Fig 1.
Distribution of asparagine side chains (gray) around an adenosine nucleoside.
All molecular graphics were created using using VMD-1.9.2 [46].
Fig 2.
Side chain clusters identified in the distribution shown in Fig 1.
The clusters are shown in colours (dark blue, vermillion, light blue, pink, green, orange).
Table 1.
Number of contacts involving individual DNA base types after redundant entries had been discarded.
Table 2.
As Table 1, but only including contacts in which the amino acid interacts directly with the DNA base.
Fig 3.
Interaction energy profile example: dAMP—asparagine dimers.
The pink bars display the interaction energies of the entire distribution; the blue bars show the interaction energies provided by the members of its most stabilising cluster. The latter are shown in dark blue in Fig 2. The interaction energies were calculated in an environment with dielectric constant ε = 4.
Table 3.
DNA base—amino acid dimer types that can contribute to direct recognition.
Table 4.
dNMP—amino acid dimer types that can contribute to direct recognition.
Table 5.
dNMP—amino acid dimer types that can contribute to direct recognition.
Fig 4.
Recognition of adenine by asparagine (blue), glutamine (orange), lysine (pink), and threonine (green).
Fig 5.
Recognition of guanine by arginine (blue) and aspartate (orange).
Fig 6.
Interactions of cytosine with isoleucine (blue) and glutamine (orange).
Fig 7.
Recognition of thymine by threonine (blue), serine (orange), tyrosine (pink), and glutamine (green).