We thank Professor L.N. Johnson for providing a stimulating working environment.
We are grateful to the Royal Commission for the Exhibition of 1851 and the Royal Society for support.
We thank András Fiser for numerous helpful discussions and a critical review of the manuscript,
and Drs J. Kuriyan, S.K. Burley, M.J. Adams and M.E.M. Noble for providing coordinates prior to
deposition. Abbreviations
3D, three-dimensional; Ig, immunoglobulin; RMS, root mean square; SH2, src homology 2;
SH3, src homology 3; HNF-3, hepatocyte nuclear factor 3; the standard three letter and one letter
abbreviations for amino acids are also used throughout.
Figure 1
Molscript (Kraulis, 1991) drawings illustrating
example of three types of 3D structural similarities all with Mouse Ig light chain
variable domain (2FBJ_Ldomain 1). The type A similarity is between 2FBJ_Ldomain
1 and a Human Ig light chain variable domain; the type B between 2FBJ domain 1 and
2CD4 domain 1; and the type C between 2FBJ_Ldomain 1 and poplar plastocyanin. Equivalent
strand regions within the three structures similar to 2FBJ_Lare shown as arrows; non-equivalent
regions are shown as
trace.
Figure 2
Complete linkage cluster analysis dendrogram derived by a matrix of the sums of the absolute
differences between columns in Table 3. The numbers on axis correspond to the
minimum sum of absolute differences for each cluster (eg. W and F cluster together with
a sum of absolute differences of
).
Figure 3
How structurally derived sequence alignments and protein 3D structures are used to find side-chain
to side-chain contacts common to a pair of 3D structures. The sequence alignment is shown in the
top of the figure and the two structures in the same (ie. superimposed) orientation are shown in the
bottom of the figure. A pair of residues in contact in Protein 1 (,
) are equivalent to another
pair in Protein 2 (
,
). The interaction R-D in Protein 1 is ``replaced'' in Protein 2 by the
interaction F-A.
Figure 4
How the structurally similarity index behaves as a function of the percent
sequence identity (
).
Figure 5
How the percentage of positions having the same accessibility category behaves as a function of the percent
sequence identity ().
Figure 6
How the percentage of positions within structurally equivalent regions behaves as a function of
the percent sequence identity ().
Figure 7
How the percentage of positions having the same three state secondary structure assignment behaves as a
function of the percent sequence identity ().
Figure 8
How the RMS deviation for equivalent atoms behaves as a
function of the percent sequence identity (
).
Interesting outliers are specified by their
PDB four letter code, their chain letter (if any) and a Roman numeral specifying the number of the
domain considered (numbered sequentially from the N-terminus).
Figure 9
How the number of residue pairs with side-chains in contact behaves as a function of
the sequence length.
Figure 10
How the number of residues with side-chains in an energetically favourable contact behaves as a function of
the total number of residue pairs in contact.
Figure 11
How the percentage of residues with side-chains in contact common to both structures behaves as a function
of percent sequence identity (). Interesting outliers are specified as described in Figure 8.
Figure 12
How the percentage of residues with -
distances
Å common to both structures behaves
as a function of percent sequence identity (
).
Figure 13
How the percentage of residues with side-chains in an energetically favourable contact common to both structures
behaves as a function of percent sequence identity (). Interesting outliers are specified as described in Figure 8.
The dashed line shows the expected percentage of favourable interactions for
convergently related proteins of a similar 3D structure.
Figure 14
How the percentage of complementary changes behaves as a function of . Four pairs with high percentages
are shown as described for Figure 8. The dashed line shows the expected percent complementary changes for
convergently related proteins of a similar 3D structure.
Figure 15a
Figure 15b
Figure 15c
Figure 15d
Figure 15e
Five examples of complementary changes. Details are described in the text.