This kind of sounds like an exam question, but, it is 9 months old...

Just about anything can impact the protein function, in theory. Depending on the situation, you can even get a disease phenotype from an L->I mutation, one of the most innocuous and common substitutions. Without knowing your exact case, it's hard to say why.

The basic chemical properties like polarity, pH, aromaticity aren't everything -- you also have pKas and isoelectric points, steric effects, helical propensities, cation affinities, types of bonds the side chain can engage in, etc, etc. Different amino acids are different!

One structural context may be very lax with amino acid properties (free loop), while others are very fine-tuned (inter-subunit bridge). You just don't know until you know (read: have the crystal structure).

Also, you can impact function without affecting secondary or tertiary structure. A mutation can affect the ability to interact with other proteins, receive PTMs, bind ligands, etc.