Ramachandranploten

Ramachandranploten, often referred to as Ramachandran plots, are graphical representations of the permissible combinations of the backbone dihedral angles phi (φ) and psi (ψ) for amino acid residues in a polypeptide chain. Developed by G.N. Ramachandran and his colleagues in the 1960s, these plots are fundamental tools in structural biology for analyzing and understanding protein structures.

The phi (φ) angle describes the rotation around the bond between the alpha-carbon and the nitrogen atom of the peptide backbone. The psi (ψ) angle describes the rotation around the bond between the alpha-carbon and the carbonyl carbon atom. Steric hindrances, the physical repulsion between atoms, limit the possible values of these angles, leading to specific regions of favored conformations.

Ramachandran plots categorize these allowed regions into "generously allowed," "allowed," and "outlier" zones. The generously allowed regions represent the most stable and frequently observed conformations, typically corresponding to secondary structure elements like alpha-helices and beta-sheets. The allowed regions are less stable but still possible. Outliers represent conformations that are sterically disfavored and are usually indicative of errors in structure determination or the presence of unusual structural features.

By plotting the φ and ψ angles of each amino acid residue in a protein structure, researchers can quickly assess the quality of the structure and identify potential errors or unusual conformations. Ramachandran plots are widely used in validating protein crystallography and NMR structures, as well as in computational protein design and molecular dynamics simulations. They provide valuable insights into the local structural preferences of amino acids and the overall folding patterns of proteins.