I-sites 17

[Amphipathic 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
3116 (1oac A 533)		DLD EE_ R0R DDE
3162 (1phg 24)		FDF ___ 000 CDD
31020 (3sdh A 128)		GDK _HH 0QA KLM
4033 (1pox A 168)		IPVD EETT 00QA DFKL
3260 (1fc2 D 319)		YKC EEE 000 DDD
4136 (1slt B 125)		DFKI SEEE RG00 ACCF
4190 (1tsp 167)		IECK EEES 000R DDFK
5132 (1gcb 49)		DNRVF _____ B0R00 CCBDF
5036 (1ova A 124)		YPILP S_B_H G000Q CCDFK
6077 (1dpg A 348)		DIVFKA EEEE__ 000000 DDDDDD
6355 (1thv 3)		FEIVNR EEEEE_ 00000R DDDDFB
8131 (1wht A 29)		SLFYLLQE EEEEEEE_ 00000000 CDDDDDDD
9174 (1ctm 125)		EITFPILAP EEEEEEE__ G00000000 CCDDDDDDD
8173 (1fc2 D 258)		EVTCVVVD EEEEEEEE 00000000 DDDDDEHJ

[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)