Human Coronaviruses which belongs to family Coronaviridae, are generally the main cause of respiratory diseases. In addition, central nervous system failure and gastrointestinal diseases would be occurred. The nucleocapsid, as an important structural protein of coronaviruses is involved in replication of the genomic material and immunization of the host. Characteristics of secondary structure, post-translational modifications and antigenic sites of six coronaviruses from human including 229E: NC_002645, HKU1: NC_006577, MERS: KF958702, NL63: AY567487, OC43: NC_005147 and SARS: NC_004718 coronavirus, were studied bioinformatically. The highest divergence of amino acid sequence was shown between 229E and MERS while the lowest divergence was related to OC43: NC_005147 and HKU1. The rate of α-helix structure was 17% in SARS and MERS coronaviruses and 13% in 229E and NL63 strains. Percentage of β-sheet structure were different in the strains and determined 11-16%. The viral strains were classified in three distinctive groups not only based on ASN-X-SER / THR N-Glycosylation and phosphorylation sites but also according to their antigenic regions. Phylogenetic tree analyses of strains confirmed the classification. In spite of previous reports about highly conserved properties of nucleocapsid gene sequences in coronaviruses, the viruses from human were grouped based on the protein characteristics that could be reflect to various performance in the host organs. Also obtained information could be noticed in effective controlling of the infections.
