phi:

                          R1       
                          |        
		          Ca       
                       \ / \ /      
                        N   C    
                        |   "    
                        H   O     

psi:

                          R1       
                          |        
		          Ca       
                       \ / \ /      
                        N   C    
                        |   "    
                        H   O     

Ca stands for alpha-carbon, not calcium

Phi and psi are two tortion angles that define the shape of a protein backbone. Imagine if you made a 2-D graph with phi on one axis and psi on the other (each ranging from -180 to +180 degrees) and then went through a protein and plotted the value for each amino acid. You would then have a Ramachandran plot, named after the scientist who invented it.

Looking at the points on this plot, you would discover that the dots are not scattered randomly. Instead, they tend to cluster in very specific regions of the graph. Because of basic forces that determine chemical geometries, phi and psi are statistically limited to a narrow set of values. The clusters represent different types of secondary structure. Amino acids in an alpha helix tend to fall in one part of the plot and those in a beta sheet in another.

This plot is also used as a tool for evaluating new structures. If a protein is well behaved, most of its amino acids should fall within the allowed regions. Areas of great conformational flexibility (e.g. with glycine) or those which are under conformational strain may appear in regions outside those generally allowed.

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