Protein structure dihedral angles

Einally, structural properties that depend directly neither on the data nor on the energy parameters can be checked by comparing the structures to statistics derived from a database of solved protein structures. PROCHECK-NMR and WHAT IE [94] use, e.g., statistics on backbone and side chain dihedral angles and on hydrogen bonds. PROSA [95] uses potentials of mean force derived from distributions of amino acid-amino acid distances. 

The structures of amino acids incorporated into polypeptides and proteins may be characterized by a pair of dihedral angles involving the so-called a carbon for each amino acid. 

Fig. 7.17 Bend structure resulting from the HF/4-21G geometry refinement of a type-II bend of N-formyl pentaglycine amide. The torsional angles in this structure are not common in proteins due to the effects of the end groups on the dihedral angles in the bend.

Fig. 7. Plot of main chain dihedral angles and (see Fig. 5 for definition) experimentally determined for approximately 1000 nonglycine residues in eight proteins whose structures have been refined at high resolution (chosen to be representative of all categories of tertiary structure).

Fig. 8. Plot of main chain dihedral angles and i/i experimentally determined for the glycines in 20 high-resolution protein structures.

The dihedral angles of disulfides in proteins are very difficult to determine with any accuracy except in refined high-resolution structures. In the first few protein structures to show disulfides at 2 A resolution, attention was paid mostly to the dihedral angle around the S—S bond (x3), since it is the most characteristically interesting... 

Now that about 70 different disulfides have been seen in proteins and more than 20 of those have been refined at high resolution, it is possible to examine disulfide conformation in more detail, as it occurs in proteins. Many examples resemble the left-handed small-molecule structures extremely closely Fig. 46 shows the Cys-30-Cys-115 disulfide from egg white lysozyme. The x > Xs and x dihedral angles and the Ca-Ca distance can be almost exactly superimposed on Fig. 45 the only major difference is in Xi All of the small-molecule structures have Xi close to 60°. Figure 47 shows the Xi values for halfcystines found in proteins. The preferred value is -60° (which puts S-y trans to the peptide carbonyl), while 60° is quite rare since it produces unfavorable bumps between S-y and the main chain except with a few specific combinations of x value and backbone conformation. 

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