"Average" HMG-1 Box

Energy scaffolds for an "average" HMG-1 box

A subset of 48 HMG-1 box sequences was selected in order to identify the most important contacts within the HMG-1 box. The subset does not skew the data set in favor of identical sequences that have been determined in a number of different organisms. The individual pairwise interaction energies determined in the course of threading experiments were averaged over the entire subset.

The alpha-carbon backbone of the protein is depicted as a curving "worm." Within the backbone, segments of the HMG-1 box domain comprising the core folding motif are shown in blue, while the intervening loop regions are shown in yellow.

Pairwise residue interaction energies between core residues are indicated by the thickness and coloring of the connected alpha-carbon positions on the protein backbone. Thick, magenta-colored cylinders indicate the most favorable interactions. Thick, cyan-colored cylinders indicate the least favorable interactions. Intermediate colors and cylinder widths represent interactions falling between these extremes.

All pairwise interaction energies with E < -0.4 kcal/mol or E > 0.4 kcal/mol are indicated. 60 of the 62 interactions shown are favorable. The range of pairwise interaction energies is from -1.54 to 0.54 kcal/mol.

Indicated interactions are limited to those with pairwise interaction energies < -1 kcal/mol. The 11 residues shown in the figure are involved for maintaining the most important contacts within the HMG-1 box.