The only possibility is the presence of an Histidine residue whose imidazole ring fits with your observation. The possibility of the presence of a residue of the His-tag often used for protein purification may give you an answer. Probably is present in a non stoichiometric ratio with other residues.

According to the search results, aprotinin is a polypeptide extracted from bovine lung and composed of 58 amino acids with a molecular weight of 6’512 Daltons. It has a single polypeptide chain with three crosslinking disulfide bridges. A heterocyclic compound is a ring structure that contains at least one atom of an element other than carbon within the ring. Nitrogen is one of the most common heteroatoms in heterocyclic compounds. Aprotinin does not contain any heterocyclic rings in its chemical structure, so it does not contain a heterocyclic compound with nitrogen.

I undestand your question in this way. Aprotinin is ....58 etc . But I find an heterocyclic moiety . thus I cite your question :

"Need to confirm the presence of heterocyclic compound with Nitrogen in it’s structure."

I answered how to explain this presence if any. Otherwise I did not understand your question. It is well known that aprotinin does not contain aromatics aminoacids.

Your protein has been extracted or produced by E. Coli?.