Database proton NMR chemical shifts for RNA signal assignment and validation

Barton, Shawn; Heng, Xiao; Johnson, Bruce A.; Summers, Michael F.

doi:10.1007/s10858-012-9683-9

Table 1 Sequence variables and chemical shift corrections calculated by Pace regression

From: Database proton NMR chemical shifts for RNA signal assignment and validation

Atom	const	pre_a	pre_c	pre_g	pre_gu	pre_ug	suc_a	suc_c	suc_g	suc_gu
Part 1
A–H₂	7.0299	0.6672	0.2521	0.6899	0.7637	0.2555	−0.5934	0.0658	0.2814	−0.3321
A–H₈	8.1525	−0.4169	−0.1145	−0.3709	−0.3808	0.2107	−0.1006	0.0379	−0.0723	0.0458
G–H₈	7.7036	−0.5622	−0.1595	−0.497	−0.5083	0.2215	−0.0383	0.0562	−0.0265	0.0369
C–H₅	5.6724	−0.4611	−0.1625	−0.4304	−0.2815	0.0377	−0.0222	−0.0368	−0.0249	−0.032
U–H₅	5.5639	−0.5133	−0.1778	−0.5018	−0.3641	−0.0469	0.0333	0.0165	0	0.0348
C–H₆	7.8627	−0.3901	−0.0867	−0.2215	−0.2059	0.085	−0.0253	0.0363	−0.0288	−0.0833
U–H₆	7.9946	−0.3643	−0.1083	−0.2523	−0.3392	0.0832	−0.0402	0.0332	−0.0555	−0.0809
A–H₁′	5.9905	−0.1042	−0.05	0	−0.0639	0	−0.0823	0	−0.0324	0.0528
G–H₁′	5.7539	−0.1822	−0.0584	−0.019	−0.068	−0.0373	0	0.0216	0.0198	0.0777
C–H₁′	5.56	−0.1805	−0.0825	−0.0446	−0.0492	0.039	−0.0226	−0.0139	0.0134	0.0711
U–H₁′	5.6203	−0.1679	−0.0865	−0.1049	−0.1992	0.0234	−0.0405	0.0097	0.0196	0.0571
A–H₂′	4.4575	−0.0269	0.0268	0.0309	−0.0499	0.1174	0.1041	0.0496	0.1613	0.1416
G–H₂′	4.4582	−0.0666	0.0389	0	0	0.0794	0.1367	0.0248	0.1286	0.0705
C–H₂′	4.3454	−0.1298	0.0188	0.0499	−0.0867	0.0363	0.1475	0	0.1557	0.1724
U–H₂′	4.4078	−0.0599	0.0404	0.0658	−0.0445	0.0618	0.0807	0.059	0.174	0.1431
A–H₃′	4.6788	−0.1275	−0.0229	−0.0794	−0.083	0.0436	−0.0377	0.006	0.0105	0.0593
G–H₃′	4.5076	−0.1292	−0.029	−0.0537	−0.1527	0.0644	0.0445	0.0459	0.0333	0.0674
C–H₃′	4.4794	−0.1336	−0.0189	−0.0431	0.0221	0.0364	0.0498	−0.0147	0.0454	−0.043
U–H₃′	4.495	−0.119	−0.0065	−0.0447	0.0458	0.0506	0.1024	0.0229	0.0657	0.0839

Atom	suc_ug	5ter	3ter	3loop	5loop	GU	corr	rms	nobs	xcorr	xrms	ntrim
Part 2
A–H₂	0.0804	0.1558	0	0.0274	0.0622	0	0.9868	0.0562	162	0.9845	0.0608	1
A–H₈	−0.0261	0.3206	0	−0.0175	0.08	0	0.9535	0.0575	157	0.9406	0.065	0
G–H₈	−0.0671	0.3563	−0.0607	−0.0253	0.0332	−0.0529	0.9655	0.0658	288	0.9612	0.0697	2
C–H₅	−0.0958	0.1245	−0.016	−0.0205	0.01	0	0.9674	0.0478	256	0.9635	0.0505	5
U–H₅	0.047	0	0	0	0.0216	0.2747	0.9692	0.0537	178	0.9623	0.0594	0
C–H₆	−0.1132	0.2326	−0.0359	−0.0428	0.0311	0	0.9332	0.0558	260	0.9249	0.0591	0
U–H₆	−0.0457	0	−0.0287	−0.0341	0.0268	−0.0412	0.9444	0.0446	172	0.9331	0.0489	4
A–H₁′	−0.0353	0.0966	0	−0.0173	0.0061	0	0.8476	0.0332	157	0.7905	0.0384	0
G–H₁′	0	0.1435	−0.0376	0	0	0	0.9278	0.0415	284	0.9209	0.0434	3
C–H₁′	−0.0224	0.1351	0.0114	−0.0168	0.0121	0	0.8355	0.0427	253	0.7872	0.0482	5
U–H₁′	0.0328	0	0.0183	0.0145	0.0403	−0.0316	0.7411	0.053	172	0.6451	0.0609	1
A–H₂′	0.1044	0.0702	0	−0.0115	0.0291	0	0.7512	0.0618	143	0.6531	0.0714	0
G–H₂′	0.1022	0.074	−0.1122	−0.0326	−0.0257	0.1211	0.8675	0.0516	246	0.8359	0.057	2
C–H₂′	0.1198	0.085	−0.1316	0	0	0	0.9014	0.0589	217	0.8774	0.0654	4
U–H₂′	0.1691	0	−0.229	−0.0488	−0.03	−0.3095	0.92	0.0609	146	0.8999	0.0679	2
A–H₃′	0.0283	0.0235	0	−0.0248	0.0202	0	0.5997	0.064	129	0.4933	0.0708	0
G–H₃′	−0.0887	0.1061	−0.0416	−0.0146	0.0244	−0.1527	0.7307	0.0807	226	0.6391	0.0914	3
C–H₃′	−0.1182	0.1326	−0.0178	0.0096	−0.0224	0	0.7442	0.062	191	0.6942	0.0669	4
U–H₃′	−0.0268	0	−0.0432	−0.0187	0.0159	0.0266	0.7047	0.0482	121	0.5928	0.0552	2

Output from the Pace Regression analysis. Each row represents an individual atom type in the specified nucleotide (e.g., A-H₂ is the H₂ proton of Adenine). The column labeled const represents the chemical shift of that atom in the triplet uXu when none of the additional attributes represented in subsequent columns are present. Contributions with values equal to 0 represent attributes that the Pace Regression algorithm found could not be supported by the data and were thereby automatically excluded from the regression analysis. The contribution from columns labeled pre_x and suc_x, where x is a,c,g, or gu are used where the preceding or succeeding nucleotide is not a u. A GU attribute represents the case where the nucleotide is in a GU, rather than GC, base pair, and can apply to the i − 1 (pre_gu), i + 1 (suc_gu) or central (GU) triplet (with the same approach used for UG wobbles). The 5ter attribute indicates the triplet is at the 5′ end (so there is no i − 2 nucleotide), and 3ter indicates the triplet is at the 3′ end (so there is no i + 2 nucleotide). The loop attributes indicate that the i − 2 (5loop) nucleotide or i + 2 (3loop) nucleotide is in a loop or mismatched base pair. The columns labeled corr and rms represent the correlation coefficient (corr) and the square root of the mean of squared deviations between predicted and experimental values (rms) for all the data in the fit. The columns labeled xcorr and xrms represent the same values, but calculated with 10-fold stratified cross-validation. The column labeled nobs represents the number of observations available and ntrim the number that were automatically eliminated as outliers

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