Both the homology model and the equivalent part of 5uke chain 2 (residues 16:105 in the canonical numbering) were analysed with WHAT_IF (TWINSET). For this the following commands were used in sequence: DelHyd, HB2NET, HB2GRA, HB2LIS. HB2NET produces an optimized hydrogen bonding network. HB2GRA then graphically displays the hydrogen bonds and HB2LIS lists them. We also performed a WHAT_CHECK analysis on the hydrogen bonding network. Below we list the number of burried unsatisfied hydrogen bond donors and acceptors for both the homology model and for the equivalent portion of 5uke chain 2.

Displayed in the tophalf are the homology model (left) and the corresponding portion of 5uke chain 2 (right) along with all hydrogen bonds. In the bottom half only the hydrogen bonds are shown. Clearly the homology model has more hydrogen bonds than 5uke.

List of hydrogen bonds that WHAT_IF identified for the homology model and for 5uke chain 2:16-105 . WHAT_IF identified 103 hydrogen bonds for the homology model and 71 for 5uke chain 2.

WHAT_CHECK results for both the homology model and 5uke chain 2.

5uke chain 2:16-105 Homology model
Buried donors: 70 63
- without H-bond: 26 5
- essentially without H-bond: 0 0
- with only a very poor H-bond: 0 1
- with a poor H-bond: 1 4
- with a H-bond: 43 53
Buried acceptors: 40 47
- without H-bond: 12 6
- essentially without H-bond: 0 0
- with only a very poor H-bond: 0 1
- with a poor H-bond: 1 1
- with a H-bond: 27 39
For the same number of residues, the model displays both fewer burried unsatisfied donors as well as fewer unsatisfied acceptors.