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Table 3 Comparison of cumulative contact and readout position weight matrices for 4 prokaryotic (top) and 4 eukaryotic (bottom) transcription factors

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

SCOP v1.73
superfamily
TF [PDB id] Resolution (Å) Robs E-valuecontacts E-valuereadout
Winged helix CRP [1cgp] 3 0.24 7.93E-03 3.76E-05
C-terminal domain of the bipartite response regulators NarL [1je8] 2.12 0.23 3.58E-05 7.01E-07
lambda repressor-like DNA-binding domains PurR [2pua] 2.9 0.16 4.33E-15 5.51E-01
(7.58E-04)
ribbon-helix-helix MetJ [1cma] 2.8 0.22 1.22E-01 3.30E-01
Zn2/Cys6 DNA-binding domain LEU3 [2er8] 2.85 0.23 4.97E-06 5.52E-05
HLH, helix-loop-helix DNA-binding domain PHO4 [1a0a] 2.8 0.23 3.57E-07 3.97E-07
Homeodomain-like RAP1 [1ign] 2.25 0.21 5.52E-03 1.89E-02
(6.40E-04)
C2H2 and C2HC zinc fingers ZIF268 [1aay] 1.6 0.19 7.93E-14 1.99E-14
  1. In the first column we include the name of the structural superfamily of each TF according to SCOP [37]. In the second column the name of each TF is followed by the PDB identifier of the structure used enclosed in brackets. The following two columns contain the resolution and the R-value of the crystals respectively. The last two columns report the E-values resulting from STAMP [38] local alignments between the structure-based PWMs obtained with the method of Morozov and Siggia [32] (E-valuecontacts) or our approach (E-valuereadout) and the corresponding cognate PWMs, extracted from the literature [43, 49, 53]. Parenthesized E-values were calculated after sampling interface rotamers with DNAPROT.