Amino acid replacement

Amino acid replacement is a change from one amino acid to a different amino acid due to point mutation in DNA sequence. It is caused by nonsynonymous missense mutation which alters the codon sequence to code other amino acid instead of the originals.

Not all amino acid replacements have the same effect on function or structure of protein. The magnitude of this process may vary depending on how similar or dissimilar the replaced amino acids are, as well as on their position in the sequence or the structure. Similarity between amino acids can be calculated based on substitution matrices, physico-chemical distance, or simple properties such as amino acid size or charge (see also amino acid chemical properties). Usually amino acids are thus classified into two types:

Physicochemical distance is a measure that assesses the difference between replaced amino acids. The value of distance is based on properties of amino acids. There are 134 physicochemical properties that can be used to estimate similarity between amino acids. Each physicochemical distance is based on different composition of properties.

Grantham's distance depends on 3 properties: composition, polarity and molecular volume.

Distance difference D for each pair of amino acid i and j is calculated as: ${\displaystyle D_{ij}=[\alpha (c_{i}-c_{j})^{2}+\beta (p_{i}-p_{j})^{2}+\gamma (v_{i}-v_{j})^{2}]}$

...
Wikipedia