I-sites 18

[Non-polar beta strand]

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
3026 (1erw 77)		FQF EEE 000 DDD
3035 (1dhr 79)		ILC EEE 00O CDF
3041 (1dhr 193)		ADF S_G G0Q CFK
5057 (1arb 80)		CRAPN ___TT 0000R CDEHI
5069 (1gca 86)		PVVFF _EEEE 00000 CDDEH
3084 (1pvd A 69)		CII EEE 000 DDF
3092 (2min B 442)		MIG EEE 000 CFK
4021 (1pre A 93)		IPDG E___ 0000 DEHJ
6139 (1ice A 280)		IIIQAC EEEE__ 000000 DDDDDE
5107 (2isd A 499)		CKSVH _EEE_ G0000 CCDDD
6288 (1ice A 278)		KVIIIQ EEEEEE 000000 DDDDDD
7428 (1ice A 278)		KVIIIQA EEEEEE_ 0000000 DDDDDDD

[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)