The native structure of Antimicrobial peptides is stabilized by a large number of individually weak forces; a complete understanding of folding implies the need to evaluate the contribution of each of these, including nonconventional hydrogen bonds. In this work, we have analyzed the influence of C-H...O interactions in the structural stability of Antimicrobial peptides by comparison with conventional hydrogen bond. There are a number of amino acid residues that can form hydrogen bonds via their side chains in addition to their peptide group. Perhaps highest contribution in this category is polar residue (Cys) and charged residues such as Lys and Arg. A total of 2513 C-H...O interactions were found in a data set of 53 Antimicrobial peptides. Among the 2513 nonconventional interactions observed in the data set, 40% of interactions are bonded to alpha carbon. This is consistent with the fact that the hydrogens are more acidic than others. Most prominent were side-chain to main-chain C-H...O interactions (SM-C-H...O). 92% of the stabilizing centers in the Antimicrobial peptides were found to be involved in C-H...O interactions. These interactions are mainly formed by short range contacts. Moreover, the study shows that, there is an average of more than one C-H...O interactions observed for every single residue in the Antimicrobial peptides data set. It is concluded that the C-H...O interaction can, indeed, be categorized as a true stabilizing force like hydrogen bond in Antimicrobial peptides.