Table 2.

Averages and standard deviations of helical parameters for the different dinucleotide steps

Step	Shift	Slide	Rise	Tilt	Roll	Twist
AA•TT (4/55)	−0.19 ± 0.11	−0.42 ± 0.13	3.33 ± 0.04	−2.02 ± 0.40	2.74 ± 0.60	33.57 ± 1.25
	−0.30 ± 0.02	−0.00 ± 0.02	3.37 ± 0.03	−3.28 ± 0.63	5.89 ± 0.41	35.62 ± 0.74
	0.11 ± 0.30	−0.16 ± 0.36	3.25 ± 0.15	−1.32 ± 2.13	1.43 ± 4.78	35.77 ± 3.87
AC•GT (7/18)	0.05 ± 0.09	−0.74 ± 0.14	3.37 ± 0.05	−1.06 ± 0.30	0.01 ± 0.70	33.38 ± 0.98
	0.37 ± 0.05	−0.16 ± 0.08	3.20 ± 0.06	0.12 ± 0.82	3.44 ± 0.13	31.96 ± 1.02
	0.35 ± 0.40	−0.39 ± 0.28	3.20 ± 0.19	0.02 ± 2.10	1.73 ± 2.22	32.37 ± 3.07
AG•CT (4/10)	−0.33 ± 0.04	−0.65 ± 0.20	3.39 ± 0.08	−2.70 ± 0.31	2.83 ± 0.88	32.06 ± 1.29
	0.00 ± 0.03	−0.19 ± 0.09	3.31 ± 0.07	−3.02 ± 0.66	6.45 ± 0.50	31.45 ± 1.41
	0.35 ± 0.29	0.34 ± 0.39	3.23 ± 0.15	−2.19 ± 1.73	5.54 ± 3.73	28.80 ± 5.70
AT•AT (3/44)	0.00 ± 0.14	−0.77 ± 0.06	3.14 ± 0.03	0.00 ± 0.49	1.47 ± 0.35	28.59 ± 0.91
	0.00 ± 0.08	−0.36 ± 0.05	3.16 ± 0.02	0.00 ± 0.42	5.02 ± 0.64	28.12 ± 1.23
	0.00 ± 0.33	−0.57 ± 0.19	3.27 ± 0.19	0.00 ± 2.85	−1.02 ± 3.64	31.32 ± 3.78
CA•TG (5/32)	−0.33 ± 0.13	−0.22 ± 0.07	3.21 ± 0.06	0.43 ± 0.49	9.25 ± 0.93	28.44 ± 1.59
	−0.23 ± 0.13	−0.07 ± 0.02	3.46 ± 0.07	−0.12 ± 0.23	9.64 ± 1.77	33.43 ± 0.97
	0.01 ± 0.26	1.85 ± 1.01	3.14 ± 0.32	0.05 ± 2.76	−0.87 ± 6.76	43.65 ± 8.31
CC•GG (8/21)	0.11 ± 0.12	−0.76 ± 0.17	3.56 ± 0.07	−0.44 ± 0.69	4.58 ± 0.62	34.19 ± 1.82
	0.01 ± 0.08	−0.18 ± 0.12	3.55 ± 0.03	−0.38 ± 0.58	5.34 ± 0.98	35.50 ± 1.51
	0.16 ± 0.58	0.47 ± 0.54	3.29 ± 0.20	3.46 ± 2.74	5.35 ± 3.72	34.60 ± 7.57
CG•CG (8/64)	0.00 ± 0.14	−0.07 ± 0.08	3.26 ± 0.12	0.00 ± 0.78	6.45 ± 1.06	31.89 ± 3.66
	0.00 ± 0.14	0.29 ± 0.16	3.46 ± 0.08	0.00 ± 1.06	8.99 ± 1.15	33.92 ± 1.40
	0.00 ± 0.54	0.52 ± 0.47	3.31 ± 0.34	0.00 ± 3.76	3.83 ± 4.83	33.48 ± 6.44
GA•TC (5/47)	−0.21 ± 0.16	−0.29 ± 0.19	3.37 ± 0.03	−0.50 ± 0.74	2.14 ± 1.13	36.47 ± 1.01
	−0.28 ± 0.06	0.26 ± 0.04	3.35 ± 0.01	−0.80 ± 0.62	3.78 ± 0.54	38.65 ± 0.42
	−0.20 ± 0.49	0.00 ± 0.39	3.50 ± 0.46	−0.99 ± 2.81	0.33 ± 3.76	41.85 ± 6.04
GC•GC (5/67)	0.00 ± 0.12	−0.29 ± 0.12	3.41 ± 0.02	0.00 ± 0.33	−1.08 ± 0.68	36.07 ± 0.60
	0.00 ± 0.08	−0.18 ± 0.04	3.27 ± 0.01	0.00 ± 0.54	3.19 ± 0.26	35.58 ± 0.37
	0.00 ± 0.86	0.31 ± 0.41	3.46 ± 0.31	0.00 ± 4.40	−6.41 ± 5.22	41.35 ± 3.97
TA•TA (3/9)	0.00 ± 0.30	−0.15 ± 0.07	3.27 ± 0.04	0.00 ± 1.89	8.32 ± 1.37	32.66 ± 0.43
	0.00 ± 0.30	0.30 ± 0.06	3.39 ± 0.07	0.00 ± 1.21	5.57 ± 2.36	36.63 ± 0.95
	0.00 ± 0.37	0.38 ± 0.74	3.34 ± 0.21	0.00 ± 2.47	−0.58 ± 4.12	43.45 ± 5.17
Generic	0.00 ± 0.20	−0.47 ± 0.24	3.35 ± 0.11	0.00 ± 1.28	3.64 ± 3.12	32.84 ± 2.51
	0.00 ± 0.21	−0.04 ± 0.20	3.36 ± 0.11	0.00 ± 1.61	5.74 ± 2.06	34.22 ± 2.72
	0.00 ± 0.20	0.30 ± 0.67	3.29 ± 0.11	0.00 ± 1.56	1.43 ± 3.11	36.48 ± 5.17

The parmbsc0, CHARMM27 (italics) and X-ray values (bold) are shown. Values for simulations were obtained from the time averages computed for individual steps in each sequence. The standard deviations thus refer to the environment dependence of the parameters and not to their fluctuations in time. The generic values are means and standard deviations computed from the sequence-dependent averages shown in the table, weighting equally all the 16 possible steps. Rotational parameters are in degrees and translational ones in Å. Complementary steps (e.g. AG and CT) have the same average except for a change in sign of shift and tilt, and the same standard deviation. In parentheses is the number of copies of each step taken from the simulated oligomers and from the X-ray database (bold).