ramachandran plot by krunal chodvadiya
DESCRIPTION
Ramachandran plot for structural validation of protein will give information whether your protein or model protein is allowed or not in three dimensional point of view.TRANSCRIPT
Ramachandran plot
ByKrunal Chodvadiya10MBT001
Ramachandran plot
A Ramachandran plot (also known as a Ramachandran diagram or a [φ,ψ] plot), originally developed in 1963 by G. N. Ramachandran, C. Ramakrishnan and V. Sasisekharan, is a way to visualize backbone dihedral angles ψ against φ of amino acid residues in protein structure.
Plot of φ vs. ψ
The conformations of peptides are defined by the values of φ and ψ.
Each peptide bond has partial double-bond character due to resonance and cannot rotate.
Three bonds separate sequential Ca in a polypeptide chain. The N-Ca and Ca– C bonds can rotate, with bond angles designated φ and ψ respectively. The peptide C-N bond is not free to rotate.
Other single bonds in the backbone may also be rotationally hindered, depending on the size and charge of the side chain R groups.
Both φ and ψ increases as the carbonyl and amide nitrogen (respectively) rotate clockwise.
• By convention, both φ and ψ are defined as 00 when the two peptide bonds flanking that Ca carbon are in the same plane.
• In a protein, this conformation is prohibited by steric overlap between an carbonyl oxygen and an amino hydrogen atom.
Ramachandran plot for L-Ala residues.
• Conformations deemed possible are those that involve little or no steric interference, based on calculations using known van der Waals radii and bond angles.
• The areas shaded dark blue reflect conformations that involve no steric overlap and thus are fully allowed.
• Medium blue indicates conformations allowed at the extreme limits for unfavorable atomic contacts.
• lightest blue area reflects conformations that are permissible if a little flexibility is allowed in the bond angles.
• Unshaded portion indicates sterically disallowed conformations
values of φ and ψ for various allowed 20 structures
Every type of secondary structure can be completely described by the bond angles φ and ψ at each residue.
The structure of cytochrome C shows many segments of -a helix and the Ramachandran plot shows a tight grouping of φ = -60 and psi = -45 to -50.
a-helix cytochrome CRamachandran plot
Similarly, repetitive values in the region of φ = -110 to -140 and ψ = +110 to +135 give beta sheets. The structure of plastocyanin is composed mostly of beta sheets; the Ramachandran plot shows values in the –110, +130 region:
beta-sheet plastocyanin Ramachandran plot
Glycine Ramachandran Plot
Because its side chain, a single hydrogen atom, is small, a Gly residue can take part in many conformations that are sterically forbidden for other amino acids.
Proline Ramachandran Plot
The range for Pro residues is greatly restricted because φ is limited by the cyclic side chain to the range of -35 to -85.
Significance A Ramachandran plot can be used in 2 somewhat different ways.
i. One is to show in theory which values, or conformations, of the ψ and φ angles are possible for an amino-acid residue in a protein.
ii. A second is to show the empirical distribution of datapoints observed in a single structure in usage for structure validation, or else in a database of many structures.
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