Post-translational modifications (PTMs) increase protein functional diversity by modifying an amino acid at specific locations called modification sites (MSs) in protein. It is believed that domains are being influenced by PTMs at interacting MSs to determine the unique functional changes in protein and, in this scenario, it is likely that the exact position of the MS, relative to the domain, plays a major part in structural changes by PTM influence. In this study, we present a system called 'PTM Tracker', built from two main parts to study the general distances of MS amino acids which are relative to protein functional domains. In the first part, we apply our system to illustrate that unique organisms appear to have distinguishing locations where PTMs may be found in the proteome. These crowded locations of MS sites (called, 'neighbourhoods') are relative to protein domains. We describe how these MS neighbourhoods may be a conserved extension of the already-conserved domain. Since specific protein domain types may be found in diverse proteins, the second part of our system studies MS neighbourhood clusters, relative to user-selected domains. From the study of many different proteins containing the same domain type, we conclude trends to suggest that MS neighbourhoods have specific locations in protein, relative to the domains (where-ever the domain occurs naturally), with which they are likely to interact. We conclude that the study of these distances may help to understand interaction mechanisms and describe types of protein folding requirements.