Phi, psi plot

Residues Receptor Atoms Cheek Phi-Psi Plot V Plot /Date I ... 

The phi (O) angle of a polypeptide is the angle about the C —bond the psi (T ) angle is that about the C -C bond. Most combinations of phi-psi angles are disallowed due to steric hindrance. The phi-psi angles that form the a helix and the P sheet fall within the lower and upper left-hand quadrants of a Ramachandran plot, respectively. 

The favoured dihedral angles for protein main chains were derived from energy considerations of steric clashes in peptides giving the well known Ramachandran plot (Ramachandran and Sasisekharan, 1968). These phi/psi combinations characterize the elements of secondary structure. Accurate main chain models can be constructed from spare parts, that is short pieces of helices, sheets, turns, and random coils taken from highly refined structures, provided a series of C-alpha positions can be established from the electron density map... 

The PROCHECK stmcture validation program (Laskowski et al, 1993) deploys a multitude of quality checks using both aoss-validation and standard checks for geometric deviations. The Ramachandran plot it produces is its most attractive and useful feature (Ramakrishnan and Ramachandran, 1965). The plot consists of a two dimensional plot of phi/psi values for each amino acid residue. Steric overlap between side chain and main chain atoms limits the energetically allowed values... 

Each atom of every individual amino acid present in the complexes was processed to extract the associated sets of phi-psi angles to generate a statistically significant cumulative Ramchandran plot for chain A of all proteins [60] (Fig. 5.62). 

Figure 5-1. Ramachandran plot of the main chain phi (< ) and psi (T) angles for approximately 1000 nonglycine residues in eight proteins whose structures were solved at high resolution. The dots represent allowable combinations and the spaces prohibited combinations of phi and psi angles. (Reproduced, with permission, from Richardson JS The anatomy and taxonomy of protein structures. Adv Protein Chem 1981 34 167.)...

By convention, the bond angles resulting from rotations at Ca are labeled (phi) for the N—C bond and i// (psi) for the C —C bond. Again by convention, both and extended conformation and all peptide groups are in the same plane (Fig. 4-2b). In principle, and i// can have any value between —180° and +180°, but many values are prohibited by steric interference between atoms in the polypeptide backbone and amino acid side chains. The conformation in which both and i// are 0° (Fig. 4-2c) is prohibited for this reason this conformation is used merely as a reference point for describing the angles of rotation. Allowed values for and i// are graphically revealed when i// is plotted versus in a Ramachandran plot (Fig. 4-3), introduced by G. N. Ramachandran. 

A protein is a linear sequence of amino acids linked together by peptide bonds. The peptide bond is a covalent bond between the oi-amino group of one amino acid and the a-carboxyl group of another. The peptide bond has partial double bond character and is nearly always in the trans configuration. The backbone conformation of a polypeptide is specified by the rotation angles about the Ca-N bond phi, (j>) and Ca-C bond psi, amino acid residues. The sterically allowed values of 0 and yr are visualized in a Ramachandran plot. When two amino acids are joined by a peptide bond they form a dipeptide. Addition of further amino acids results in long chains called oligopeptides and polypeptides. 

Carp http //www.glycosciences.de/tools/carp/ Generation of psi-phi plot... 

Lastly, the number of Ramachandran outliers is often reported in the coordinate data file, or they can be calculated by submission of the coordinate file to a web-based server (Davis et al, 2007). Outliers are residues whose peptide phi and psi values fall in energetically unfavorable regions of the Ramachandran plot, suggesting that there is an error in the conformation in at least that region of the protein. Typically, the number of outliers should be <5%. 

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