Table 1.

Activity of HIV-1 PR mutants

Level of activity	Substitutions at indicated flap positions
	M46	I47	G48	G49	I50	G51	G52	F53	I54	K55	V56
Wild-type	Val		Ser		Leu			Tyr	Leu	Thr	Thr
	Trp		Thr					Leu	Val	Asn	Cys
	Phe		His					Ile		Ile
	Leu		Gln					Val		Arg
			Arg					Trp		Gln
			Ala					Met
			Lys
Intermediate
Nearly  wild-type	His	Val	Phe		Val			Ser
	Arg		Val
In between	Asn	Cys	Asn			Ala		Glu	Cys
	Ser		Ile					Gly
			Glu					Asp
			Trp					Arg
Nearly  negative	Gln								Thr		Gly
	Gly
Negative	Pro	Asp	Asp	Trp	Tyr	Leu	Asn		His		Leu
		Ala	Pro	Ala	Asn	Thr	His		Asp		Ile
		Leu		Asp	Thr	Arg	Lys		Asn		Trp
		Arg		Ser	Ala	Pro	Asp		Arg		Ser
		Met		Phe	Trp	Cys	Ala		Lys		Ala
		Asn		Gln	Ser	Lys	Phe		Gly		Glu
		Gln		Arg	Gln	Val	Val		Pro		Arg
		Gly		Val	Lys	Met	Ser		Ala		Lys
		Tyr		Glu	Met	Phe	Pro		Ser
		Glu		Lys	Arg	Ile	Arg		Phe
		Ser		Leu			Cys
		Lys		His			Met
		Thr					Gln
							Leu

The level of protease activity was assessed based on results from Western analysis. A mutant was considered to have a wild-type level of activity if the Pro–Pol precursor was completely processed. A negative phenotype was assigned when no correct processing to generate either the p66 or p51 form of RT was seen. An intermediate phentoype was assigned when some, but not complete, processing was observed. The intermediate phentoype was further subdivided based on whether the activity was nearly wild-type, nearly negative, or in between. One-letter abbrevations for amino acids are used, followed by the position number.