color=limegreen>Glu</font>-Ser-<font color=blue>Ala</font>'''. With Ser having values of ψ = -116<sup>o</sup> and φ = 55<sup>o</sup> the Ser side chain is in contact with the Ala, colored blue. In plots of native peptides the data points will form clusters in the several areas in which steric hindrance does not occur. These regions are illustrated in the Figure on the left. The core regions (blue in the Figure) contain the most favorable combinations of ψ and φ and contain the greatest number of points.[[Image:Ramaplot.png|thumb|left|Figure: Ramachandran Plot showing two core regions (blue) and four allowed regions (green).]] Plots of some proteins contain a small third core region in the upper right quadrant. The allowed regions (green in the Figure) can be located around the core regions or can be unassociated with a core region, but they contain fewer data points than the core regions. The generous regions (not shown in the Figure)extend beyond the allowed regions. The remaining areas are the disallowed regions. Observe that the data point -116<sup>o</sup>, 55<sup>o</sup> for Ser of the above tripeptide would fall in the lower right quadrant which contains only a disallowed region. If the Ser in the tripeptide has ψ and φ values of -47<sup>o</sup> and -57<sup>o</sup> which are in the core region in the lower left, the <scene name='Ramachandran_Plots/Tripeptide_allowed/1'>Ser side chain</scene> is rotated away from the Ala and is not in contact with the Ala. Most, if not all, of the points in the above plots for α-helix and β-sheet are in one of the core areas.<p> | ||
=== Glycine === | === Glycine === | ||