Phi-psi angle

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. 

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.)...

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... 

Table 9. Dihedral angles phi, psi, and omega from the isolated biantennary decasaccharide calculated by the GESA program [138] and from the x-ray structure analysis of human lgG1 [33, 34]... 

The authors thank Rik Moereels (Janssen Research Foundation, Beerse, Belgium) for his direction during the de novo model building stage of the project and Harold Almond, Jr., for helpful discussions. We also thank Marco Ceruso for his advice and analysis of the final receptor model in particular, he examined phi-psi space for angle violations and relaxed the relevant regions through molecular dynamics simulations. 

For polysaccharide, choose connectivity (01-C[l-6]), anomer (alpha or beta), isomer (l or d), and conformation (define phi and psi angle with omega = 180). Add sugars (alsohexoses or aldopentoses) to build polysaccharide chain. 

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