Bone is a biological nanocomposite composed primarily of collagen and hydroxyapatite. The collagen molecules self-assemble to from a structure known as a fibril that comprises of about 85–95% of the total bone protein. In a fibril, the molecular level interactions at the interface between molecular collagen and hydroxyapatite nanocrystals have a significant role on its mechanical response. In this study, we have used molecular dynamics and steered molecular dynamics to study directional dependence of deformation response of collagen with respect to the hydroxyapatite surface. We have also studied mechanical response of collagen in the proximity of (0 0 0 1) and (1 0 1¯0) surfaces of hydroxyapatite. Our simulations indicate that the mechanics of collagen pulled in different directions with respect to hydroxyapatite is significantly different. Similar results were obtained for collagen pulled in the proximity of different crystallographic surfaces of hydroxyapatite.