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Table 3 Components of the free energies (in kcal/mol) calculated according to the MM/DDDC-HP(+HB) model. The distance dependent dielectric constant is 1r. The constant term x const is -13.355 kcal/mol

From: Identification of DNA-binding protein target sequences by physical effective energy functions: free energy analysis of lambda repressor-DNA complexes.

Original base Mutated ΔGexp ΔGcalc vdW Coul H P HB
T3-A39 C-G 0.400 0.311 -50.460 -12.925 36.028 47.532 -6.508
  G-C 0.600 0.204 -50.326 -12.684 35.875 47.203 -6.508
  A-T 0.400 -0.091 -50.384 -12.669 35.965 46.861 -6.508
A4-T38 C-G 1.000 1.245 -49.982 -13.112 35.965 48.057 -6.327
  T-A 1.400 2.666 -49.455 -13.227 35.992 48.858 -6.147
  G-C 1.100 1.456 -49.704 -13.341 36.114 48.070 -6.327
C5-G37 T-A 0.800 1.681 -50.791 -13.042 36.270 49.108 -6.508
  A-T 0.600 0.404 -50.786 -12.985 36.360 47.860 -6.689
  G-C 0.700 0.659 -50.921 -12.952 36.417 47.978 -6.508
C6-G36 T-A 0.900 1.176 -50.637 -12.833 36.068 48.622 -6.689
  A-T 1.000 1.918 -50.517 -12.560 35.698 49.161 -6.508
  G-C 0.600 1.016 -50.216 -12.680 35.837 47.939 -6.508
T7-A35 G-C 0.400 0.018 -50.525 -13.005 35.845 47.387 -6.327
  A-T -0.200 0.301 -50.387 -13.076 35.731 47.715 -6.327
  C-G 0.900 0.725 -50.472 -12.987 36.267 47.781 -6.508
C8-G34 T-A 0.500 1.878 -50.138 -13.246 36.020 48.924 -6.327
  A-T 3.600 2.417 -49.584 -12.945 35.415 49.213 -6.327
  G-C 3.400 1.965 -49.762 -13.259 36.086 48.583 -6.327
T9-A33 A-T 2.800 2.387 -49.570 -12.933 36.187 48.386 -6.327
  G-C 1.000 1.111 -49.390 -13.552 36.308 47.427 -6.327
  C-G 0.300 0.489 -50.729 -12.988 36.235 47.834 -6.508
G10-C32 A-T 0.400 0.974 -50.711 -12.531 36.073 48.187 -6.689
  T-A 0.500 1.377 -50.195 -13.338 36.243 48.530 -6.508
  C-G 0.200 0.654 -51.175 -12.775 36.602 48.227 -6.870
G11-C31 C-G 1.400 -0.061 -50.889 -13.098 36.203 47.768 -6.689
  A-T 1.100 0.760 -50.512 -13.375 35.925 48.766 -6.689
  T-A 2.300 0.451 -51.217 -12.921 36.481 48.332 -6.870
C12-G30 G-C 2.500 2.764 -48.826 -13.604 36.091 48.425 -5.966
  A-T 2.500 1.043 -50.496 -12.687 36.059 48.030 -6.508
  T-A 2.700 2.161 -49.468 -13.250 35.898 48.845 -6.508
G13-C29 A-T 2.900 2.337 -50.000 -12.972 36.226 48.766 -6.327
  C-G 3.400 2.413 -49.823 -12.729 36.460 48.188 -6.327
  T-A 3.200 2.546 -49.982 -12.803 36.574 48.621 -6.508
G14-G28 C-G 3.700 2.728 -49.462 -12.929 36.226 48.215 -5.966
  T-A 3.700 2.834 -49.692 -12.379 35.851 48.556 -6.147
  A-T 3.100 2.202 -50.081 -13.153 36.145 48.793 -6.147
T15-A27 G-C 2.900 1.728 -50.522 -12.607 36.887 47.834 -6.508
  A-T 2.000 1.089 -50.515 -12.812 36.617 47.663 -6.508
  C-G 2.500 0.966 -50.540 -12.811 36.544 47.637 -6.508
G16-C26 C-G 0.900 1.793 -49.675 -12.665 36.140 47.676 -6.327
  T-A 1.000 1.767 -50.112 -12.163 35.993 47.912 -6.508
  A-T 0.600 1.276 -50.287 -13.133 36.279 48.280 -6.508
A17-T25 C-G 0.200 1.168 -50.790 -12.598 36.796 47.624 -6.508
  T-A -0.100 1.134 -50.710 -12.660 36.638 47.729 -6.508
  G-C -0.200 1.256 -50.358 -12.788 36.760 47.506 -6.508
T18-A24 C-G 2.000 1.796 -49.628 -13.518 36.648 47.978 -6.327
  A-T 2.800 2.799 -49.290 -13.722 36.428 48.885 -6.147
  G-C 1.100 1.749 -49.774 -13.455 36.261 48.399 -6.327
A19-T23 T-A 0.400 1.239 -50.111 -12.649 36.212 47.650 -6.508
  C-G 0.500 1.378 -50.196 -12.587 36.216 47.808 -6.508
  G-C 0.400 0.780 -50.410 -12.892 36.243 47.703 -6.508
wild- type -- 0.000 1.158 -50.404 -13.063 36.234 48.254 -6.508