Ramachandran Plot: Difference between revisions

<applet load='1MBO.pdb' size='600' frame='true' align='right' scene ='User:Karl_Oberholser/Ramachandran_Plots/Myoglobin/2' caption='' />

  <scene name='User:Karl_Oberholser/Ramachandran_Plots/Myoglobin/2'>View of structure</scene> : Secondary structure consist of &alpha;-helix, loops and ordered, nonrepetitive structures.<br>

  <scene name='User:Karl_Oberholser/Ramachandran_Plots/Plot_myoglobin/1'>Ramachandran plot</scene>: Red data points outside of the area expected for &alpha;-helix most likely involve residues at the end of the &alpha;-helix because often these have angle values that are not typical for &alpha;-helix.  White points are those for loops and ordered, nonrepetitive structures. The few residues that map to the disallowed region are Gly.<br>

<scene name='User:Karl_Oberholser/Ramachandran_Plots/Plot_myoglobin_model/1'>Return to model</scene> after viewing plot </p>

'''[[1scr|Concanavalin A]]'''<p>

<scene name='User:Karl_Oberholser/Ramachandran_Plots/Concanavalin_a/3'>View of structure</scene>: Twisted &beta;-sheet with small segments of &alpha;-helix.<br>

<scene name='User:Karl_Oberholser/Ramachandran_Plots/Plot_concanavalin_a/1'>Ramachandran plot</scene>: Most of the yellow points are located in the area for twisted &beta;-sheets where one would expect them, and again the points in the disallowed region are Gly. <br>

<scene name='User:Karl_Oberholser/Ramachandran_Plots/Plot_concanavalin_a_model/1'>Return to model</scene> after viewing plot. </p>

'''[[Acetylcholinesterase]]''' <p>

<scene name='User:Karl_Oberholser/Ramachandran_Plots/Acetylcholinesterase/2'>View structure</scene> <br>

<scene name='User:Karl_Oberholser/Ramachandran_Plots/Plot_acetylcholinesterase/1'>Ramachandran Plot</scene>: Close to equal amounts of &alpha;-helix, &beta;-sheet, and ordered, nonrepetitive structures. One important exception to Gly in the disallowed region is Ser:200.  Locate this residue that is located in a disallowed region (lower right quadrant). An interesting aspect concerning Ser:200 is that it is one of a triad of residues that are part of the catalytic site and are involved in the catalytic action of this enzyme.  The unique &phi; and &psi; values for Ser:200 is the major factor in positioning the side chain so that it can participate in the catalysis.<br>

<scene name='User:Karl_Oberholser/Ramachandran_Plots/Plot_ache_model/1'>Return to model</scene> after viewing plot.</p>

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