1. Volume 75, Issue 5, Pages 2170-2177 (November 1998)
An Analysis of the Relationship between Hydration and Protein-DNA Interactions 
Juliana Woda, Bohdan Schneider, Ketan Patel, Kavin Mistry, Helen M. Berman 
Biophysical Journal 
Volume 75, Issue 5, Pages (November 1998)
DOI: /S (98)77660-X
Copyright © 1998 The Biophysical Society Terms and Conditions

2. Figure 1
The DNA sequences in the two CAP-DNA complexes for which protein interaction sites were predicted. Sequence (a) (Parkinson et al., 1996a) shows both base and phosphate hydration while sequence (b) (Parkinson et al., 1996b) shows only base hydration. The consensus sequences are bold. The interacting protein residues are indicated by one-letter amino acid codes. Triple dots indicate that the predicted sites are within 1.0Å of the observed sites; double dots indicate the agreement is between 1.0 and 1.5Å; single dots 1.5–2.0Å. (>), the hydration site is >2.0Å from the observed protein atoms.
Biophysical Journal  , DOI: ( /S (98)77660-X)
Copyright © 1998 The Biophysical Society Terms and Conditions

3. Figure 2
The interface between CAP and DNAGCE in the high resolution complex (Parkinson et al., 1996a) showing base hydration in the bent part of the sequence. The predicted base hydration is drawn as pseudoelectron density in cyan and the interacting protein residues are shown in dark blue. The region shown in this figure is shaded in Fig. 1.
Biophysical Journal  , DOI: ( /S (98)77660-X)
Copyright © 1998 The Biophysical Society Terms and Conditions

4. Figure 3
A view of the three residues in the consensus region for the high resolution CAP-DNAGCE complex (Parkinson et al., 1996a). The predicted phosphate hydration is drawn as pseudoelectron density in cyan, the interacting protein residues are shown in dark brown, and the phosphate groups are red. The protein atoms that contact the DNA are shown as blue crosses. The predicted sites are the red crosses.
Biophysical Journal  , DOI: ( /S (98)77660-X)
Copyright © 1998 The Biophysical Society Terms and Conditions

5. Figure 4
The nine DNA sequences for which protein binding sites were correlated with the predicted base hydration sites of the DNA. The consensus sequences are bold. The interacting protein residues are indicated by one-letter amino acid codes; water-mediated protein-DNA contacts are labeled “W.” The closeness of prediction is coded as in Fig. 1.
Biophysical Journal  , DOI: ( /S (98)77660-X)
Copyright © 1998 The Biophysical Society Terms and Conditions

6. Figure 4
The nine DNA sequences for which protein binding sites were correlated with the predicted base hydration sites of the DNA. The consensus sequences are bold. The interacting protein residues are indicated by one-letter amino acid codes; water-mediated protein-DNA contacts are labeled “W.” The closeness of prediction is coded as in Fig. 1.
Biophysical Journal  , DOI: ( /S (98)77660-X)
Copyright © 1998 The Biophysical Society Terms and Conditions

7. Figure 5
Examples of the protein-DNA interfaces. The pseudoelectron densities are the predicted sites. The actual observed protein and DNA residues are shown. (a) OR1-DNA (Aggarwal et al., 1988); (b) OR2-DNA (Shimon and Harrison, 1993); (c) Cro-DNA (Harrison et al., 1988); (d) lambda-DNA (Beamer and Pabo, 1992); (e) mat α2-DNA (Wolberger et al., 1991); (f) gal4-DNA (Marmorstein et al. 1992); (g) engrailed homeodomain-DNA (Kissinger et al., 1990); (h) ZIF-DNA (Pavletich and Pabo, 1991).
Biophysical Journal  , DOI: ( /S (98)77660-X)
Copyright © 1998 The Biophysical Society Terms and Conditions