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Few models of sequence evolution incorporate parameters describing protein structure, despite its high conservation, essential functional role and increasing availability. We present a structurally-aware empirical substitution model for amino acid sequence evolution in which proteins are expressed using an expanded alphabet that relays both amino acid identity and structural information. Each character specifies an amino acid as well a rotamer state: the discrete geometric pattern of permitteddoi:10.1101/530634 fatcat:nb3b75ibzjadrpmay7bpjvcbay