Electrostatic interaction: In an aqueous environment, the oppositely charged groups in amino acid side chains within the active site and substrates attract each other, which is termed electrostatic interaction. For example, when a carboxylic acid (R-COOH) dissociates into RCOO and H ions, COO will attract positively charged groups such as protonated guanidine side chain of arginine.
Hydrogen bond: A hydrogen bond is a specific type of dipole-dipole interaction between a partially positive hydrogen atom and a partially negative electron donor that contain a pair of electrons such as oxygen, fluorine and nitrogen. The strength of hydrogen bond depends on the chemical nature and geometric arrangement of each group.
Van der Waals force: Van der Waals force is formed between oppositely charged groups due to transient uneven electron distribution in each group. If all electrons are concentrated at one pole of the group this end will be negative, while the other end will be positive. Although the individual force is weak, as the total number of interactions between the active site and substrate is massive the sum of them will be significant.
Hydrophobic interaction: Non-polar hydrophobic groups tend to aggregate together in the aqueous environment and try to leave from polar solvent. These hydrophobic groups usually have long carbon chain and do not react with water molecules. When dissolving in water a protein molecule will curl up into a ball-like shape, leaving hydrophilic groups in outside while hydrophobic groups are deeply buried within the centre.