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An isopeptide bond is the linkage between the side chain amino or carboxyl group of one amino acid to the α-carboxyl, α-amino group, or the side chain of another amino acid. In a typical peptide bond, also known as eupeptide bond, the amide bond always forms between the α-carboxyl group of one amino acid and the α-amino group of the second ...
In biochemistry, a Ramachandran plot (also known as a Rama plot, a Ramachandran diagram or a [φ,ψ] plot), originally developed in 1963 by G. N. Ramachandran, C. Ramakrishnan, and V. Sasisekharan, [1] is a way to visualize energetically allowed regions for backbone dihedral angles ψ against φ of amino acid residues in protein structure.
Protein structure is the three-dimensional arrangement of atoms in an amino acid -chain molecule. Proteins are polymers – specifically polypeptides – formed from sequences of amino acids, which are the monomers of the polymer. A single amino acid monomer may also be called a residue, which indicates a repeating unit of a polymer.
Peptide bond formation via dehydration reaction. When two amino acids form a dipeptide through a peptide bond, [1] it is a type of condensation reaction. [2] In this kind of condensation, two amino acids approach each other, with the non-side chain (C1) carboxylic acid moiety of one coming near the non-side chain (N2) amino moiety of the other.
Molecular geometry. Geometry of the water molecule with values for O-H bond length and for H-O-H bond angle between two bonds. Molecular geometry is the three-dimensional arrangement of the atoms that constitute a molecule. It includes the general shape of the molecule as well as bond lengths, bond angles, torsional angles and any other ...
μ (Polarity) >0. Disphenoidal or seesaw (also known as sawhorse [1]) is a type of molecular geometry where there are four bonds to a central atom with overall C 2v molecular symmetry. The name "seesaw" comes from the observation that it looks like a playground seesaw. Most commonly, four bonds to a central atom result in tetrahedral or, less ...
The standard hydrogen-bond definition for secondary structure is that of DSSP, which is a purely electrostatic model. It assigns charges of ± q 1 ≈ 0.42 e to the carbonyl carbon and oxygen, respectively, and charges of ± q 2 ≈ 0.20 e to the amide hydrogen and nitrogen, respectively.
Peptide plane flipping. Peptide plane flipping is a type of conformational change that can occur in proteins by which the dihedral angles of adjacent amino acids undergo large-scale rotations with little displacement of the side chains. The plane flip is defined as a rotation of the dihedral angles φ,ψ at amino acids i and i+1 such that the ...