Comprehensive Bending Classification of Nucleic Acid Double Helix Structures

Strong bending (M > 45 °)
Classification I (double-kink: M=a1+a2)
(Last update: November 15, 2004)

Number of structures: 114 + 22

PDB	NDB	IMB Jena Image Library	bp	molecule type	method	model	s(2)	r	a/a1	a2	a1+a2	M
1azq	pdr048	E   |    H   |    B	8	prot-nuc	diff	single-kink line	0.364		46			46
1jh9	pd0226	E   |    H   |    B	16	prot-nuc	diff	single-kink line*	0.369		46			46
1rvb	pde015	E   |    H   |    B	10	prot-nuc	diff	single-kink line	0.217		46			46
2puc	pdr042	E   |    H   |    B	16	prot-nuc	diff	single-kink line	0.442		46			46
2pud	pdr046	E   |    H   |    B	16	prot-nuc	diff	single-kink line	0.470		46			46
1cw0	pd0100	E   |    H   |    B	12	prot-nuc	diff	single-kink line	0.508		47			47
1icg	ah0015	E   |    H   |    B	8	nuc	diff	single-kink line	1.101		47			47
1id9	ah0016	E   |    H   |    B	8	nuc	diff	single-kink line	1.296		47			47
1j46	------	E   |    H   |    B	14	prot-nuc	NMR	double-kink line	0.278		13	34	47	47
1j59	pd0299	E   |    H   |    B	13	prot-nuc	diff	double-kink line	0.372		15	32	47	47
1l3l	pd0298	E   |    H   |    B	20	prot-nuc	diff	double-kink line	0.236		19	28	47	47
1mm8	pd0340	E   |    H   |    B	18	prot-nuc	diff	double-kink line	0.261		31	16	47	47
1mus	pd0350	E   |    H   |    B	18	prot-nuc	diff	double-kink line	0.209		29	18	47	47
1nk3	------	E   |    H   |    B	14	prot-nuc	NMR	double-kink line	0.446		28	19	47	47
1zme	pdt044	E   |    H   |    B	16	prot-nuc	diff	double-kink line	0.408		26	21	47	47
2pub	pdr041	E   |    H   |    B	16	prot-nuc	diff	single-kink line	0.455		47			47
1an4	pdt027	E   |    H   |    B	20	prot-nuc	diff	double-kink line	1.782		25	23	48	48
1dp7	pd0111	E   |    H   |    B	16	prot-nuc	diff	double-kink line	0.366		24	24	48	48
1j5n	------	E   |    H   |    B	15	prot-nuc	NMR	single-kink line	0.419		48			48
1muh	pd0347	E   |    H   |    B	18	prot-nuc	diff	double-kink line	0.212		29	19	48	48
1o3t	pd0401	E   |    H   |    B	13	prot-nuc	diff	double-kink line	0.306		36	12	48	48
1qrv	pd0110	E   |    H   |    B	9	prot-nuc	diff	single-kink line	0.412		48			48
1b3t	pd0024	E   |    H   |    B	18	prot-nuc	diff	double-kink line	0.196		25	24	49	49
1iha	ah0018	E   |    H   |    B	8	nuc	diff	single-kink line	0.993		49			49
1j5o	pd0316	E   |    H   |    B	18	prot-nuc	diff	double-kink line	0.807		31	18	49	49
1k3w	pd0253	E   |    H   |    B	18	prot-nuc	diff	double-kink line	0.218		19	30	49	49
1mur	pd0349	E   |    H   |    B	18	prot-nuc	diff	double-kink line	0.218		19	30	49	49
1rcs	------	E   |    H   |    B	20	prot-nuc	NMR	double-kink line	0.148		20	29	49	49
1ysa	pdt002	E   |    H   |    B	16	prot-nuc	diff	double-kink line	0.385		16	33	49	49
1b95	pd0038	E   |    H   |    B	10	prot-nuc	diff	single-kink line	0.307		50			50
1bsu	pde0145	E   |    H   |    B	10	prot-nuc	diff	single-kink line	0.050		50			50
1eon	pd0131	E   |    H   |    B	10	prot-nuc	diff	single-kink line	0.238		50			50
1g9y	pd0189	E   |    H   |    B	24	prot-nuc	diff	double-kink line	0.702		28	22	50	50
1idw	ah0017	E   |    H   |    B	8	nuc	diff	single-kink line	1.023		50			50
1lb2	pd0306	E   |    H   |    B	20	prot-nuc	diff	double-kink line	0.191		19	31	50	50
1ub8	ud0027	E   |    H   |    B	7	nuc	diff	circular line	1.997	15				50
