Phi and Psi Angles: Difference between revisions
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<table width='400' align='right' cellpadding='5'><tr><td rowspan='2'> </td><td bgcolor='#eeeeee'><applet load='LeuLeuIleTyr.pdb' size='390' frame='true' align='right' scene ='49/499178/First_view/2' caption='' /></td></tr><tr><td bgcolor='#eeeeee'><center>'''Tetrapeptide: Leu-Leu-Ile-Tyr'''<scene name='Phi_and_Psi_Angles/First_view/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.pdb' size='390' frame='true' align='right' scene ='49/499178/First_view/2' caption='' /></td></tr><tr><td bgcolor='#eeeeee'><center>'''Tetrapeptide: Leu-Leu-Ile-Tyr'''<scene name='Phi_and_Psi_Angles/First_view/1'> (Initial scene)</scene></center></td></tr></table> | ||
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 <scene name='Phi_and_Psi_Angles/First__view_planes/1'>same plane</scene> - 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 <scene name='Phi_and_Psi_Angles/Backbone/1'>backbone</scene> is determined by the values of two torsional angles. In sequence order, phi (φ) is the | 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 <scene name='Phi_and_Psi_Angles/First__view_planes/1'>same plane</scene> - 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 <scene name='Phi_and_Psi_Angles/Backbone/1'>backbone</scene> is determined by the values of two torsional angles. In sequence order, phi (φ) is the C(i-1),N(i),Ca(i),C(i) torsion angle and psi (ψ) is the N(i),Ca(i),C(i),N(i+1) torsion angle. | ||
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*Click in the lower text box of the console that comes up, type the '''Select''' command followed by the number of the residue (Obtain this number in the Jmol applet by hovering over the residue whose psi and phi you want to determine), a "''';'''" and the command '''draw rama''' and then press the '''Return''' key. | *Click in the lower text box of the console that comes up, type the '''Select''' command followed by the number of the residue (Obtain this number in the Jmol applet by hovering over the residue whose psi and phi you want to determine), a "''';'''" and the command '''draw rama''' and then press the '''Return''' key. | ||
== | == See Also == | ||
* [[Dihedral/Index]] which lists many tutorials and resources about the Ramachandran principle, and phi and psi angles in proteins. | |||
[http:// | *[http://xray.bmc.uu.se/embo2001/modval/phirot_anim.gif Animation of Phi] and [http://xray.bmc.uu.se/embo2001/modval/psirot_anim.gif Psi rotations] by [http://www.medicine.usask.ca/biochem/faculty/associate-faculty/david-sanders.php David Sanders] | ||
[http:// | *[http://www.msg.ucsf.edu/local/programs/garlic/commands/dihedrals.html Excellent description of torsional angles] by [http://www.zucic.org/damir/damir.html Damir Zucic]. | ||
[http:// | *[http://en.wikipedia.org/wiki/Torsional_angle Extensive description] of torsional angles. | ||
*[[Basics of Protein Structure]] | |||