RMS deviation

Figure 8 shows RMS deviation, calculated using the method of McLachlan (1979) for pairs of equivalent common core atoms versus . The Figure is similar to that shown by Chothia and Lesk (1986), though with substantially more spread, which one would expect given the greater structural variation of the protein pairs considered here.

Three interesting outliers are labelled on the plot. Two distantly related globin structures (Sea Hare and Leghaemoglobin; 1MBA and 2LH1) show a higher RMS deviation than other structural pairs of a similar , which might be explained by the large variations in helix packing angles seen within this family [Pastore et al., 1988]. The other two pairs have RMS deviations lower than expected for their respective values. The two helical domains within 6-phosphogluconate dehydrogenase (PGD_IIand PGD_III) are closely packed together, and might accordingly be restrained to specific symmetrical conformations in spite of sequence dissimilarity. The two plastocyanin-like structures (1PLC and 1PAZ) have a strong functional similarity, which might also restrict the degree to which their core atoms can deviate from one another.