I-sites 29

[Alpha loop, type 2]

Given below is the representative amino acid fragments, "paradigm", for each I-sites cluster of this motif:

Paradigms are given by their PDB code, (chain number,) and the PDB residue number of the first position in the fragment.
The PDB style files of the fragments contain the neighbouring two residues for each terminal.
Backbone structures are obtained using ProteinViewer, where N-terminal is colored red and C-terminal blue.
Click on thumbnail for larger images.
Rough characterization of the DSSP code, the PB label, and the 5-tile code is given below.
See also reference [3] for DSSP and [2] for PBs.

Cluster ID (paradigm)	Backbone structure	Amino acid sequence DSSP code sequence 5-tile code sequence PB sequence
7015 (1epa B 6)		FDISKFL __GGGS_ 00QAAG0 CFKLMGH
8247 (1pkm 262)		KNIKIISK TTSEEEEE QB000000 MPCCDDDD
9060 (1ctn 263)		HPDLKILPS _TT_EEEEE 0QBG00000 MMBCCDDDE

[The DSSP code]

H = alpha helix
B = residue in isolated beta-bridge
E = extended strand, participates in beta ladder
G = 3-helix (3/10 helix)
I = 5 helix (pi helix)
T = hydrogen bonded turn
S = bend
_ = no assigned structure

[The PB label]

A = N-cap beta
B = N-cap beta
C = N-cap beta
D = beta
E = C-cap beta
F = C-cap beta
G = mainly coil
H = mainly coil
I = mainly coil
J = mainly coil
K = N-cap alpha
L = N-cap alpha
M = alpha
N = C-cap alpha
O = C-cap alpha
P = C-cap alpha to N-cap beta

[The 5-tile code]

0 = DDDDD (extended strand, small blue spheres)
1 = DDDDU
2 = DDDUD
3 = DDDUU
8 = DUDDD
9 = DUDDU
A = DUDUD (helix, large red spheres)
B = DUDUU (turn, large yellow spheres)
G = UDDDD
H = UDDDU
I = UDDUD
J = UDDUU
O = UUDDD
P = UUDDU
Q = UUDUD (turn, large yellow spheres)
R = UUDUU (turn, large yellow spheres)