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![[Figure 2]](ba5270fig2mag.jpg)
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Figure 2
(a) The process of defining all-atom contacts. Small, pale dots are the van der Waals envelope of covalently bonded atoms, including H atoms. A probe sphere of 0.25 Å radius (gray) is rolled on this surface, leaving color-coded probe dots where it intersects with the surface of another atom. Favorable van der Waals contacts from just touching to 0.5 Å apart produce paired patches of green (close) and blue (more distant) contacts, while overlaps are either favorable hydrogen bonds between donor–acceptor atom pairs or repulsive overlaps in warm colors, with serious clashes of ≥0.4 Å shown by hot-pink spikes. (b) A definitive assignment of an amide `flip' for Gln115 in PDB entry 1gk8. The larger NH2 group gives clashes and there are no hydrogen bonds in the original position, while the flip shows three hydrogen bonds and no clashes. The REDUCE flip is confirmed as correct by the higher electron density in the assigned O position. |
![[Figure 2]](ba5270fig2.jpg)
 | STRUCTURAL BIOLOGY |
ISSN: 2059-7983
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