In the diagram above the dark blue and black areas correspond to conformations where atoms in the polypeptide come closer than the sum of their van der Waals radii. Angles, which cause spheres to collide correspond to sterically disallowed conformations of the polypeptide backbone. Atoms were treated as hard spheres with dimensions corresponding to their van der Waals radii. For each conformation, the structure was examined for close contacts between atoms. Ramachandran used computer models of small polypeptides to systematically vary torsional angles with the objective of finding stable conformations. These rotations are represented by the torsion angles phi ( Φ: C-N-Cα-C) and psi (ψ: N-Cα-C-N ), respectively.
JMOL RAMACHANDRAN PLOT FREE
In a polypeptide the main chain N-C α and C α -C bonds are relatively free to rotate. In rare cases a deviation of 10 ° for a cis peptide bond is observed, that usually involves Proline. The planarity of the peptide bond is restricted to 180 ° in nearly all of the main chain peptide bonds. These are phi ( Φ), psi (ψ), and omega ( Ω). The figure below shows the three main chain torsion angles of a polypeptide. 1 Backbone conformation and secondary structure The goal of this course is to revisit basic principles of protein structures and familiarize yourself with sources of experimental and theoretical protein structure models. Proteins are involved in transport (hemoglobin: oxygen), storage (myoglobin in the muscle: oxygen), movement (dynein, actin), recognition (insulin receptors: protein kinase activation through binding of the hormone insulin), signal transduction (epidermal growth factor: cell growth), protection (antibodies), energy storage (glycogenin: glycogen), metabolism (F1-ATPase: ATP generation) and structure (keratin: skin). Their correct functioning and interaction with other molecules in the cell is crucial for many aspects of life.
![jmol ramachandran plot jmol ramachandran plot](https://www.umass.edu/molvis/workshop/imgs/1000px-Amino_Acids.svg.png)
Proteins are the "worker" molecules of a cell.