Table 3.

Combined pair/surf energy score and % identities for sequence-structure alignments of the death domain-fold family sequences to the death domain-fold family structures

	DED	CARD				DD
	1a1z	1dgn	1cy5	3ygs.P	3crd	1ddf	1ngr	1d2z.A	1d2z.B	1fad	1e41
Pair/Surf score
1a1z	6.93	6.07	5.51	3.59	4.36	5.75	6.04	5.29	4.26	4.54	5.08
1dgn	5.33	7.36	6.43	7.04	7.31	4.52	6.60	4.73	3.96	5.95	5.35
1cy5	4.18	7.47	7.87	7.87	6.73	5.83	7.37	6.52	4.68	4.75	4.59
3ygs.P	2.93	6.48	6.29	7.65	7.75	6.05	5.02	5.97	4.98	5.33	4.33
3crd	2.97	7.05	4.90	6.55	6.83	3.94	4.08	4.92	4.55	3.31	4.10
1ddf	5.09	5.15	4.70	6.57	7.07	5.90	7.45	7.05	5.25	6.80	6.79
1ngr	4.85	6.09	6.01	5.50	5.72	4.39	8.81	7.33	5.75	6.14	6.26
1d2z.A	4.19	3.81	6.40	4.46	6.27	5.16	8.66	9.22	5.91	4.78	5.55
1d2z.B	4.09	4.58	5.54	4.26	3.94	4.60	7.59	7.68	9.57	5.28	6.64
1fad	4.52	6.26	5.79	5.27	7.31	5.04	7.80	6.94	4.28	6.38	6.41
% Identity
1a1z	100	14	16	19	18	18	17	15	12	14	13
1dgn	11	100	16	21	22	17	17	6	16	17	7
1cy5	13	24	100	19	13	14	15	10	12	19	18
3ygs.P	21	24	19	100	24	15	17	11	18	10	13
3crd	12	24	13	24	100	20	19	14	17	10	11
1ddf	12	21	12	15	20	100	15	14	16	19	16
1ngr	18	14	15	17	20	15	100	20	12	27	30
1d2z.A	16	6	11	14	18	13	22	100	20	20	20
1d2z.B	12	12	12	7	12	15	13	21	100	14	21
1fad	13	13	15	13	15	19	26	18	17	100	62

The pair/surf scores and % identities listed were obtained using default parameters. The PDB codes correspond to the following death domain-fold family members: 1a1z, FADD DED (Eberstadt et al. 1998); 1dgn, ICEBERG CARD (Humke et al. 2000); 1cy5, Apaf-1 CARD (Vaughn et al. 1999); 3ygs.P, caspase-9 CARD (Qin et al. 1999); 3crd, RAIDD CARD (Chou et al. 1998); 1ddf, Fas DD (Huang et al. 1996); 1ngr, p75 neurotrophin receptor DD (Liepinsh et al. 1997); 1d2z.A, Pelle DD (Xiao et al. 1999); 1d2z.B, Tube DD (Xiao et al. 1999); 1fad, mFADD DD (Jeong et al. 1999); 1e41, hFADD DD (Berglund et al. 2000) (this structure was not included in the fold-library used in this study). The gray boxes delineate CARD–CARD and DD–DD comparisons.