What causes variations and differentiation between Amino Acids?

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The largest contributor to chemical differences between amino acids is the composition of the "R side-chain". This side-chain defines whether the molecule is generally an acid or base, and hydrophobic (repels water) or hydrophilic (water soluble). There is also variation due to the placement of the amine group (NH2) relative to the carboxyl group(COOH), but these are a lesser contributor when compared to side chain composition.