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Psi and Phi Angles
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<table width='400' align='right' cellpadding='5'><tr><td rowspan='2'> </td><td bgcolor='#eeeeee'><applet load='tetr_ala.mol' size='390' frame='true' align='right' scene ='Psi_and_Phi_Angles/First_view/2' caption='' /></td></tr><tr><td bgcolor='#eeeeee'><center>'''Peptide Segments Illustrating Secondary Structures'''<scene name='Psi_and_Phi_Angles/First_view/2'> (Initial scene)</scene></center></td></tr></table> | <table width='400' align='right' cellpadding='5'><tr><td rowspan='2'> </td><td bgcolor='#eeeeee'><applet load='tetr_ala.mol' size='390' frame='true' align='right' scene ='Psi_and_Phi_Angles/First_view/2' caption='' /></td></tr><tr><td bgcolor='#eeeeee'><center>'''Peptide Segments Illustrating Secondary Structures'''<scene name='Psi_and_Phi_Angles/First_view/2'> (Initial scene)</scene></center></td></tr></table> | ||
| - | We start with a tetrapeptide with a composition and sequence of LeuLeuIleTyr. As with any peptide the conformation of the <scene name='Psi_and_Phi_Angles/Backbone/1'>backbone</scene> is determined by the values of two torsional angles - psi (ψ) and phi (φ) of each peptide bond. | + | We start with a tetrapeptide with a composition and sequence of LeuLeuIleTyr. As with any peptide the conformation of the <scene name='Psi_and_Phi_Angles/Backbone/1'>backbone</scene> is determined by the values of two torsional angles - psi (ψ) and phi (φ) of each peptide bond. Since the amide bond connecting two amino acids has pi bond character, the six atoms that constitute a peptide bond all lie in the same plane. The <scene name='Psi_and_Phi_Angles/First__view_planes/1'>planes of two peptide bonds</scene> - the orange plane is the peptide bond connecting Tyr and Ile and the yellow one connects Ile and Leu - illustrate this phenomena. |
| - | + | == Determining values for psi (ψ) and phi (φ) == | |
| + | |||
| + | The <scene name='Psi_and_Phi_Angles/First__view_psi/1'>four atoms </scene>which constitute a ψ are an amide nitrogen, a carbonyl carbon, the &alapha;-carbon bonded to the carbonyl and the nitrogen of the next peptide bond. After toggling off spin and 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 angle, 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 clicking on the atoms.) The <scene name='Psi_and_Phi_Angles/First_view_phi/1'>four atoms</scene> making up φ are a carbonyl carbon, the connecting α carbon, an amide nitrogen and the next carbonyl carbon (all marked with green halos), 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='Psi_and_Phi_Angles/First_draw_rama/1'>Confirm</scene> the direction of rotation and the values of ψ and φ. | ||
== Determine values of other ψ and φ angles == | == Determine values of other ψ and φ angles == | ||
Revision as of 20:40, 6 October 2010
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We start with a tetrapeptide with a composition and sequence of LeuLeuIleTyr. As with any peptide the conformation of the is determined by the values of two torsional angles - psi (ψ) and phi (φ) of each peptide bond. Since the amide bond connecting two amino acids has pi bond character, the six atoms that constitute a peptide bond all lie in the same plane. The - the orange plane is the peptide bond connecting Tyr and Ile and the yellow one connects Ile and Leu - illustrate this phenomena.
Determining values for psi (ψ) and phi (φ)
The which constitute a ψ are an amide nitrogen, a carbonyl carbon, the &alapha;-carbon bonded to the carbonyl and the nitrogen of the next peptide bond. After toggling off spin and 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 angle, 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 clicking on the atoms.) The making up φ are a carbonyl carbon, the connecting α carbon, an amide nitrogen and the next carbonyl carbon (all marked with green halos), 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. the direction of rotation and the values of ψ and φ.
Determine values of other ψ and φ angles
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. that you obtain the correct values.
External Links
Extensive description of torsional angles.