1eo4	pd0130	E   |    H   |    B	9	prot-nuc	diff	single-kink line	0.342		51			51
1hlv	pd0192	E   |    H   |    B	21	prot-nuc	diff	double-kink line	0.237		16	35	51	51
1rpd	------	E   |    H   |    B	42	prot-nuc	model	double-kink line	1.081		24	27	51	51
399d	adl047	E   |    H   |    B	12	nuc	diff	single-kink line	1.203		51			51
1bgb	pd0010	E   |    H   |    B	10	prot-nuc	diff	single-kink line	0.340		52			52
2bop	pdv001	E   |    H   |    B	16	prot-nuc	diff	double-kink line	0.505		26	26	52	52
1b94	pd0037	E   |    H   |    B	10	prot-nuc	diff	single-kink line	0.190		53			53
1b96	pd0039	E   |    H   |    B	10	prot-nuc	diff	single-kink line	0.211		53			53
422d	ar0007	E   |    H   |    B	8	nuc	diff	single-kink line	1.338		53			53
1b97	pd0040	E   |    H   |    B	10	prot-nuc	diff	single-kink line	0.272		54			54
1c7u	------	E   |    H   |    B	20	prot-nuc	NMR	double-kink line	0.524		27	27	54	54
1co0	------	E   |    H   |    B	20	prot-nuc	NMR	double-kink line	0.772		16	38	54	54
2stt	------	E   |    H   |    B	17	prot-nuc	NMR	double-kink line	0.722		17	37	54	54
4kbd	------	E   |    H   |    B	16	nuc	NMR	double-kink line	0.298		21	34	55	55
1au5	------	E   |    H   |    B	8	nuc	NMR	single-kink line	0.833		56			56
1bl0	pdr056	E   |    H   |    B	22	prot-nuc	diff	double-kink line	0.428		29	27	56	56
1fok	pde0127	E   |    H   |    B	19	prot-nuc	diff	double-kink line	0.483		28	28	56	56
1ir5	------	E   |    H   |    B	17	nuc	NMR	double-kink line	0.598		35	21	56	56
1eoo	pd0132	E   |    H   |    B	12	prot-nuc	diff	single-kink line	0.235		57			57
1exj	pd0146	E   |    H   |    B	21	prot-nuc	diff	double-kink line	0.605		16	41	57	57
1hbx	pd0233	E   |    H   |    B	25	prot-nuc	diff	single-kink line	1.881		57			57
4rve	pde003	E   |    H   |    B	10	prot-nuc	diff	single-kink line	0.503		57			57
1akh	pdr049	E   |    H   |    B	19	prot-nuc	diff	double-kink line	0.289		20	38	58	58
1c0w	pd0069	E   |    H   |    B	21	prot-nuc	diff	double-kink line	1.309		30	28	58	58
1eo3	pd0129	E   |    H   |    B	9	prot-nuc	diff	single-kink line	0.184		58			58
1kfo	ar0039	E   |    H   |    B	18	nuc	diff	double-kink line	0.135		29	29	58	58
1nk2	------	E   |    H   |    B	16	prot-nuc	NMR	double-kink line	0.646		32	27	59	59
1efa	pd0118	E   |    H   |    B	17	prot-nuc	diff	double-kink line	0.465		40	20	60	60
1le8	pd0308	E   |    H   |    B	19	prot-nuc	diff	double-kink line	0.366		30	31	61	61
433d	ar0008	E   |    H   |    B	14	nuc	diff	double-kink line	0.488		31	30	61	61
1ckt	pd0051	E   |    H   |    B	16	prot-nuc	diff	double-kink line	0.240		24	38	62	62
1yrn	pdt028	E   |    H   |    B	18	prot-nuc	diff	double-kink line	0.339		29	33	62	62
1ytf	pdt036	E   |    H   |    B	16	prot-nuc	diff	double-kink line	0.204		22	40	62	62
1a73	pd0002	E   |    H   |    B	20	prot-nuc	diff	double-kink line	0.238		33	30	63	63
1je8	pd0219	E   |    H   |    B	20	prot-nuc	diff	double-kink line	0.138		32	31	63	63
1nh2	pd0369	E   |    H   |    B	16	prot-nuc	diff	double-kink line	0.161		25	38	63	63
1oh8	------	E   |    H   |    B	10	prot-nuc	diff	single-kink line	1.397		63			63
1ouq	pd0404	E   |    H   |    B	21	prot-nuc	diff	double-kink line	0.663		35	28	63	63
1a74	pde140	E   |    H   |    B	20	prot-nuc	diff	double-kink line	0.237		33	31	64	64
