Nearly all of the data points in the disallowed region in the above Figure are Gly points. For that reason Gly will frequently plot in the disallowed region of a general-case Ramachandran plot. The with Gly having φ and ψ values of +55 o and -116 o respectively, does not show the steric hindrance that the Glu-Ser-Ala had. 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. 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. The lower figure plots Ramachandran values for over a million general-case residues with resolution <2.0Å and backbone B-factor <30. 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. Most, if not all, of the points in the above plots for α-helix and β-sheet are in one of the core areas. If the Ser in the tripeptide has φ and ψ values of -57 o and -47 o which are in the core region in the lower left, the is rotated away from the Ala and is not in contact with the Ala. Observe that the data point 55 o, -116 o for Ser of the above tripeptide would fall in the lower right quadrant which contains only a disallowed region in ProCheck. The remaining areas are considered disallowed. The generous regions (not shown in the Figure) extend beyond the allowed regions. 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. Plots of some proteins contain a small third core region in the upper right quadrant. General-case Ramachandran plot for >1,000,000 high-quality datapoints The core regions (blue in the Figure) contain the most favorable combinations of φ and ψ and contain the greatest number of points. of three other sheet segments more clearly defines the area in which values for twisted sheets are located. The of this twisted sheet has points clustered about the values of φ= -130 o and ψ= +140 o which are the average values for twisted sheets. Most β-sheets in globular proteins are twisted sheets which do not have flat parallel pleats. of two other helical segments demonstrates that data from all three appear in one large cluster and that the helical segments can not be distinguished by the differences in their φ and ψ values.Ī two segment twisted β-sheet. The of this peptide has points clustered about the values of φ= -57 o and ψ= -47 o which are the average values for α-helices. are drawn on some of the peptide bonds to emphasize that in an α-helix the planar peptide bonds rotate about the axis of the helix. When viewing the helix on end, observe the open center of the helix. The shows the axis of the α-helix rotating in the y-plane. Two common examples of secondary structure are illustrated below. The different secondary structures can be distinguished by their range of φ and ψ values with the values of different secondary structures mapping to different regions of the Ramachandran plot. Secondary structures of a peptide are segments of the peptide that have ordered and repetitive structure, and the repetitive structure is due to a repetitive conformation of the residues and, ultimately, repetitive values of φ and ψ. 2 Plot regions limited by steric hindrance.The scene on the right is the Ramachandran plot of ribonuclease H. By making a Ramachandran plot, protein structural scientists can determine which torsional angles are permitted and can obtain insight into the structure of peptides. Many of the angle combinations, and therefore the conformations of residues, are not possible because of steric hindrance. The torsional angles of each residue in a peptide define the geometry of its attachment to its two adjacent residues by positioning its planar peptide bond relative to the two adjacent planar peptide bonds, thereby the torsional angles determine the conformation of the residues and the peptide. Plotting the torsional angles in this way graphically shows which combination of angles are possible. by plotting the φ values on the x-axis and the ψ values on the y-axis, as for the image at left. In sequence order, φ is the C(i-1),N(i),Ca(i),C(i) torsion angle and ψ is the N(i),Ca(i),C(i),N(i+1) torsion angle. The Ramachandran plot is a plot of the torsional angles - phi (φ)and psi (ψ) - of the residues (amino acids) contained in a peptide. Ramachandran plot and contours from 100,000 high-quality general-case datapoints
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