journal menu
![[Figure 2]](ba0002fig2mag.jpg)
|
|
Figure 2
A schematic plot, or `wiring diagram', of protein chain A in the PDB file 1ber, giving its sequence, secondary structure, domains and motifs. The amino-acid sequence is coloured by domain: red for residues belonging to domain 1, blue for domain 2, and black for fragments belonging to neither. Domains are assigned as described in Jones et al. (1998  ). The CATH classification, based on the domains, can identify which other proteins contain structurally similar domains. The motifs, defined by the PROMOTIF analysis, are marked on the diagram; here they include β- and γ-turns, β-hairpins, and helices and strands (labelled H1–H6 and A–C, respectively). The small blue dots identify residues interacting with the DNA. Further details on all the annotations are provided by the PROMOTIF links below the wiring diagram. The link labelled TOPS leads to a protein topology cartoon generated by the TOPS program. The SAS link finds similar sequences in the PDB using FASTA (Pearson & Lipman, 1988) and annotates the alignment by structural features. Finally, the last of the links generates a MolScript (Kraulis, 1991) picture of the chain in question. |
![[Figure 2]](ba0002fig2.jpg)
 | STRUCTURAL BIOLOGY |
ISSN: 2059-7983