1mnm	pdr036	E   |    H   |    B	25	prot-nuc	diff	double-kink line	1.552		40	24	64	64
1cz0	pd0097	E   |    H   |    B	20	prot-nuc	diff	double-kink line	0.259		34	31	65	65
1jj4	pd0227	E   |    H   |    B	16	prot-nuc	diff	double-kink line	0.518		32	33	65	65
1cyq	pd0096	E   |    H   |    B	20	prot-nuc	diff	double-kink line	0.291		35	31	66	66
1ic8	pd0208	E   |    H   |    B	21	prot-nuc	diff	double-kink line	0.737		18	48	66	66
1tc3	pde0128	E   |    H   |    B	19	prot-nuc	diff	double-kink line	0.407		34	32	66	66
1ewq	pd0142	E   |    H   |    B	21	prot-nuc	diff	double-kink line	0.660		27	40	67	67
2lef	------	E   |    H   |    B	15	prot-nuc	NMR	double-kink line	0.407		37	30	67	67
1e3m	pd0201	E   |    H   |    B	17	prot-nuc	diff	single-kink line	1.164		70			70
1jwl	pd0250	E   |    H   |    B	14	prot-nuc	diff	double-kink line	0.786		40	31	71	71
1lwt	pd0320	E   |    H   |    B	36	prot-nuc	diff	double-kink line	1.483		52	19	71	71
1ng9	pd0367	E   |    H   |    B	17	prot-nuc	diff	single-kink line	1.020		71			71
1gt0	------	E   |    H   |    B	23	prot-nuc	diff	double-kink line	0.821		55	17	72	72
2gli	pdt008	E   |    H   |    B	20	prot-nuc	diff	double-kink line	1.264		31	41	72	72
1iaw	pd0207	E   |    H   |    B	16	prot-nuc	diff	double-kink line	0.590		52	21	73	73
1lws	pd0319	E   |    H   |    B	34	prot-nuc	diff	double-kink line	1.163		56	17	73	73
1qn4	pd0154	E   |    H   |    B	14	prot-nuc	diff	double-kink line	0.307		41	32	73	73
1ipp	pde0144	E   |    H   |    B	20	prot-nuc	diff	double-kink line	0.311		62	12	74	74
2cgp	pdt049	E   |    H   |    B	26	prot-nuc	diff	double-kink line	0.153		37	37	74	74
1gdt	pde0115	E   |    H   |    B	34	prot-nuc	diff	double-kink line	0.588		44	31	75	75
1n14	------	E   |    H   |    B	13	nuc	NMR	double-kink line	0.990		37	38	75	75
1a84	------	E   |    H   |    B	12	nuc	NMR	single-kink line	0.852		78			78
1ais	pdr031	E   |    H   |    B	17	prot-nuc	diff	double-kink line	0.617		49	29	78	78
1k6o	pd0258	E   |    H   |    B	23	prot-nuc	diff	double-kink line	1.853		21	57	78	78
2kbd	------	E   |    H   |    B	16	nuc	NMR	double-kink line	0.231		30	48	78	78
1jfi	pd0221	E   |    H   |    B	17	prot-nuc	diff	double-kink line	0.508		41	39	80	80
2rve	pde002	E   |    H   |    B	16	prot-nuc	diff	double-kink line	0.454		43	40	83	83
1qne	pd0163	E   |    H   |    B	14	prot-nuc	diff	double-kink line	0.376		49	37	86	86
1c9b	pd0112	E   |    H   |    B	17	prot-nuc	diff	double-kink line	0.914		43	44	87	87
1owf	pd0406	E   |    H   |    B	20	prot-nuc	diff	double-kink line	0.579		24	65	89	89
1run	pdr024	E   |    H   |    B	30	prot-nuc	diff	double-kink line	0.527		48	42	90	90
1cgp	pdr006	E   |    H   |    B	30	prot-nuc	diff	double-kink line	0.389		48	44	92	92
1l1m	------	E   |    H   |    B	23	prot-nuc	NMR	double-kink line	0.217		51	41	92	92
1ouz	pd0405	E   |    H   |    B	20	prot-nuc	diff	double-kink line	0.574		25	67	92	92
1ruo	pdr025	E   |    H   |    B	30	prot-nuc	diff	double-kink line	1.164		46	47	93	93
1ngm	pd0368	E   |    H   |    B	19	prot-nuc	diff	double-kink line	0.573		57	38	95	95
1owg	pd0407	E   |    H   |    B	20	prot-nuc	diff	double-kink line	0.468		28	67	95	95
1d3u	pd0070	E   |    H   |    B	23	prot-nuc	diff	double-kink line	0.683		58	44	102	102
1cdw	pdt034	E   |    H   |    B	16	prot-nuc	diff	double-kink line	0.533		56	48	104	104

