Certain orientations are forbidden. Two charged groups, having the same charge will not be very near one another. The sulfhydral groups of the Cysteine tend to react together to form a covalent disulfide bond. A helical conformation often adapted by a polypeptide chain and stabilized by H-bonding between every fourth amino acid. There are 3.6 aa's per turn.
Side chains stick outside of the core.
The side chains can then form tertiary folding interactions. Some combinations of side chains can be disruptive. Hydrogen bonds between H donors and acceptors in side chains. Hydrophobic clustering between nonpolar, hydrocarbon side chains. Metal ion coordination complexes between amino, hydroxyl, and carbonyl groups, ring nitrogens and pairs of SH groups.