A Ramachandran plot can be used in two somewhat different ways. 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 (as at top right).

MODELLER

Ab initio- or de novo- protein modelling methods seek to build three-dimensional protein models “from scratch”, i.e., based on physical principles rather than (directly) on previously solved structures.

The Ramachandran Plot • The two torsion angles of the polypeptide chain, describe the rotations of the polypeptide backbone around the bonds between N-Cα (called Phi, φ) and Cα-C (called Psi, ψ) • It provides an easy way to view the distribution of torsion angles of a protein structure.

In a protein chain three dihedral angles are defined as φ (phi), ψ (psi) and ω (omega), as shown in the diagram. The planarity of the peptide bond usually restricts ω to be 180° (the typical trans case) or 0° (the rare cis case).

A dihedral angle or torsional angle (symbol: θ) is the angle between two bonds originating from different atoms in a Newman projection.

Dihedral angle has important stabilizing effects on flying bodies because it has a strong influence on the dihedral effect. Dihedral effect of an aircraft is a rolling moment resulting from the vehicle having a non-zero angle of sideslip. Increasing the dihedral angle of an aircraft increases the dihedral effect on it.

The Formula for Calculating Dihedral Angle Say, ax+by+cz+d =0. Here, the vector is denoted as n. And, n =(a,b,c).

The Angle of Attack is the angle at which relative wind meets an Aerofoil. It is the angle formed by the Chord of the aerofoil and the direction of the relative wind or the vector representing the relative motion between the aircraft and the atmosphere.

Torsion angle φ = Tor(p1, p2, p3, p4). The angle is measured in the plane perpendicular to b = p3 − p2. of the atoms. Let a = p2 − p1 (1) b = p3 − p2 c = p4 − p3.

A dihedral angle of a protein is the internal angle of polypeptide backbone at which two adjacent planes meet. A Ramachandran plot is a way to visualize dihedral angles φ against ψ of amino acid residues in protein structure. It shows the correlation of φ and ψ angles in a real polypeptide.

A torsion angle, also known as a dihedral angle, is formed by three consecutive bonds in a molecule and defined by the angle created between the two outer bonds. The backbone of a protein has three different torsion angles.

Phi (Φ; C, N, Cα, C) and psi (Ψ; N, Cα, C, N) are on either side of the Cα atom and omega (ω; Cα, C, N, Cα) describes the angle of the peptide bond. This is a result of the partial double bond character of the peptide bond which is caused by resonance effects, i.e. delocalized electrons (N-C=O.

As with any peptide the conformation of the backbone is determined by the values of two torsional angles. In sequence order, phi (φ) is the C(i-1),N(i),Ca(i),C(i) torsion angle and psi (ψ) is the N(i),Ca(i),C(i),N(i+1) torsion angle.

3.6 residues

Domains are distinct functional and/or structural units in a protein. Usually they are responsible for a particular function or interaction, contributing to the overall role of a protein. Domains may exist in a variety of biological contexts, where similar domains can be found in proteins with different functions.

Many proteins consist of several domains. One domain may appear in a variety of different proteins. Molecular evolution uses domains as building blocks and these may be recombined in different arrangements to create proteins with different functions.

A motif is similar 3-D structure conserved among different proteins that serves a similar function. Domains, on the other hand, are regions of a protein that has a specific function and can (usually) function independently of the rest of the protein.

Hydrophobic effect Since it is known that protein folding is a spontaneous reaction, then it must assume a negative Gibbs free energy value.