The structures of interleukin-1 β , basic fibroblast growth factor and Erythrina trypsin inhibitor have been analysed in order to determine whether the hydrophobic core remains conserved, even when the structures have extremely low sequence similarities. We find that there are significant differences in the way each protein achieves a satisfactory arrangement of core residues and that positions which contribute to the core of one structure are not guaranteed to contribute to the integrity of another. Furthermore, the side-chain packing arrangements of these core residues vary significantly between the three structures. During this analysis the side-chain rotamers for three independently determined interleukin-1 β structures were also compared. It was found that although buried residues are generally in agreement the remaining residues frequently occupy different rotamers in the three structures. This suggests that although meaningful studies are possible for buried side-chains the results obtained from equivalent analyses of accessible residues should be treated with caution. These results are discussed with specific reference to the optimization of side-chain packing in proteins of known structure.
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