In this study we attempt to determine the interconnection of the nanocrystal and amorphous phases in two states of spider dragline silk, native, and supercontracted with water. Infrared spectroscopy is employed to measure crystal stress with a high time resolution, while varying mechanical fields are applied to the silk. The results show that in both states of silk a serial arrangement between the crystalline and amorphous phase dominates the nanostructure. However, water can break the hydrogen bonds of the amorphous chains, and, in combination with hydrophobic effects, it induces the formation of a physical network in the amorphous phase. This network increases in stiffness, until a stress limit is reached. At higher stress, the nanostructure of supercontracted silk is irreversibly transformed to one similar to native silk. This enables one to make a complete description of the mechanical properties of silk in both states, by taking into account the energy required to break these bonds in the previous structural model that assumed a pre-strain distribution of worm-like amorphous chains.