Table 1.

Correlation between Functional Sites from Experiments and Computations

			Experimental Datac		Theoretical Resultsd,e
PDBa	Protein Name	Sizeb	Catalytic Res.	Ligand Binding Res.	Key Mechanical Res.	Odds Ratio
10GS	Human glutathione S-transferase P1-1	2 × 209	7, 8, 13, 38, 44, 51, 52, 64, 65, 98	A, B: 8, 10, 13, 38, 51, 52, 64, 65, 98, 108	A, B: 47–50	6.4
1A16	Aminopeptidase P	440	260, 271, 354, 361, 383, 406	350, 354, 361, 404	168–181	4.2
1A30	HIV-1 protease	2 × 99	A25, A30, B25	A27, A29, A48–A50, B23, B81, B84	A, B: 25–28, 47–54	4.2
1A3B	Human α-thrombin heavy chain	245 + 14	57, 195	57, 60A, 60D, 189, 194,195, 215, 219	95–102, 121–123, 132–138, 158–176, 198–208, 212–220, 221–228	2.1
1A42	Human carbonic anhydrase II	260	64, 92, 94, 96, 119	64, 92, 106, 131, 198, 199, 200, 202	44–53, 142–148, 186–191, 210–215, 243–245	2.3
1A47	CGTase	683	101, 141, 228, 230, 258, 328, 329	197, 371	131–148, 247–262, 496–510	3.1
1A5I	Plasminogen activator	244	57, 102, 156, 194, 195	57	90–105, 120–123, 135–141, 155–161, 183–192, 194–209	2.8
1A5V	Asv integrase	54–199	64, 121, 157	62, 119, 154, 155, 158	62–67, 76–82, 153–158	5.4
1AEC	Actinidin	218	25	19 ,24, 26, 66, 68, 69, 162	7–19, 113–115	5.6
1AL8	Glycolate oxidase	359	24, 108, 129, 257	24, 108, 129, 161, 254, 257	80–106, 150–161, 225–258	2.4
1ARZ	E. coli dihydrodipicolinate reductase	4 × 273	B–D: 159, 160, 163	B–D: 12, 13, 16, 17, 34, 39, 81, 84, 88, 102, 104, 127, 129, 163, 169, 170	A, B: 134–195, 197–239; C, D: 147–164, 189–216	.61
1B3N	β-ketoacyl carrier protein synthase	412	163, 398–401	107, 108, 111, 163, 193, 198, 202, 303, 340, 342, 398–401	41–56, 145–219	3.6
1B6A	Methionine aminopeptidase 2	110–478	231	219, 328, 331, 339, 340, 376, 444, 447	163–271, 363–381, 445–462	2.4
1BGQ	N-terminal domain of yeast Hsp90	214	40, 44, 79, 80, 84, 92, 93, 98, 123, 124, 171, 173	34, 44, 79, 83, 124, 171	27–42, 82–93, 127–141, 149–165	1.4
1BH6	Subtilisin DY	275	32, 64, 221	64, 99–101, 125– 127, 155, 221	20–26, 122–126, 204–207, 214–217	2.15
1BVV	Endo-1,4-xylanase	185	69, 78, 172	9, 80, 112, 116, 166	59–109, 128–140, 162–177	2.2
1BLC	β-lactamase	31–290	70	69, 70, 234	65–72, 206–215	6.2
1BR6	Ricin	268	80, 81, 121,123, 177, 180	78, 80, 81, 121, 180	14–33, 45–52, 168–180	3.3
1BIO	Complement factor D	16–243	57, 102, 195	195, 189, 214, 218	122–124, 136–153, 155–160	6.9
1BK9	Phospholipase A2	134	48, 52, 99	5, 9, 30, 45, 48, 49	3–22, 43–54, 100–111	5.0
1BXO	Penicillopepsin	323	33, 213	75, 216	146–180	5.3
1CP3	Apopain	35 + 227	121, 122, 161–165	64, 161, 163, 205, 207, 209, 214	169–195, 261–274	1.2
1CQQ	Human rhinovirus 3C protease	180	40, 71, 145, 147	142, 143, 144, 145, 147, 161, 165, 170	61–63, 70–72, 86–89	2.9
1CR6	Murine soluble epoxide hydrolase	2 × 544	A, B: 333, 334, 465, 495, 523	A, B: 333, 334, 465, 523	A, B: 225–241	-

^aReferences: 10GS: (Oakley et al., 1997); 1A16: (Wilce et al., 1998); 1A30: (Louis et al., 1998); 1A3B: (Zdanov et al., 1993); 1A42: (Stams et al., 1998); 1A47: (Wind et al., 1998); 1A5I: (Renatus et al., 1997); 1A5V: (Lubkowski et al., 1998); 1AEC: (Varughese et al., 1992); 1AL8: (Stenberg and Lindqvist, 1997); 1ARZ: (Scapin et al., 1997); 1B3N: (Moche et al., 1999); 1B6A: (Liu et al., 1998); 1BGQ: (Roe et al., 1999); 1BH6: (Eschenburg et al., 1998); 1BVV: (Sidhu et al., 1999); 1BLC: (Chen and Herzberg, 1992); 1BR6: (Yan et al., 1997); 1BIO: (Jing et al., 1998); 1BK9: (Zhao et al., 1998); 1BXO: (Khan et al., 1998); 1CP3: (Mittl et al., 1997); 1CQQ: (Matthews et al., 1999); 1CR6: (Argiriadi et al., 1999).

^b1A3B has two subunits of 14 and 245 residues. 1A5V, 1B6A, and 1BLC PDB coordinates refer to the indicated ranges.

^cUnderlined residues have mobility scores < 0.10 and exhibit minima of types I–III in mode 1.

^dHinge residues with mobility scores < 0.05, at crossover between positive and negative displacements in mode 1.

^eOdds ratio = p/p₀ (probability of finding a catalytic residue among key mechanical sites, relative to that in all residues).