Table 1.
Position-specific energy matrices based on direct interaction energies and interaction energies plus bending corrections
| ΔE
interaction
|
ΔE
interaction + ΔE
DNA deform
|
||||||
|---|---|---|---|---|---|---|---|
| A | C | G | T | A | C | G | T |
|
|
|
||||||
| 0.0 | −0.5 | −0.7 | −0.7 | 0.0 | 0.3 | −0.6 | 0.2 |
| 1.3 | 0.0 | 0.4 | −0.6 | 1.9 | 0.0 | 0.0 | 0.4 |
| 4.7 | 14.3 | 0.0 | 8.4 | 7.6 | 19.6 | 0.0 | 15.1 |
| −1.0 | 0.0 | 2.3 | 1.2 | 2.3 | 0.0 | 2.4 | 0.1 |
| 0.0 | 2.1 | 3.7 | 3.4 | 0.0 | 1.6 | 2.2 | 4.2 |
| 0.0 | 3.5 | 3.4 | 3.8 | 0.0 | 4.4 | 4.5 | 5.7 |
| 0.0 | 2.0 | 0.6 | 2.1 | 0.0 | 0.5 | 2.8 | 0.4 |
| 6.2 | 0.0 | 0.1 | 5.2 | 2.3 | 0.0 | −0.6 | 3.3 |
| 5.3 | 0.1 | 0.0 | 6.0 | 3.8 | −0.8 | 0.0 | 1.4 |
| 2.2 | 0.6 | 2.1 | 0.0 | 0.4 | 2.7 | 0.3 | 0.0 |
| 3.9 | 3.4 | 3.6 | 0.0 | 8.4 | 4.8 | 6.7 | 0.0 |
| 3.4 | 3.8 | 2.1 | 0.0 | 3.3 | 2.4 | 0.3 | 0.0 |
| 0.9 | 2.3 | 0.0 | −0.9 | −0.2 | 2.1 | 0.0 | 2.2 |
| 8.4 | 0.0 | 14.4 | 4.6 | 14.9 | 0.0 | 19.3 | 7.8 |
| −0.6 | 0.6 | 0.0 | 1.4 | −0.1 | 0.2 | 0.0 | 1.8 |
| −0.7 | −0.6 | −0.6 | 0.0 | −0.2 | −0.5 | −0.2 | 0.0 |
The energies are normalized to the consensus sequence, which has, accordingly zero binding energy. This is why a ‘Δ’ appears in front of the energies. All contributions from each base pair (including bending) were considered to be independent of the other base pairs. Energies are given in units of kilo calories per mole. Only the first decimal place is shown.