Comment on “Revisiting the Ramachandran plot from a new angle”
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Comment on "Revisiting the Ramachandran plot from a new angle".
that the ‘‘forbidden [bridge] region is well-populated in folded proteins, which can provide longer-range intramolecular hydrogen-bond partners.’’ However, using only a hard sphere model, Ramachandran and colleagues predicted the f and c combinations as a function of s that are observed in proteins of known structure. In particular, they showed that f and c combinations in the bridge region are...
متن کاملRevisiting the Ramachandran plot from a new angle.
The pioneering work of Ramachandran and colleagues emphasized the dominance of steric constraints in specifying the structure of polypeptides. The ubiquitous Ramachandran plot of backbone dihedral angles (ϕ and ψ) defined the allowed regions of conformational space. These predictions were subsequently confirmed in proteins of known structure. Ramachandran and colleagues also investigated the in...
متن کاملRamachandran plot on the web
A graphics package has been developed to display the main chain torsion angles phi, psi (phi, Psi); (Ramachandran angles) in a protein of known structure. In addition, the package calculates the Ramachandran angles at the central residue in the stretch of three amino acids having specified the flanking residue types. The package displays the Ramachandran angles along with a detailed analysis ou...
متن کاملRevisiting the Ramachandran plot: hard-sphere repulsion, electrostatics, and H-bonding in the alpha-helix.
What determines the shape of the allowed regions in the Ramachandran plot? Although Ramachandran explained these regions in terms of 1-4 hard-sphere repulsions, there are discrepancies with the data where, in particular, the alphaR, alphaL, and beta-strand regions are diagonal. The alphaR-region also varies along the alpha-helix where it is constrained at the center and the amino terminus but d...
متن کاملObjectively judging the quality of a protein structure from a Ramachandran plot
MOTIVATION Statistical methods that compare observed and expected distributions of experimental observables provide powerful tools for the quality control of protein structures. The distribution of backbone dihedral angles ('Ramachandran plot') has often been used for such quality control, but without a firm statistical foundation. RESULTS A new and-simple method is presented for judging the ...
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ژورنال
عنوان ژورنال: Protein Science
سال: 2011
ISSN: 0961-8368
DOI: 10.1002/pro.724