4NOD: Base Pair Morphology Parameters

A Portal for Three-dimensional Structural Information about Nucleic Acids
As of 22-Jun-2022 number of released structures: 12128

Search for released structures

NDB ID: NA2797 PDB ID: 4NOD

Base Pair Morphology Parameters

CSV Format

Model Number	Pair Number	Pair Name	Shear	Stretch	Stagger	Buckle	Propellor	Opening
1	25	C_BRU19:DA4_D	0.349	-0.082	0.492	2.062	-7.566	9.856
1	16	C_DA8:DT15_D	0.034	-0.298	-0.438	0.673	-9.882	4.133
1	11	C_DG3:DC20_D	-0.108	-0.284	0.081	0.613	-6.488	-3.628
1	12	C_DG4:DC19_D	0.201	-0.186	0.379	16.602	-8.623	1.298
1	13	C_DG5:DC18_D	0.603	0.064	0.376	23.531	1.078	-5.551
1	14	C_DG6:DC17_D	0.442	-0.219	-0.211	-17.519	-1.191	-1.092
1	18	C_DG10:DC13_D	-0.117	0.134	0.67	1.932	-13.471	6.454
1	19	C_DG12:DC11_D	2.395	0.831	0.02	-9.442	-24.236	26.068
1	20	C_DG13:DC10_D	0.281	1.385	0.539	-18.564	-19.706	26.007
1	23	C_DG17:DC6_D	0.214	0.204	0.002	19.796	14.257	4.164
1	24	C_DG18:DC5_D	1.398	0.4	-0.162	-16.503	-1.48	-1.478
1	27	C_DG21:DC2_D	0.205	-0.154	-0.08	-11.278	-12.977	1.693
1	28	C_DG22:DC1_D	1.933	0.207	0.074	-11.912	-6.401	-1.724
1	9	C_DT1:DA22_D	-1.249	0.248	-0.015	-8.633	-14.14	-4.017
1	10	C_DT2:DA21_D	-0.582	-0.033	0.402	-11.823	-8.047	-9.778
1	15	C_DT7:DA16_D	-0.188	-0.172	-0.415	-27.287	-13.334	5.662
1	17	C_DT9:DA14_D	0.123	0.088	-0.418	12.126	-12.938	-2.665
1	21	C_DT15:DA8_D	0.284	0.163	0.248	-31.129	-9.857	4.218
1	22	C_DT16:DA7_D	-1.207	0.048	-0.001	6.761	10.169	3.914
1	26	C_DT20:DA3_D	-0.841	-0.182	0.129	5.71	-6.786	7.574
1	5	E_BRU19:DA4_F	0.259	-0.27	0.554	3.431	-8.537	9.584
1	36	E_DA8:DT15_F	0.193	-0.233	-0.574	1.279	-12.063	4.206
1	31	E_DG3:DC20_F	-0.177	-0.446	-0.033	0.074	-5.541	-4.122
1	32	E_DG4:DC19_F	-0.022	-0.239	0.264	16.873	-8.514	0.588
1	33	E_DG5:DC18_F	0.44	0.059	0.4	22.514	0.175	-6.321
1	34	E_DG6:DC17_F	0.342	0.008	-0.485	-19.556	-3.092	-2.082
1	38	E_DG10:DC13_F	-0.051	0.083	0.516	2.163	-13.616	6.163
1	39	E_DG12:DC11_F	2.35	0.781	-0.044	-10.106	-24.18	26.01
1	40	E_DG13:DC10_F	0.217	1.365	0.416	-19.162	-19.04	25.693
1	3	E_DG17:DC6_F	0.316	0.135	-0.056	19.629	14.914	4.554
1	4	E_DG18:DC5_F	1.42	0.242	-0.067	-16.236	-1.255	-0.895
1	7	E_DG21:DC2_F	0.048	-0.21	-0.039	-12.078	-12.648	2.09
1	8	E_DG22:DC1_F	1.78	0.32	0.096	-13.11	-6.448	-1.173
1	29	E_DT1:DA22_F	-0.956	0.081	-0.085	-6.721	-15.296	-4.488
1	30	E_DT2:DA21_F	-0.489	-0.202	0.297	-12.634	-10.581	-10.137
1	35	E_DT7:DA16_F	-0.076	-0.025	-0.475	-27.073	-13.498	5.257
1	37	E_DT9:DA14_F	0.282	0.119	-0.547	11.918	-13.161	-2.137
1	1	E_DT15:DA8_F	0.34	0.202	0.135	-31.529	-9.194	4.31
1	2	E_DT16:DA7_F	-1.097	0.059	-0.027	7.057	11.427	4.003
1	6	E_DT20:DA3_F	-0.925	-0.339	0.272	6.221	-6.023	8.027
1	65	I_BRU19:DA4_J	0.202	-0.33	0.414	4.589	-7.253	10.131
