4NOD: Base Pair Morphology Step Parameters

A Portal for Three-dimensional Structural Information about Nucleic Acids
As of 19-Jan-2022 number of released structures: 11891

Search for released structures

NDB ID: NA2797 PDB ID: 4NOD

Base Pair Morphology Step Parameters

CSV Format

Model Number	Step Number	Step Name	Shift	Slide	Rise	Tilt	Roll	Twist	X-Displacement	Y-Displacement	Helical Rise	Inclination	Tip	Helical Twist
1	24	CC_BRU19DT20:DA3DA4_DD	0.482	-1.102	3.095	2.56	3.58	24.009	-3.646	-0.398	2.936	8.514	-6.089	24.403
1	16	CC_DA8DT9:DA14DT15_DD	-0.428	0.32	3.019	0.671	7.197	26.307	-1.002	1.065	2.988	15.445	-1.441	27.265
1	11	CC_DG3DG4:DC19DC20_DD	0.073	1.446	3.087	-1.367	-5.134	38.455	2.75	-0.263	2.874	-7.75	2.064	38.806
1	12	CC_DG4DG5:DC18DC19_DD	0.3	0.526	3.218	1.582	4.852	29.577	0.019	-0.253	3.272	9.415	-3.07	30.005
1	13	CC_DG5DG6:DC17DC18_DD	-1.043	0.194	4.999	-0.61	46.745	34.964	-3.932	1.026	3.271	55.194	0.72	57.784
1	14	CC_DG6DT7:DA16DC17_DD	-1.473	0.123	3.578	5.923	43.064	4.01	-4.486	2.621	0.258	84.192	-11.579	43.645
1	18	CC_DG10DG12:DC11DC13_DD	0.423	-0.216	6.895	11.501	-1.45	71.734	-0.081	0.446	6.891	-1.229	-9.751	72.54
1	19	CC_DG12DG13:DC10DC11_DD	0.579	-0.317	2.822	6.774	17.005	32.671	-2.435	-0.132	2.442	27.689	-11.03	37.327
1	22	CC_DG17DG18:DC5DC6_DD	-0.177	1.085	5.465	5.301	47.805	22.951	-4.886	0.875	3.385	65.57	-7.27	52.998
1	23	CC_DG18BRU19:DA4DC5_DD	0.484	-0.389	3.087	-5.308	5.902	23.904	-2.478	-2.537	2.744	13.772	12.385	25.169
1	26	CC_DG21DG22:DC1DC2_DD	-1.847	0.334	3.36	-0.536	11.214	44.701	-0.581	2.314	3.367	14.475	0.692	46.019
1	27	CE_DG22DT1:DA22DC1_FD	-0.565	-1.055	3.103	0.251	-2.261	14.076	-2.23	2.503	3.22	-9.148	-1.015	14.257
1	9	CC_DT1DT2:DA21DA22_DD	-0.17	-0.388	3.418	-2.899	1.809	36.403	-0.879	-0.146	3.398	2.888	4.627	36.558
1	10	CC_DT2DG3:DC20DA21_DD	1.072	1.078	3.09	5.89	-0.743	41.75	1.572	-0.906	3.187	-1.036	-8.215	42.151
1	15	CC_DT7DA8:DT15DA16_DD	-0.912	2.044	2.927	-8.609	13.518	24.715	0.841	-0.232	3.658	28.12	17.908	29.388
1	17	CC_DT9DG10:DC13DA14_DD	0.841	2.163	3.569	-4.894	-0.798	43.962	2.953	-1.606	3.423	-1.061	6.513	44.227
1	20	CC_DT15DT16:DA7DA8_DD	-0.432	1.242	3.183	-0.741	25.306	13.586	-4.459	0.669	2.622	62.2	1.821	28.68
1	21	CC_DT16DG17:DC6DA7_DD	-0.147	1.123	3.318	-2.853	19.894	27.372	-1.718	-0.27	3.357	36.459	5.228	33.844
1	25	CC_DT20DG21:DC2DA3_DD	0.052	-0.143	3.585	1.531	3.571	44.183	-0.552	0.087	3.563	4.736	-2.031	44.345
1	5	EE_BRU19DT20:DA3DA4_FF	0.501	-1.1	3.129	1.703	2.856	24.516	-3.386	-0.682	3.01	6.687	-3.987	24.737
1	35	EE_DA8DT9:DA14DT15_FF	-0.423	0.325	3.007	0.841	7.825	26.033	-1.143	1.098	2.962	16.886	-1.814	27.177
1	30	EE_DG3DG4:DC19DC20_FF	0.036	1.494	3.068	-1.846	-4.426	38.203	2.768	-0.264	2.879	-6.73	2.807	38.492
1	31	EE_DG4DG5:DC18DC19_FF	0.251	0.55	3.237	-0.052	5.109	29.551	0.006	-0.497	3.283	9.923	0.1	29.98
