Ramachandran Plot: Difference between revisions
added image, changed order to phi,psi, definition, etc |
→Plot regions limited by steric hindrance: Adding modern validation, image; fix order of phi,psi, etc |
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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, '''<font color=limegreen>Glu</font>-Ser-<font color=blue>Ala</font>'''. With Ser having values of & | 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 φ = 55<sup>o</sup> and ψ = -116<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, according to our understanding in the early 1990's when the first validation programs such as ProCheck were developed [[Image:Ramaplot.png|thumb|left|Figure: Ramachandran Plot showing two core regions (blue) and four allowed regions (green).]] The core regions (blue in the Figure) contain the most favorable combinations of ψ and φ and contain the greatest number of points. 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 considered disallowed. Observe that the data point 55<sup>o</sup>, -116<sup>o</sup> for Ser of the above tripeptide would fall in the lower right quadrant which contains only a disallowed region in ProCheck. 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> | ||
[[Image:Ramachandran_general-case_data_and_contours_T8000.png|thumb|left|General-case Ramachandran plot for >1,000,000 high-quality datapoints]] | |||
Since the 1990's, great expansion in the number and quality of macromolecular crystal structures and advances in methodology have greatly improved understanding of the energetically favored, allowed, and truly disallowed conformations of proteins and nucleic acids. The lower figure plots Ramachandran values for over a million general-case residues with resolution <2.0Å and backbone B-factor <30. Over half the plot is entirely empty, but there are further clusters evident that have moderate population and presumably have somewhat unfavorable energy but are possible; this actually includes the region near +55, -116, which is found in one type of beta turn. | |||
=== Glycine === | === Glycine === | ||
Since Gly has only a hydrogen as a side chain, steric hindrance is not as likely to occur as & | Since Gly has only a hydrogen as a side chain, steric hindrance is not as likely to occur as φ and ψ are rotated through a series of values. The <scene name='Ramachandran_Plots/Tripeptide_gly/1'>tripeptide Glu-Gly-Ala</scene> with Gly having φ and ψ values of +55<sup>o</sup> and -116<sup>o</sup> respectively, does not show the steric hindrance that the Glu-Ser-Ala had. For that reason Gly will frequently plot in the disallowed region of a general-case Ramachandran plot. Nearly all of the data points in the disallowed region in the above Figure are Gly points. Therefore modern Ramachandran criteria use separate functions for subsets of the amino-acids that have different local steric-hindrance properties. </p> | ||
===Functionally relevant residues=== | ===Functionally relevant residues=== | ||