The configuration is a concept that is related to the order (poition) by which different substituents linked to the same central atom, in the case of amino acids, around the central carbon atom. So, amino acids can be divided in two groups, L- and D- forms, analogous to left-handed and right-handed configurations.
On the other hand, protein folding (folded structure of peptides) is the physical process by which a protein chain acquires its conformation (3D structure) that is usually biologically functional.
