This document summarizes different types of molecular interactions that are important for protein structure: 1) Bonded interactions such as covalent bonds, ionic bonds, and metallic bonds directly involve the sharing or transfer of electrons between atoms and strongly hold molecules together. 2) Non-bonded interactions like van der Waals forces, hydrogen bonds, electrostatic interactions, and hydrophobic interactions occur between molecules and parts of molecules not directly bonded and help maintain three-dimensional structure through weaker attractive forces. 3) Computational tools like ERRAT and Verify 3D can analyze protein structures, identify errors, and score how well an amino acid sequence matches a proposed three-dimensional structure model.

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2. C
C

3. Phi and Psi Angles
The angle of rotation
(also called torsion
angle or dihedral
angle) around the N
Cα bond is called phi
(φ) and that around
the Cα C bond is
called psi (ψ)

5. Server to predict the ramachandran plot

8. Bonded Interactions: Forces that hold atoms together within a molecule. These interactions involve the sharing
or transfer of electrons between atoms
a. Covalent Bonds: Covalent bonds are formed when atoms share electrons. They are strong and directional,
meaning the atoms involved are held together in specific orientations. Covalent bonds are common in organic
molecules, such as proteins, DNA, and carbohydrates.
b. Ionic Bonds: Ionic bonds occur when there is a complete transfer of electrons from one atom to another,
resulting in charged ions. The attraction between the oppositely charged ions leads to the formation of an ionic
bond. Ionic bonds are common in salts and other ionic compounds.
c. Metallic Bonds: Metallic bonds are found in metals, where electrons are delocalized and shared among all the
atoms in the metal lattice, creating a cohesive force that holds the metal together.

9. Non-bonded Interactions: Non-bonded interactions, also known as non-covalent interactions, occur
between molecules or parts of a molecule that are not directly involved in chemical bonding. These
interactions are generally weaker than covalent bonds and are essential for maintaining the three-
dimensional structure of molecules and the interactions between different molecules. There are four
primary types of non-bonded interactions:
a. Van der Waals Interactions: Van der Waals forces are weak attractive forces that arise
due to temporary fluctuations in electron density around atoms or molecules. They include London
dispersion forces and dipole-dipole interactions.
Hydrogen Bonds: Hydrogen bonds are a type of strong dipole-dipole interaction between a
hydrogen atom covalently bonded to an electronegative atom (e.g., nitrogen, oxygen, or fluorine) and
another electronegative atom in a different molecule or in a different part of the same molecule.
Hydrogen bonding is crucial for the stability of many biological molecules, such as proteins and DNA.
Electrostatic Interactions: These interactions arise from the attraction between oppositely
charged ions or polar molecules. They can be strong if the charges are large and close together, or
weak if the charges are small or distant.
Hydrophobic Interactions: Hydrophobic interactions occur between nonpolar molecules or
parts of molecules in an aqueous environment. They are responsible for the "clustering" of nonpolar
molecules in water to minimize their contact with the polar solvent.

10. Error values are plotted as a function of the position of a sliding 9-residue
window. The error function is based on the statistics of non-bonded atom-atom
interactions in the reported structure (compared to a database of reliable high-
resolution structures).
The figure shows a plot of an initial model and a final model. Regions of the
structure that can be rejected at the 95% confidence level are yellow; 5% of a
good protein structure is expected to have an error value above this level.
ERRAT
Plot

11. Verify
3D
The three-dimensional (3D) profile of a protein structure is a table computed from the
atomic coordinates of the structure that can be used to score the compatibility of the 3D
structure model with any amino acid sequence. Three-dimensional profiles computed
from correct protein structures match their own sequences with high scores. An
incorrectly modeled segment in an otherwise correct structure can be identified by
examining the profile score in a moving-window scan.