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![[Figure 4]](ba0002fig4mag.jpg)
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Figure 4
A NUCPLOT of a segment of the DNA in 1ber and the protein residues of chain A that interact with it. Bases are represented by one-letter codes and are coloured according to their type. Base pairs are connected by a solid black line between them. The DNA backbones are drawn next to the bases: sugars as brown pentagons and phosphates as purple circles. The base numbers, as given in the PDB file, are written inside the sugars. Interactions are plotted on either side of the DNA strands with hydrogen bonds drawn as blue dotted lines and non-bonded contacts as red dotted lines. Interacting protein residues are represented by their atom name, residue name and number and the chain identifier in brackets. The atom names are coloured blue for nitrogen and red for oxygen, although they are omitted from residues interacting only by non-bonded contacts. Water molecules are drawn as light green circles and labelled by their PDB number. A break in the DNA backbone is shown on the left-hand strand between bases 9 and 10. The chain above the break is labelled C and the chain below is D in accordance with the original PDB file. |
![[Figure 4]](ba0002fig4.jpg)
 | STRUCTURAL BIOLOGY |
ISSN: 2059-7983
