Zika virus (ZIKV) remains a public health threat as climate change may increase infections and associated neurotropic illnesses. Interferon antagonism by ZIKV nonstructural protein 5 (NS5) is essential to ZIKV infection and pathogenesis due to STAT2 binding. This study assessed the genetic flexibility of NS5 residues that directly contact human STAT2 (hSTAT2) through combination of yeast two-hybrid (Y2H) protein-protein interaction and deep mutational scanning (DMS). We hypothesized that these NS5 residues would exhibit a range of mutational tolerances, and that this interface could be programmed to be stronger or weaker with individual amino acid substitution. Our results showed that DMS with Y2H can define the hierarchy of ZIKV NS5 residues to tolerate mutations and still bind hSTAT2. We could increase the sensitivity of this analysis by weakening the STAT2 interface and use this system to predict emerging pathogens and identify targets for therapeutics, live-attenuated vaccines, and mouse-adapted viruses.