1	32	EE_DG5DG6:DC17DC18_FF	-1.053	0.227	5.082	-0.014	45.721	34.307	-4.048	1.109	3.34	55.025	0.017	56.603
1	33	EE_DG6DT7:DA16DC17_FF	-1.403	0.147	3.509	4.628	43.75	4.332	-4.418	2.353	0.351	84.185	-8.906	44.197
1	37	EE_DG10DG12:DC11DC13_FF	0.406	-0.201	6.884	11.132	-1.637	71.867	-0.056	0.431	6.88	-1.386	-9.427	72.625
1	38	EE_DG12DG13:DC10DC11_FF	0.575	-0.322	2.837	6.74	17.134	32.585	-2.469	-0.125	2.445	27.933	-10.988	37.304
1	3	EE_DG17DG18:DC5DC6_FF	-0.153	1.107	5.431	4.689	47.826	22.713	-4.879	0.772	3.378	65.853	-6.456	52.864
1	4	EE_DG18BRU19:DA4DC5_FF	0.463	-0.395	3.04	-5.158	6.191	23.612	-2.583	-2.462	2.69	14.594	12.159	24.931
1	7	EE_DG21DG22:DC1DC2_FF	-1.842	0.368	3.413	-0.705	10.59	44.64	-0.504	2.301	3.437	13.713	0.913	45.821
1	8	EC_DG22DT1:DA22DC1_DF	-0.513	-1.144	3.138	0.028	-1.489	13.238	-3.397	2.239	3.244	-6.434	-0.122	13.322
1	28	EE_DT1DT2:DA21DA22_FF	-0.189	-0.343	3.506	-2.203	4.041	36.121	-1.149	-0.025	3.454	6.485	3.536	36.403
1	29	EE_DT2DG3:DC20DA21_FF	0.979	1.136	3.062	4.515	-0.799	41.945	1.656	-0.92	3.125	-1.113	-6.284	42.183
1	34	EE_DT7DA8:DT15DA16_FF	-0.912	2.033	2.94	-7.763	12.486	24.732	1.047	-0.06	3.652	26.383	16.404	28.713
1	36	EE_DT9DG10:DC13DA14_FF	0.809	2.163	3.535	-5.172	-0.742	43.954	2.946	-1.586	3.388	-0.987	6.881	44.248
1	1	EE_DT15DT16:DA7DA8_FF	-0.423	1.239	3.191	-1.056	25.673	13.64	-4.447	0.558	2.617	62.441	2.568	29.037
1	2	EE_DT16DG17:DC6DA7_FF	-0.143	1.129	3.322	-2.219	19.711	27.3	-1.71	-0.164	3.368	36.305	4.086	33.634
1	6	EE_DT20DG21:DC2DA3_FF	0.011	-0.176	3.567	2.695	4.11	44.106	-0.648	0.258	3.533	5.453	-3.576	44.365
1	62	II_BRU19DT20:DA3DA4_JJ	0.496	-1.13	3.185	1.633	2.947	24.239	-3.544	-0.683	3.054	6.975	-3.864	24.469
1	54	II_DA8DT9:DA14DT15_JJ	-0.433	0.31	3.017	1.403	6.752	26.458	-0.907	1.241	2.976	14.444	-3.001	27.326
1	49	II_DG3DG4:DC19DC20_JJ	0.056	1.467	3.123	-1.15	-3.539	37.991	2.661	-0.221	2.977	-5.42	1.762	38.167
1	50	II_DG4DG5:DC18DC19_JJ	0.224	0.62	3.214	-0.051	5.371	30.211	0.116	-0.434	3.273	10.203	0.097	30.674
1	51	II_DG5DG6:DC17DC18_JJ	-1.19	0.138	4.87	-2.409	45.992	35.01	-3.884	1.031	3.213	54.639	2.862	57.268
1	52	II_DG6DT7:DA16DC17_JJ	-1.484	0.058	3.638	6.054	42.664	5.24	-4.578	2.668	0.3	82.569	-11.717	43.394
1	56	II_DG10DG12:DC11DC13_JJ	0.417	-0.203	6.917	11.105	-1.446	71.922	-0.07	0.423	6.914	-1.224	-9.399	72.672
1	57	II_DG12DG13:DC10DC11_JJ	0.573	-0.31	2.813	7.078	16.809	32.568	-2.413	-0.087	2.443	27.455	-11.561	37.206
1	60	II_DG17DG18:DC5DC6_JJ	-0.137	1.076	5.35	4.836	47.773	23.232	-4.762	0.757	3.355	65.34	-6.614	53.04
1	61	II_DG18BRU19:DA4DC5_JJ	0.468	-0.434	3.063	-4.844	6.405	23.721	-2.724	-2.385	2.707	15.039	11.375	25.024
1	64	II_DG21DG22:DC1DC2_JJ	-1.851	0.364	3.323	-1.526	10.065	44.437	-0.449	2.253	3.382	13.105	1.987	45.53
1	65	IK_DG22DT1:DA22DC1_LJ	-0.576	-1.649	3.215	0.696	-2.713	12.549	-4.196	3.386	3.454	-12.215	-3.135	12.857
