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| A Ramachandran plot has the values of psi (ψ) torsional angles on the y-axis and the values of phi (φ)torsional angles on the x-axis. More [http://en.wikipedia.org/wiki/Ramachandran_plot detailed description]. | | A Ramachandran plot has the values of psi (ψ) torsional angles on the y-axis and the values of phi (φ)torsional angles on the x-axis. More [http://en.wikipedia.org/wiki/Ramachandran_plot detailed description]. |
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| ==Torsional (dihedral) angles==
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| <applet load='tetr_ala.mol' size='300' frame='true' align='right' scene ='User:Karl_Oberholser/Ramachandran_Plots/First_view/1' caption='Tetrapeptide' />[http://en.wikipedia.org/wiki/Torsional_angle Extensive description] of torsional angles. Each peptide bond has two torsional angles - psi (ψ) and phi (φ) - which determine the geometry about the peptide bond. A tetrapeptide is used to describe and illustrate these two angles.
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| <scene name='User:Karl_Oberholser/Ramachandran_Plots/First_view_planes/2'>Draw planes </scene> of two peptide bonds. The <scene name='User:Karl_Oberholser/Ramachandran_Plots/First_view_halos_psi/6'>four atoms </scene>making up ψ remain translucent, and the remaining atoms become transparent. After rotating the structure so that you can clearly see that you are not clicking on a transparent atom, determine and display the numerical value of ψ by double clicking on a nitrogen of the peptide bond, single clicking on the next two atoms and then double clicking on the second nitrogen. (If the structure rotates in the course of clicking on the atoms or if you encounter some other problem, re-click on the green link 'four atoms' and restart the clicking on the atoms.) The <scene name='User:Karl_Oberholser/Ramachandran_Plots/First_view_halos_phi/5'>four atoms</scene> making up φ remain translucent, and the remaining atoms become transparent. After rotating the structure so that the four atoms can be clearly seen, measure and display the numerical value of φ using the technique described above. <scene name='User:Karl_Oberholser/Ramachandran_Plots/First_view_draw_rama/5'>Confirm</scene> the direction of rotation and the values of ψ and φ.
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| == Determine values of other ψ and φ angles ==
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| <scene name='User:Karl_Oberholser/Ramachandran_Plots/First_view_planes2/4'>Draw the planes</scene> of two other peptide bonds, and then using the technique described above identify the atoms contained in and the numerical values of the ψ and φ angles of the α-carbon connected to these two planes. <scene name='User:Karl_Oberholser/Ramachandran_Plots/First_view_draw_rama2/2'>Confirm</scene> that you obtain the correct values.
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| == Plots of segments of [http://en.wikipedia.org/wiki/Alpha_helix α-helix] == | | == Plots of segments of [http://en.wikipedia.org/wiki/Alpha_helix α-helix] == |
