Table 4.
Average values and dispersion of base-pair parameters in RNA helical fragments.†
| Rigid-body parameters |
|||||||
|---|---|---|---|---|---|---|---|
| Base pair | Shear (Å) | Stretch (Å) | Stagger (Å) | Buckle (deg) | Propeller (deg) | Opening (deg) | V (deg3Å3) |
| G·C_WC | −0.20(0.41) | −0.15(0.17) | −0.04(0.40) | −3.4(8.4) | −8.7(8.5) | 0.5(4.5) | 6.5 |
| A·U_WC | 0.04(0.34) | −0.14(0.15) | 0.04(0.39) | −0.3(8.4) | −9.0(8.7) | 0.9(5.2) | 6.4 |
| G·U_w | −2.11(0.84) | −0.52(0.27) | −0.04(0.43) | −0.1(8.2) | −7.4(7.5) | −0.6(6.9) | 25.1 |
| G·A_s | 6.78(0.23) | −4.40(0.55) | 0.14(0.52) | 1.5(11.0) | −3.2(9.1) | −5.4(8.4) | 27.1 |
| A·U_H | −4.06(0.80) | −1.92(0.84) | 0.07(0.61) | −0.4(7.3) | 1.0(10.8) | −95.1(17.4) | 25.9 |
| U·U_w | −2.34(0.59) | −1.63(0.31) | −0.09(0.47) | 0.6(8.8) | −11.1(7.8) | −0.2(17.4) | 49.8 |
| G·A_WC | 0.00(0.64) | 1.52(0.40) | −0.29(0.41) | 7.8(10.8) | −10.8(9.6) | −17.2(13.5) | 86.2 |
†
Mean values and standard deviations (subscripted values in parentheses) for steps in all helical contexts. Subscripts correspond to designations in Tables 2,3. Parameters defined such that the first of the two bases in a given pair lies in the primary strand I. Values are identical for the reverse pair, defined with respect to the secondary strand II, except that Shear and Buckle are of the opposite sign.