The following structures cannot be described by one of the models adopted for the description of the helical axis, like the superhelical structures 1aoi, 1eqz, 1f66 and 1id3, or have goodness-of-fit values larger than 2. The latter duplexes can nevertheless roughly be classified as double-kink structures. This Table includes the most strongly bent structures currently known: 1aoi, 1ihf, 5crx, 4crx. 

Number of structures: 22

PDB	NDB	IMB Jena Image Library	bp	molecule type	method	model	s(2)	r	a/a1	a2	a1+a2	M
2d47	adl025	E   |    H   |    B	12	nuc	diff	single-kink line	3.186		53			53
1j9h	ar0034	E   |    H   |    B	9	nuc	diff	circular line	3.280	12				60
1fjl	pde025	E   |    H   |    B	41	prot-nuc	diff	double-kink line	2.521		31	31	62	62
1ju1	------	E   |    H   |    B	23	nuc	NMR	double-kink line	3.481		32	32	64	64
1dfu	pr0018	E   |    H   |    B	15	prot-nuc	diff	double-kink line	3.516		62	31	93	93
1n96	------	E   |    H   |    B	8	nuc	NMR	circular line	34.159	9				76
1bpz	pde0124	E   |    H   |    B	16	prot-nuc	diff	double-kink line	2.241		64	32	96	96
1nzb	pd0392	E   |    H   |    B	36	prot-nuc	diff	double-kink line	4.446		24	78	102	102
4crx	pd0047	E   |    H   |    B	34	prot-nuc	diff	double-kink line	3.227		24	82	107	107
5crx	pd0048	E   |    H   |    B	32	prot-nuc	diff	double-kink line	2.926		29	83	111	111
1ihf	pdt040	E   |    H   |    B	34	prot-nuc	diff	double-kink line	3.423		92	82	174	174
1nyd	------	E   |    H   |    B	9	nuc	NMR	circular line	2.264	3				188
-	-	-	-	-	-	-	-	-	-	-	-	-
1aoi	pd0001	E   |    H	146	prot-nuc	diff	-	-	-	-	-	-	-
1eqz	pd0137	E   |    H	146	prot-nuc	diff	-	-	-	-	-	-	-
1f66	pd0171	E   |    H	146	prot-nuc	diff	-	-	-	-	-	-	-
1id3	pd0209	E   |    H	146	prot-nuc	diff	-	-	-	-	-	-	-
1kx3	pd0285	E   |    H	146	prot-nuc	diff	-	-	-	-	-	-	-
1kx4	pd0286	E   |    H	146	prot-nuc	diff	-	-	-	-	-	-	-
1m1a	pd0330	E   |    H	146	prot-nuc	diff	-	-	-	-	-	-	-
1m18	pd0328	E   |    H	146	prot-nuc	diff	-	-	-	-	-	-	-
1m19	pd0329	E   |    H	146	prot-nuc	diff	-	-	-	-	-	-	-
1kx5	pd0287	E   |    H	147	prot-nuc	diff	-	-	-	-	-	-	-

Abbreviations