1	56	I_DA8:DT15_J	0.121	-0.131	-0.513	1.096	-12.045	4.484
1	51	I_DG3:DC20_J	-0.253	-0.46	0.004	-0.595	-5.115	-4.112
1	52	I_DG4:DC19_J	-0.147	-0.232	0.217	13.941	-6.943	1.565
1	53	I_DG5:DC18_J	0.392	0.039	0.287	20.626	1.38	-5.021
1	54	I_DG6:DC17_J	0.373	-0.016	-0.219	-16.508	-2.357	-3.207
1	58	I_DG10:DC13_J	-0.049	0.142	0.432	2.218	-12.882	5.92
1	59	I_DG12:DC11_J	2.438	0.792	-0.114	-10.921	-23.417	25.972
1	60	I_DG13:DC10_J	0.338	1.353	0.358	-18.803	-18.811	25.989
1	63	I_DG17:DC6_J	0.26	-0.024	-0.071	19.987	15.655	4.888
1	64	I_DG18:DC5_J	1.389	0.055	-0.137	-13.88	-0.064	-1.084
1	67	I_DG21:DC2_J	-0.063	-0.142	-0.197	-12.164	-10.845	3.322
1	68	I_DG22:DC1_J	1.767	0.358	-0.046	-11.746	-3.468	-1.236
1	49	I_DT1:DA22_J	-0.968	-0.017	0.018	-6.602	-13.901	-5.035
1	50	I_DT2:DA21_J	-0.614	-0.268	0.442	-11.181	-6.552	-12.283
1	55	I_DT7:DA16_J	-0.093	0.028	-0.458	-27.306	-13.907	5.558
1	57	I_DT9:DA14_J	0.259	0.172	-0.579	11.674	-13.247	-2.195
1	61	I_DT15:DA8_J	0.342	0.059	0.17	-31.117	-9.557	4.031
1	62	I_DT16:DA7_J	-1.096	-0.083	0.03	6.988	11.623	4.292
1	66	I_DT20:DA3_J	-1.021	-0.365	0.221	5.042	-6.374	8.276
1	45	K_BRU19:DA4_L	0.218	-0.163	0.408	3.819	-6.076	10.345
1	76	K_DA8:DT15_L	0.132	-0.257	-0.442	1.211	-9.734	4.059
1	71	K_DG3:DC20_L	-0.265	-0.343	-0.147	-0.496	-4.87	-4.136
1	72	K_DG4:DC19_L	0.133	-0.16	0.146	13.907	-7.664	1.76
1	73	K_DG5:DC18_L	0.667	0.084	0.305	21.748	0.845	-5.555
1	74	K_DG6:DC17_L	0.474	-0.143	-0.238	-17.394	-4.184	-1.771
1	78	K_DG10:DC13_L	-0.089	0.135	0.568	1.776	-13.921	6.337
1	79	K_DG12:DC11_L	2.429	0.836	0.01	-9.876	-22.402	25.682
1	80	K_DG13:DC10_L	0.334	1.388	0.465	-18.117	-18.2	25.84
1	43	K_DG17:DC6_L	0.157	0.072	-0.056	18.573	14.876	5.153
1	44	K_DG18:DC5_L	1.268	0.255	-0.212	-16.582	-2.557	-1.176
1	47	K_DG21:DC2_L	0.165	-0.074	-0.141	-11.355	-9.42	2.618
1	48	K_DG22:DC1_L	1.931	0.306	0.141	-11.228	-2.992	-1.379
1	69	K_DT1:DA22_L	-1.157	0.113	-0.179	-6.909	-13.861	-4.56
1	70	K_DT2:DA21_L	-0.818	-0.118	0.179	-9.647	-5.201	-12.522
1	75	K_DT7:DA16_L	-0.07	-0.12	-0.415	-26.507	-12.509	5.416
1	77	K_DT9:DA14_L	0.174	0.092	-0.433	11.737	-11.818	-2.516
1	41	K_DT15:DA8_L	0.343	0.083	0.259	-31.457	-9.505	4.299
1	42	K_DT16:DA7_L	-1.185	-0.055	0.06	5.795	10.648	4.49
1	46	K_DT20:DA3_L	-0.942	-0.26	0.041	4.326	-7.008	8.037

The above values were obtained using first alternate conformation only and calculated by 3DNA program.
Xiang-Jun Lu & Wilma K. Olson (2003). '3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures', Nucleic Acids Res.31(17), 5108-21.
Xiang-Jun Lu & Wilma K. Olson (2008). '3DNA: a versatile, integrated software system for the analysis, rebuilding and visualization of three-dimensional nucleic-acid structures', Nat Protoc.3(7), 1213-27.