Editing Sequence motif (section)

===Three-dimensional chain codes===
The ''[[E. coli]]'' lactose [[operon]] repressor LacI ({{PDB|1lcc}} chain A) and ''E. coli'' catabolite gene activator ({{PDB|3gap}} chain A) both have a ''helix-turn-helix'' motif, but their amino acid sequences do not show much similarity, as shown in the table below. In 1997, Matsuda, ''et al.'' devised a code they called the "three-dimensional chain code" for representing the protein structure as a string of letters. This encoding scheme reveals the similarity between the proteins much more clearly than the amino acid sequence (example from article):<ref name="Matsuda1997">{{cite journal | vauthors = Matsuda H, Taniguchi F, Hashimoto A | title = An approach to detection of protein structural motifs using an encoding scheme of backbone conformations | journal = Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing | pages = 280–91 | year = 1997 | pmid = 9390299 | url = http://psb.stanford.edu/psb-online/proceedings/psb97/matsuda.pdf }}<!--https://www.researchgate.net/publication/13840372--></ref> The code encodes the [[torsion angle]]s between alpha-carbons of the [[protein backbone]]. "W" always corresponds to an alpha helix.
{| cellpadding="5"
|-
! !! 3D chain code !! Amino acid sequence
|-
! 1lccA
| <code>TWWWWWWWKCLKWWWWWWG</code> || <code>LYDVAEYAGVSYQTVSRVV</code>
|-
! 3gapA
| <code>KWWWWWWGKCFKWWWWWWW</code> || <code>RQEIGQIVGCSRETVGRIL</code>
|}