Table 2.

Hydrogen bonds between SUB (or INT) and HIV-1 PR

	Presence of the interaction (%)
Substrate-protein hydrogen bonds	4HVP	WT/SUB	M46I/SUB	WT/INT	M46I/INT
N-H1,2,3(P3). . .Oδ1,2(48)	100	30	100	99	100
N-H(29). . .O(P3)	100	27	95	97	100
N-H(P2). . .O(48)	100	100	99	93	100
O-H(wat_b). . .O(P2)	100	99	100	100	99
N-H(P1). . .O(27)	100	1	3	39	27
O-H(wat_b). . .O(P1')	100	98	99	100	99
N-H(P2'). . .O(27')	100	84	89	12	95
Nɛ-Hɛ1(P2'). . .O(30')	0	100	100	99	94
N-H(29'). . .Oɛ(P2')	0	81	90	25	79
N-H(P3'). . .O(48')	100	95	79	99	99
N-H(48). . .O1,2(P3')	0	9	20	100	100

Labeling as in Chart 2 ▶. In the Table, the A-H. . .B H-bond is present at each step of the dynamics if d(H. . .A) < 3.0 Å and |nj(B-H. . .A) < 120°. 4HVP is the crystal structure of HIV-1 PR complexed with MVT101 (Miller et al. 1989). The overall agreement is fairly good, as most of the H-bonds present in the crystal structure are maintained in the molecular dynamics simulations. The few exceptions (presence < 50%) that are marked in bold face, are located at the cleavage site region. The largest discrepancy, which involves N-H_(P2'). . .O_(27'), could be a consequence of the structural differences between the MVT101 inhibitor (Miller et al. 1989) and SUB/INT (Rose et al. 1996). Other significant discrepancies are found for the two hydrogen bonds that restrain the P3 terminal substrate in wild type/SUB, indicating a large flexibility of this residue (Fig. 4B ▶) and for the two hydrogen bonds at the P2' site in wild type/INT. In this case, the side chain of GlnP2' adopts a different binding mode and there does not seem to be a large effect on the INT flexibility at the P2' site (Fig. 4C ▶).