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Psi and Phi Angles
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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, an α-carbon and a second nitrogen . 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). 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/2'>Confirm</scene> the direction of rotation and the values of ψ and 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, an α-carbon and a second nitrogen . 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). 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/2'>Confirm</scene> the direction of rotation and the values of ψ and φ. | ||
| - | <scene name='Psi_and_Phi_Angles/First_view_planes2/1'>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='Psi_and_Phi_Angles/Second_draw_rama/ | + | <scene name='Psi_and_Phi_Angles/First_view_planes2/1'>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='Psi_and_Phi_Angles/Second_draw_rama/2'>Confirm</scene> that you obtain the correct values. |
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<table width='400' align='right' cellpadding='5'><tr><td rowspan='2'> </td><td bgcolor='#eeeeee'><applet load='LeuLeuIleTyr_2models.pdb' size='390' frame='true' align='right' scene ='Psi_and_Phi_Angles/Model_1_ile_angles/1' caption='' /></td></tr><tr><td bgcolor='#eeeeee'><center>'''Tetrapeptide: Leu-Leu-Ile-Tyr'''<scene name='Psi_and_Phi_Angles/Model_1_ile_angles/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='LeuLeuIleTyr_2models.pdb' size='390' frame='true' align='right' scene ='Psi_and_Phi_Angles/Model_1_ile_angles/1' caption='' /></td></tr><tr><td bgcolor='#eeeeee'><center>'''Tetrapeptide: Leu-Leu-Ile-Tyr'''<scene name='Psi_and_Phi_Angles/Model_1_ile_angles/1'> (Initial scene)</scene></center></td></tr></table> | ||
| - | The initial scene shows psi and phi values for Ile. Notice the three colored triangular planes. The yellow plane serves as the references in measuring the two angles. The purple plane is part of planar peptide bond between Tyr and Ile, and the orange one is part of the planar bond between Ile and Leu. | + | The initial scene shows psi and phi values for Ile. Notice the three colored triangular planes. The yellow plane serves as the references in measuring the two angles. The purple plane is part of <scene name='Psi_and_Phi_Angles/Model_1_plane_psi/1'>planar peptide bond</scene> between Tyr and Ile, and the orange one is part of the planar bond between Ile and Leu. |
== External Links == | == External Links == | ||
[http://en.wikipedia.org/wiki/Torsional_angle Extensive description] of torsional angles. | [http://en.wikipedia.org/wiki/Torsional_angle Extensive description] of torsional angles. | ||
Revision as of 23:57, 9 October 2010
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A tetrapeptide, such as Leu-Leu-Ile-Tyr, contains four amino acids connected together with three amide or peptide bonds. Since an amide bond has pi bond character, the six atoms that constitute a peptide bond all lie in the - the orange plane is the peptide bond connecting Tyr and Ile and the yellow one connects Ile and Leu. As with any peptide the conformation of the is determined by the values of two torsional angles - psi (ψ) and phi (φ) of each interior amino acid.
Determining values for psi (ψ) and phi (φ)
The which constitute a ψ are an amide nitrogen, a carbonyl carbon, an α-carbon and a second nitrogen . 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). 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.
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.
Psi and Phi More Detail
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The initial scene shows psi and phi values for Ile. Notice the three colored triangular planes. The yellow plane serves as the references in measuring the two angles. The purple plane is part of between Tyr and Ile, and the orange one is part of the planar bond between Ile and Leu.
External Links
Extensive description of torsional angles.
