The overall three-dimensional shape of a protein molecule is called the tertiary structure.
Although the shape may appear random, the protein takes these forms due to the many stabilizing forces and bonding interactions between the side chain groups. The most stable form of a protein is called the native conformation of the protein.
The four main side chain interactions that stabilize the native conformation are hydrophobic/hydrophilic forces, Van der Waal forces, Electrostatic bonds, and Hydrogen bonds.
To become functional, some proteins require a prosthetic group. The apoprotein lacks the prosthetic group and the holoprotein includes the prosthetic group. This attachment can either be covalent or noncovalent.
Biotin: Covalent attachment to the Lysine side chain.
Heme: Non Covalent attachment to hydrophobic Heme binding site.
The orientation of the side chains depends on a few factors: whether it is hydrophobic or hydrophilic, polar or nonpolar, and acidic or basic.
Hydrophobic interactions would result in the side chains being found on the interior of the protein. On the other hand, hydrophilic interactions would find the side chains on the exterior, exposed to the cellular membrane.
Certain structures, such as disulfide and salt bridges add stability to the tertiary structure. The disulfide bridges allow different parts of the protein chain to be held together by covalent bonds, whereas the salt bridges add ionic interactions between positive and negative sides of the side chains.