Alanine and phenyalanine would react in both tertiary or quaternary structure with least chances in former than later. The protein's size, shape and reactive properties depend on the number, type and sequence of amino acids. The most important level of bonding in terms of chemical properties is represented by protein's tertiary structure. A protein's attains maximum stability and lowest energy state or reactivity in its tertiary structure. So, in tertiary structure there are least chances of reactivity.
The tertiary structure of a protein is stabilised by various ionic recations between positively and negatively charged sites on amino acid side chains, salt bridges etc.
The quarternary structure of a protein relates to inter relation and arrangement of polypeptides in a protein with more than 2 polypeptide chains.
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