I-sites 14

[Type-I beta hairpin]

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
3009 (1gsa 238)		AGG GT_ BR0 OPA
3047 (1ptx 10)		VNC TS_ BR0 OPA
3148 (1lgr 277)		NGT TTE RRG HIA
9920 (1abr B 179)		ALYTDGSIR EE_TTS_EE 000QBR000 DDFKLPACD
12031 (1eri A 178)		NISITRPDGRVV _EEEE_SSS_EE 000000QBR000 CDDDDFKLPACD
13202 (1msa A 53)		FLSMQTDGNLVVY EEEE_TTS_EEEE 000R0QBR00000 CDDDFKLPACDDD
3027 (2pgd 165)		TGE TS_ BO0 LPA
6015 (1hpm 214)		DGIFEV TTEEEE RR000R HIACDF
6111 (3cox 270)		EQGNVV TTS_EE QBR00R LOPAFB
7156 (1tie 6)		NGEVVQN TS_B__T BR00000 LPACDEH
9102 (1eri A 99)		DDYGEWRVV _TTS_EEEE 0QBR0000R KNOPACDFB

[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)