Proteins differ in the arrangements of 20 naturally occurring amino acids. This difference in protein sequence can also be captured at atom level. Carbon is the only element that contributes towards the hydrophobic interactions that drives the protein to carry out its biochemical reactions. Understanding the difference in protein sequence at atomic level could be very useful both to compare sequence from different origin and to define threshold carbon content for bar-coding of proteins. A new methodology for comparing protein sequences at atomic level is proposed. Viral sequences and aquaporins from various plants and animal origin have been analyzed based on the designed algorithm and the demarcation at carbon level was found to be very prominent