The crystal structure of glycyl-L-threonine dihydrate reveals a large number of intermolecular contacts made to each molecule in the crystal. It is not surprising that the charged atom groups of each dipeptide, the alpha-ammonium group of the glycyl residue and the terminal carboxylate of the threonyl residue, interact with each other in a tight ion-ion hydrogen bond (Table 1.1). Likewise all polar atom groups, such as carbonyls, hydroxyls and amide nitrogens take part in some variety of electrostatic interaction. A couple of interesting observations stem from the number of van der Waal's contacts made by the carbonyl oxygen of the glycyl residue.
Table 1.1 List of contacts made to each non-hydrogen atom of molecule A in the model of Glycyl-L-threonine dihydrate, in file glythr.pdb.
| Atom A | Atom X | Type of Interaction | Distance |
| 1A@N | 2J@OG1 | ion-dipole hydrogen bond | 3.12 Å |
| 2J@OXT | ion-ion hydrogen bond | 2.85 Å | |
| 4A*@O | ion-dipole hydrogen bond | 2.87 Å | |
| 1A@CA | 1K@O | vdW | 3.27 Å |
| 2G@OG1 | vdW | 3.43 Å | |
| 1A@C | 1K@O | vdW | 3.67Å |
| 1A@O | 2J@N | dipole-dipole hydrogen bond | 3.05 Å |
| 2C@CB | vdW | 3.67 Å | |
| 2J@C | vdW | 3.67 Å | |
| 2J@CA | vdW | 3.27 Å | |
| 2A@N | 1K@O | dipole-dipole hydrogen bond | 3.05 Å |
| 2A@CA | 2C@CG2 | vdW | 3.95 Å |
| 2A@CB | 1E@O | vdW | 3.67Å |
| 2A@OG1 | 2G@O | ion-dipole hydrogen bond | 2.78 Å |
| 1K@N | ion-dipole hydrogen bond | 3.12 Å | |
| 2A@CG2 | 2E@C | vdW | 3.55 Å |
| 2E@CA | vdW | 3.95 Å | |
| 2A@C | 2C@CG2 | vdW | 3.55 Å |
| 2A@O | 2F@OG1 | ion-dipole hydrogen bond | 2.78 Å |
| 4E*@O | ion-dipole hydrogen bond | 2.73 Å | |
| 2A@OXT | 1K@N | ion-ion hydrogen bond | 2.85 Å |
| 4H*@O | ion-dipole hydrogen bond | 2.74 Å |
One interesting observation to be made in the crystal structure of the gly.thr dipeptide is that the threonine side chain has not adopted the same conformation that has been observed in solution. Specifically, the dihedral angle about Ca-Cb is -62.5 degrees in the crystal and 180 degrees in solution. Clearly, 180 degrees offers a better orientation for the side chain relative to the dipeptide backbone (Figure 1.1). In this conformation, all substituents are staggered, and a maximum number of trans- relationships exist. At -62.5 degrees, the hydroxyl group of the side chain is in a gauche conformation with respect to both the carboxylate group and the alpha-nitrogen, which is less sterically favorable.
Figure 1.1 Two conformations of the threonine sidechain (chi is the dihedral angle defined by N, Ca, Cb and CG2).
Despite the apparent preferability of the 180 degree dihedral angle, the crystal structure cannot accomodate that conformation. The side chain methyl group (@CG2) is within 2.2 Å of the carbonyl oxygen of a glycyl residue on an adjacent dipeptide and the side chain hydroxyl (@OG1) is not correctly positioned to take advantage of any hydrogen bonding opportunities. Contrasted with the favorable contacts made to the side chain when the dihedral is at -62.5 degrees, it is clear that rotating the side chain results in the loss of stabilizing intermolecular contacts. This evidence demonstrates that the conformation of a molecule in the crystalline state may reflect that molecule's local environment more than it does the lowest energy conformation of the molecule under isolated conditions. This is an important caveat to keep in mind when examining models of protein structures built from crystallographic data.