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Table 5 Contribution of hydrogen bonds, hydrophobic contacts and water-mediated hydrogen bonds to specific DNA recognition in terms of interface binding score (A) and STAMP E-value of structure-based PWMs (B)

From: Prediction of TF target sites based on atomistic models of protein-DNA complexes

A) Fraction of interface binding score contributed by:
  H-bonds Hydrophobic contacts Water-mediated
# atomic interactions
CRP 1.00 0.00 0.00 8
PurR 0.76 0.24 0.00 6
MetJ 0.89 0.00 0.11 6
NarL 0.61 0.34 0.05 11
LEU3 1.00 0.00 0.00 4
PHO4 1.00 0.00 0.00 7
RAP1 1.00 0.00 0.00 12
ZIF268 0.70 0.00 0.30 21
B) E -value of PWM derived from:
  H-bonds Hydrophobic contacts Water-mediated
All atomic interactions
NarL 1.049E-02 4.837E-04 - 7.010E-07
ZIF268 1.359E-11 - 6.957E-05 1.998E-14
  1. A) Transcription factors in Table 3 where further analyzed by assessing the fraction of the interface binding score, obtained after summing all log-likelihood atomic scores, contributed by each interaction type. The number of atomic interactions found by the DNAPROT protocol in the native PDB structure is indicated in the rightmost column. B) A further analysis of two notable examples, NarL with an important hydrophobic contribution and ZIF268 with a remarkable contribution of water-mediated hydrogen bonds, in which structurally derived PWMs that consider exclusively H-bonds, hydrophobic contacts or water-mediated H-bonds are compared with default DNAPROT PWMs, which integrate all three atomic interactions.