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Beta bulges

A beta bulge is a region of irregularity in a beta sheet, where the normal pattern of hydrogen bonding is disrupted e.g. by the insertion of an extra residue. Using the definition of beta strands and main-chain hydrogen bonds provided by the Kabsch and Sander algorithm such irregularities are identified and classified as described in Chan et al. (1993). The bulges are defined as parallel or antiparallel depending on whether they occur in parallel or antiparallel regions of beta sheet. Within each of these categories bulges are further subdivided into classic, wide, bent, G1 and special types depending on the number of residues involved and the hydrogen bonding pattern. Classic and wide bulges both involve an extra residue on one beta strand relative to its neighbouring strand. In antiparallel beta sheets the classic bulges occur where the extra residue is between two narrowly spaced pairs of hydrogen bonds, whilst in the case of the wide bulges the extra residue is between the widely spaced pairs of hydrogen bonds. Corresponding hydrogen bonding patterns for parallel classic and wide bulges can be found in Chan et al. (1993). Bent bulges occur much less frequently, and have one extra residue on both strand partners. The term special bulges is used to refer to several possible situations where there can be up to 3 extra residues in one strand. G1 bulges occur only in antiparallel sheets; in these cases residue 1 is in the alpha left conformation and is therefore usually glycine. This usually occurs at the end of a beta strand.

Plots

The plots show a Ramachandran plot for each bulge, showing the phi,psi angles of the residues involved in the bulge. The phi,psi angles of residue X are indicated by a red circle on the Ramachandran plot, residues 1 and 2 are represented by green and blue squares, respectively, and any remaining residues (3 and 4 if they occur) are represented by purple squares. The type of bulge is indicated above the Ramachandran plot. To the right of the Ramachandran plot is a schematic diagram indicating the residues and hydrogen bonding patterns in and around the beta bulge.

A PostScript or PDF version of the plots (showing 8 bulges per page) can be generated by clicking on the appropriate icon below the Table.

Table

The following information is given for each bulge: bulge type, and residues X, 1, 2, 3 and 4. Most of the bulges will have just residues X, 1 and 2; the special bulges may have one or more of residues 3 and 4, and the bent bulges will just have residues 1 and 2.

References

Chan AWE, Hutchinson EG, Harris D and Thornton JM (1993). Identification, classification and analysis of beta-bulges in proteins. Protein Science, 2, 1574-1590.
Kabsch W and Sander C (1983). Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers, 22, 2577-2637.

 

Gail Hutchinson 22nd May, 1996 spacer
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