I-sites 31

[Miscellaneous motifs]

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
10073 (1bco 330)		DFHITIDNTR S_EEE___TT G000000RQB DCDDDDFKNO
3111 (4sbv A 176)		CPD _S_ 0RG FBF
3117 (1ptd 223)		EDL T_S BRQ FBF
3133 (1pbe 158)		CDG ___ R00 EHJ
3014 (1crl 267)		GCG T_T RRQ PMM
3016 (2cdv 32)		DCH HHS B1B MMG
3025 (1fjm A 169)		IFC EEE 000 CCD
3030 (1esc 210)		ADI TT_ 0R0 MAC
3031 (1tpl A 429)		QHK TTG ABQ MMM
3051 (1irk 1057)		HHV TTB QBG KBC
3059 (1oac A 440)		HQE E__ 0R0 DDE
4103 (1gpc 81)		HGDY GT__ BRRQ OPAM
4175 (1hlb 133)		FNEK __TH R0PA GHKL
4179 (1bgl A 599)		RQFC GGGG 0RQB JMMP
5108 (3pmg A 260)		HPDPN ____S 0R00G CDDBF
5123 (1har 75)		VDFRE E_THH 0R00G E_THH
8192 (1lcp A 322)		NGKTIQV TS_EEEE BR0000R LPACDDF

[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)