Ramachandran plot

A ramachandran plot (example above from [1]) is a graphical representation of all the phi-psi angles (image below from[2] ) of amino acids in a protein. There exist only so many different ways an amino acid can orient itself in a protein, given the constraints of its own structure and the structure and context of neighboring amino acids, so plotting out all the orientations of all amino acids in a given protein can help determine if the predicted protein structure is consistent with or violates biochemical ‘rules’ for phi-psi angles. Ramachandran plots can also help identify secondary structures that are made apparent by phi-psi angles that commonly exist together in beta sheets, alpha helices, or other structures within a protein.