2011_09_19_secondary_structure

2011_09_19_secondary_structure - Typical covalent bond...

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Unformatted text preview: Typical covalent bond lengths Bond Bond length () Bond energy (kcal/mol) CC 1.51 85 C=N 1.27 175 C C 1.20 >250 C !-C ! 3.80 The dihedral angle (also known as a torsion angle) between four atoms A- B-C-D is defined as the angle between the the planes ABC (marked by red lines) and BCD (marked in purple): Dihedral angles Dihedral angles in the peptide backbone - Three distinct dihedral angles in the peptide backbone - Dihedral angles determine protein structure and conformation # = phi $ = psi % = omega N Peptide bond (omega) is planar due to its partial double bond character Phi ( # ) look along N-C ! bond Angle between carbonyls Positive is clockwise C'N to C ! C' Psi ( $ ) look along C !-C' bond Angle between nitrogens Positive is clockwise NC ! to C'N (positive when read from N to C using backbone atoms with " cis " being a zero angle) Definition of phi & psi Phi/Psi projections Phi/Psi Values of phi and psi angles determine the conformation of the protein All values of phi/psi are not possible due to steric clash Restriction of phi/psi it one reason why proteins can fold into defined structures Ramachandran plot visualizes phi/psi distribution Red represents most populated regions Yellow represents less populated regions The Ramachandran Plot ~3/4 of angles are excluded Ramachandran plot for glycine Least sterically hindered amino acid Largest range of possible phi and psi angles Shown are the conformations of glycine residues in 30 high-resolution protein X-ray structures. Ramachandran plot for alanine Typical amino acid Phi essentially limited to -45 to -170 Shown are the conformations of alanines in 30 high-resolution protein X-ray structures. Ramachandran plot for proline Most constrained amino acid Phi restricted to -70 Psi restricted to just two values: 140 and -30 Average Ramachandran plot for non-glycine...
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2011_09_19_secondary_structure - Typical covalent bond...

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