A typical protein has four levels of organisation, which are primary, secondary, tertiary and quaternary structures.
A mutation that result in the replacement of the side chain of an amino acid will affect the tertiary structure of the protein. This is because the tertiary structure of a protein is primarily due to the interactions between the R groups of the amino acids that make up the protein. If the tertiary structure is affected, the function of the protein too will be negatively affected because the function of a protein depend on its tertiary structure.