How do you tell the difference between the non-polar R group and the polar but neutral R group?
The major difference is that polar R groups can either become charged (ionic) or can participate in hydrogen bonding through partial charges; whereas non-polar groups cannot. Hence the key is to look at the chemical properties of the side chain and decide whether it can become charged or carry polar charge. This answer will explain how to do this.
You may know from your studies that simple hydrocarbon chains are unable to carry polar charge, whereas groups with O, N and H atoms in close proximity can carry polar charge due to the atoms' different affinity for electrons. This differential results in slight charges (+ or -) on the atoms, giving the molecule the capacity to participate in hydrogen bonding and hence being more hydrophilic. In addition, some types of groups can become ionized through acid-base reactions: carboxylic acid (COOH) and amine (NH2) groups are the ...
This comprehensive answer explains how to look at the chemical properties of the side chain and decide whether it can become charged or carry polar charge. It also identifies six groups of amino acids and evaluates why, or why not, they are polar or non-polar: aliphatic amino acids, sulfur side chains, hydroxyl side chains, aromatic amino acids, acidic residues and amide derivatives, and basic amino acids.