1	47	II_DT1DT2:DA21DA22_JJ	-0.185	-0.43	3.484	-2.421	3.796	35.5	-1.28	-0.068	3.426	6.195	3.951	35.775
1	48	II_DT2DG3:DC20DA21_JJ	1.048	1.077	3.107	5.879	-1.262	42.134	1.608	-0.869	3.186	-1.745	-8.128	42.542
1	53	II_DT7DA8:DT15DA16_JJ	-0.932	2.001	2.928	-8.235	12.527	24.342	0.957	-0.148	3.636	26.714	17.56	28.528
1	55	II_DT9DG10:DC13DA14_JJ	0.808	2.162	3.523	-4.989	-0.512	43.934	2.923	-1.569	3.392	-0.681	6.642	44.205
1	58	II_DT15DT16:DA7DA8_JJ	-0.421	1.222	3.219	-1.103	25.135	13.746	-4.512	0.546	2.643	61.738	2.71	28.617
1	59	II_DT16DG17:DC6DA7_JJ	-0.13	1.132	3.342	-2.043	19.206	27.506	-1.64	-0.159	3.4	35.394	3.764	33.502
1	63	II_DT20DG21:DC2DA3_JJ	0.029	-0.16	3.595	3.117	3.842	43.849	-0.609	0.283	3.564	5.125	-4.159	44.114
1	43	KK_BRU19DT20:DA3DA4_LL	0.426	-1.129	3.152	2.495	4.136	24.54	-3.766	-0.284	2.953	9.612	-5.798	25.004
1	73	KK_DA8DT9:DA14DT15_LL	-0.403	0.302	3.022	0.678	6.659	26.145	-0.94	1.026	2.994	14.421	-1.469	26.974
1	68	KK_DG3DG4:DC19DC20_LL	-0.017	1.518	3.07	-1.776	-3.999	39.318	2.674	-0.166	2.906	-5.921	2.63	39.551
1	69	KK_DG4DG5:DC18DC19_LL	0.19	0.526	3.202	0.057	4.88	29.906	0.03	-0.352	3.246	9.377	-0.109	30.293
1	70	KK_DG5DG6:DC17DC18_LL	-1.135	0.219	4.943	-1.214	46.275	33.694	-3.993	1.084	3.213	55.845	1.465	56.704
1	71	KK_DG6DT7:DA16DC17_LL	-1.501	0.099	3.544	5.595	43.132	4.59	-4.446	2.61	0.287	83.568	-10.841	43.724
1	75	KK_DG10DG12:DC11DC13_LL	0.426	-0.223	6.892	10.547	-1.598	71.621	-0.076	0.38	6.893	-1.358	-8.964	72.306
1	76	KK_DG12DG13:DC10DC11_LL	0.562	-0.326	2.804	7.023	17.01	32.733	-2.425	-0.085	2.421	27.631	-11.408	37.428
1	41	KK_DG17DG18:DC5DC6_LL	-0.165	1.106	5.366	4.93	48.789	22.605	-4.776	0.789	3.305	66.409	-6.71	53.703
1	42	KK_DG18BRU19:DA4DC5_LL	0.453	-0.384	3.03	-6.121	5.795	23.78	-2.401	-2.644	2.665	13.53	14.292	25.209
1	45	KK_DG21DG22:DC1DC2_LL	-1.861	0.316	3.348	-1.273	9.248	44.464	-0.443	2.295	3.394	12.064	1.66	45.385
1	46	KI_DG22DT1:DA22DC1_JL	-0.603	-1.637	3.172	0.416	-2.835	12.748	-4.02	3.116	3.43	-12.562	-1.843	13.065
1	66	KK_DT1DT2:DA21DA22_LL	-0.205	-0.416	3.434	-2.083	3.603	34.931	-1.25	0.015	3.382	5.977	3.455	35.17
1	67	KK_DT2DG3:DC20DA21_LL	1.073	1.102	3.187	5.032	0.59	42.59	1.448	-0.969	3.302	0.809	-6.898	42.877
1	72	KK_DT7DA8:DT15DA16_LL	-0.958	2.043	2.95	-8.474	12.437	24.611	1.057	-0.153	3.676	26.272	17.9	28.788
1	74	KK_DT9DG10:DC13DA14_LL	0.825	2.164	3.555	-4.339	-0.149	44.105	2.884	-1.527	3.455	-0.198	5.761	44.308
1	39	KK_DT15DT16:DA7DA8_LL	-0.408	1.228	3.207	-0.731	25.827	13.673	-4.467	0.614	2.607	62.547	1.769	29.177
1	40	KK_DT16DG17:DC6DA7_LL	-0.139	1.143	3.344	-2.323	19.202	27.339	-1.648	-0.199	3.406	35.536	4.299	33.383
1	44	KK_DT20DG21:DC2DA3_LL	0.022	-0.121	3.578	0.705	3.047	44.085	-0.472	0.043	3.563	4.053	-0.938	44.191

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.