I-sites 9

[Alpha-alpha corner, type 1]

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
4114 (1bdm B 27)		EMLG TTT_ R000 MNOP
10063 (1lpb B 138)		SAFGYSPSNV HHH___GGGE AB0R00QABG MNOPAFKLPC
11068 (1cmb A 91)		IMREMGINPET HHHHTT__TTS ASSSBR00QAB MMMNOPAFKLP
12010 (1phg 163)		FMLLAGLPEEDI HHHHHT__GGGH AAAABR00QABQ MMMNOPAFKLMM
13057 (1nfp 110)		YQAAAAKFNVDIA HHHHHHHHT___T AAAAAAABR00RQ MMMMMMNOPAFKL
7111 (2acq 68)		KREELFI _TTTHHH 0QABG00 FKLPCCD
10093 (2bnh 204)		CGLTPANCKD S___HHHHHH RR00QAAAAA LPAFKLMMMM
13066 (1tpl A 18)		MIPRDERLKKMQE ___HHHHHHHHHH R00QAAAAAAAAA IAFKLMMMMMMMN
3144 (1pnk A 122)		FGF HT_ B0G OPA

[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)