We have studied the vapor-phase deposition of L-cysteine on the Au(110) surface by means of synchrotron-based techniques. Relying on a comparison with previous X-ray photoemission analysis, we have assigned the fine structure of the C K-shell X-ray absorption spectra to the nonequivalent carbon bonds within the molecule. In particular, the C1s ->sigma* transition, where the sigma* state is mainly localized on the C-S bond, is shifted well below the ionization treshold, at similar to -5 eV from the characteristic pi* transition line related to carboxylic group. From the polarization dependence of the absorption spectra in the monolayer coverage range, the molecules are found to lay flat on the surface with both the C-S bond and the carboxylic group almost parallel to the surface. We performed in situ complementary surface X-ray diffraction, SXRD, measurements to probe the rearrangement of the Au atoms beneath the L-cysteine molecules. Since the early stage of deposition, L-cysteine domains are formed which display an intermediate fourfold symmetry along [001]. The self-assembly of molecules into paired rows, extending along the [1<(1over bar>0] direction, is fully compatible with our observations, as has been reported for the case of D-cysteine molecules grown on Au(110).