Table 2. Examples of known functional motifs found in ArchDB.
| Subclass | Functional motif | (φ,ψ) conformation | Sequence consensus |
|---|---|---|---|
| AR 5.9.1 | Kinases: activation loop (DFG) | bb{laaap}bb | hh{DFGhh}Xh |
| AR 6.2.1 | H1 canonical loop | bb{lbpaa}bp | hS{GhpFpp}YW |
| AR 8.2.1 | Kinases: catalytic loop (HRD) | bb{alapbaaa}bb | Ih{HXDhpPpN}hh |
| AR 8.2.2 | Kinases: catalytic loop (HRD) | bb{alapbaaa}bb | hh{HRDLphXN}hL |
| EH 3.1.1 and EH 3.1.2 | NAD(P)-binding loop | bb{eap}aa | hh{GXG}Xh |
| EH 6.1.1 and EH 6.1.2 | P-loop | bb{eppgag}aa | hh{GXXGXG}Kp |
| EH 6.1.3 | P-loop | bb{eppgag}aa | hh{GhhXXG}Kp |
| EH 6.4.1 | P-loop | bb{epplag}aa | hh{GpXpXG}Kp |
| EH 6.4.2 | P-loop | bb{epplag}aa | hX{GXXXXG}Kp |
| HE 6.6.1 | EF-hand | aa{paalal}bb | ph{DhDpDG}pI |
| HE 6.6.2 | EF-hand | aa{paalal}bb | hh{DTNXDG}ph |
| HH 9.1.1 | EF-hand | aa{paalalbbp}aa | ph{DXDXpGXhp}Xp |
Subclasses were identified by motif type and the three number code (see text). Motif names shown in the table were extracted from the literature. Regions in (φ,ψ) space are α, αL, γ, β, βP and ε (described here as a, l, g, b, p and e). Consensus sequence was derived from the multiply aligned loops. A code was used to represent the chemical properties of the consensus at every position: (1) the one letter amino acid code; (2) p for polar; (3) h for non-polar residues; (4) X denotes no sequence consensus.