5CD1: Base Pair Morphology Parameters

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As of 12-Aug-2022 number of released structures: 12231

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NDB ID: 5CD1 PDB ID: 5CD1

Base Pair Morphology Parameters

CSV Format

Model Number	Pair Number	Pair Name	Shear	Stretch	Stagger	Buckle	Propellor	Opening
1	8	M_A7:U66_M	-0.026	0.193	-0.386	4.717	-25.885	6.779
1	17	M_A23:U12_M	-0.499	0.463	0.516	9.231	-19.824	1.39
1	20	M_A26:G44_M	0.499	1.905	0.267	26.495	-24.866	-31.233
1	23	M_A29:U41_M	-0.012	-0.061	-0.084	7.01	-25.1	-5.571
1	25	M_A31:U39_M	-0.618	0.237	0.257	-9.84	-31.494	11.742
1	10	M_A50:U64_M	-0.32	0.087	-0.134	-2.769	-21.253	-7.961
1	3	M_C2:G71_M	-0.363	-0.153	-1.411	15.933	-27.176	1.232
1	4	M_C3:G70_M	-0.083	-0.07	0.512	-1.506	-14.514	-3.172
1	5	M_C4:G69_M	-0.802	0.387	-0.677	0.492	-1.962	-3.315
1	19	M_C25:G10_M	-0.147	0.126	-0.509	10.317	-9.448	-6.725
1	22	M_C28:G42_M	-0.152	0.29	0.678	10.165	-15.869	4.136
1	26	M_C32:A38_M	1.244	-0.011	0.883	-20.794	-20.281	4.681
1	9	M_C49:G65_M	-0.908	-0.063	1.277	-2.251	-16.557	-4.512
1	1	M_G0:G73_M	-7.149	-1.579	-0.658	-5.161	25.568	-36.309
1	2	M_G1:C72_M	-0.362	0.161	-0.904	3.089	-6.223	-19.434
1	6	M_G5:C68_M	0.423	0.623	0.242	-14.939	-11.291	10.29
1	7	M_G6:U67_M	-1.878	-0.22	0.652	-0.842	-8.524	2.242
1	16	M_G22:C13_M	0.175	0.195	-0.089	-18.592	-7.191	-0.693
1	18	M_G24:C11_M	0.135	-0.13	-0.477	8.941	-19.798	-3.99
1	24	M_G30:C40_M	-0.53	-0.244	-0.546	-4.541	-31.084	-5.198
1	11	M_G51:C63_M	0.682	0.103	-1.664	-21.441	-10.493	-17.818
1	12	M_G52:C62_M	1.001	0.372	-1.405	-27.555	-2.666	-25.116
1	13	M_G53:C61_M	0.031	0.281	-0.023	-10.495	3.017	-1.943
1	15	M_U8:A21_M	-0.887	-0.394	1.953	5.541	-20.701	-176.295
1	21	M_U27:A43_M	0.54	0.276	0.532	11.726	-29.028	-13.565
1	14	M_U54:U60_M	2.754	-1.982	-1.779	6.826	13.902	-9.862
1	34	N_A7:U66_N	0.302	-0.118	-0.515	5.913	-17.328	1.44
1	41	N_A23:A9_N	4.736	-4.985	0.822	-42.952	-15.506	177.281
1	44	N_A26:G44_N	0.263	1.615	0.039	27.618	-19.344	-23.172
1	47	N_A29:U41_N	0.139	0.056	0.279	2.637	-23.764	-1.743
1	49	N_A31:U39_N	0.882	0.001	-0.052	-10.197	-31.874	-2.392
1	36	N_A50:U64_N	-0.407	-0.105	-0.921	-9.455	-23.112	-9.856
1	29	N_C2:G71_N	-0.143	0.413	0.013	9.216	-17.727	9.213
1	30	N_C3:G70_N	0.557	0.175	-0.216	19.708	-15.526	1.07
1	31	N_C4:G69_N	-0.286	0.395	-0.702	16.265	-16.644	-0.351
1	43	N_C25:G10_N	-0.615	0.092	-1.175	14.219	-4.643	-15.262
1	46	N_C28:G42_N	0.367	0.009	0.136	10.746	-21.948	2.838
1	50	N_C32:A38_N	2.61	-0.365	0.782	-16.514	-13.753	-4.657
1	35	N_C49:G65_N	-0.735	0.392	-0.677	19.957	7.983	-10.388
1	27	N_G0:C75_N	-0.562	0.072	0.288	-5.567	31.887	1.882
1	28	N_G1:C72_N	-1.03	-0.23	0.003	-11.742	-17.727	-10.218
1	32	N_G5:C68_N	0.277	0.37	-0.383	1.821	-17.221	9.146
1	33	N_G6:U67_N	-1.685	-0.085	1.12	11.141	-10.273	4.412
1	40	N_G22:C13_N	-0.323	0.121	-0.682	-15.225	1.882	-1.755
1	42	N_G24:C11_N	0.167	-0.052	-0.426	5.932	-20.941	-7.045
1	48	N_G30:C40_N	-0.738	-0.363	-0.046	0.484	-29.689	-11.587
1	37	N_G51:C63_N	0.84	0.527	-1.132	-21.457	-12.81	7.695
1	38	N_G52:C62_N	0.991	0.037	-1.704	-19.504	-8.346	-12.302
1	39	N_U8:A14_N	3.126	-6.877	-0.408	-18.081	9.104	142.037
1	45	N_U27:A43_N	1.185	-0.194	1.114	10.4	-29.972	-4.784
1	51	N_U33:A37_N	0.729	0.13	-0.316	14.763	10.303	1.922
1	52	N_U55:C61_N	4.156	-1.314	1.012	4.111	46.698	37.482

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.