I-sites 3

[Glycine alpha-C-cap (Schellman) Type 3]

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
6283 (1gtr A 115)		NKGLAY HTTSEE ABRR00 NOPACC
7141 (2acq 148)		VDEGLVK HHTTSEE AABRR0R MNOPAFB
10034 (1omp 213)		AEAAFNKGET HHHHHHTT_E AAAAAABRR0 MMMMMNOMAF
11040 (1pda 66)		LEVALLENRAD HHHHHHTTS_S AAAAAABRR0O MMMMMNOPAFB
3106 (1crl 515)		DNF S_S RG0 CEH
8103 (1cnv 26)		NNYKIVFI ___SEEEE RRGR000R MAFBDCDD
8162 (1pda 72)		ENRADIAV TTS_SEEE BRR0O000 OPAFBDCD
9033 (1pda 72)		ENRADIAVH TTS_SEEEE BRR0O0000 OPAFBDCDD

[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)