The findings in this work were enabled by the combination of site-specific labeling with the CLIR-MS protocol, which provides enhanced knowledge of cross-linking sites at single nucleotide and amino acid resolution. This technology is inherently flexible, and we are exploring further improvements to the the method (Götze et al, submitted). Our findings here demonstrate the importance of local environment to cross-linking in the binding site, i.e. beyond the simple proximity of photo-reactive nucleotides and amino acids, thereby helping to explain at least in part why cross-links occur only at specific sites in an RNA-RBP motif. Because of the inherent variations in the ways that RBPs recognize their RNA targets, predictive modeling of RBP selectivity is extremely challenging. Our findings can be implemented into the development of new tools for de novo motif discovery. In a broader sense, we expect our findings also to be of value in understanding RNA-protein interactions from the analysis of CLIP data sets, which is currently an area of intense research .