List of Figures

• The homeodomain-DNA complex scheme.
• The initial structure of the wild type complex interface.
• The Gln50$\to$Lys mutation in the protein.
• The C6C7$\to$GG mutation in the DNA.
• Time dependence of root mean square deviation in two runs (wild type and protein mutant).
• Time dependence of root mean square deviation in two runs (DNA mutant and double mutant).
• Time dependence of root mean square deviation for all DNA bases in the four runs.
• Direct intermolecular contacts in the four complexes.
• Direct intermolecular contacts in the four complexes formed by residue 50.
• Direct intermolecular contacts in the four complexes formed by Asn51.
• Time development of the backbone and side chain angles of residue 51 in the complex with protein mutant and of the distances between Asn51 and base pairs 9 and 10.
• Number of hydrophobic contacs formed by Ile47 and Met54 in the four complexes.
• The number of water bridges to residues 50 and 51 in the four complexes.
• The interface of the wild type complex after 50 ps of the run.
• Contacts formed by two representative water molecules in wild type and protein mutant complexes.
• Contacts formed by two representative water molecules in DNA mutant and double mutant complexes.
• Movement of water molecules in the wild type complex.