User:Tilman Schirmer/Sandbox 99
From Proteopedia
Peptide bond
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The (highlight in ) formation is a condensation reaction between the carboxyl group of the amino acid i and the amino group of the amino acid i+1.
The peptide bond is a resonance structure between two limiting states. Therefore the N-C bond has a partial double bond character and the atoms/groups Cα, HN, C, C=O are within one plane. Peptide bonds are usually in trans conformation (ω torsion angle= 180°) due to sterical hindrance between Cβ and the C=O carbonyl. Cis conformation can occur only for the peptide bonds preceding Pro or Gly residue, where no Cβ is interfering.
If the three torsion angles phi, psi and omega of every amino acids within a protein are known, the secondary structure of this protein can approximated (?).
is defined by the four atoms φ = C - N - Cα - C (in green).
is defined by the four atoms ψ = N - Cα - C - N (in green).
is defined by the four atoms ω = Cα - C - N - Cα (in green).
Cis peptide bonds
The ω torsion angle can adopt a value close to 0° (cis-conformation), when a Pro residue is the following residue (Xaa-Pro peptide bond). In this situation a and a are similarily unfavorable, since there is a steric clash between Cα,i with Cα,i+1 or Cδ,i+1, respectively.
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