I-sites 11

[DP alpha N-cap]

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
6513 (1jap A 113)		IKDAFE HHHHHH AAAAAA MMMMMM
9022 (2dkb 310)		PAAVGLRVL HHHHHHHHH AAAAAAAAA MMMMMMMMM
11317 (1dea A 15)		WAARHIVNRIN HHHHHHHHHHH AAAAAAAAAAA MMMMMMMMMMM
12019 (1ceo 106)		FEDPNQQKRFVD TT_HHHHHHHHH ABGQAAAAAAAA MMMMLMMMMMMM
12023 (1eft 142)		DDPELLDLVEME __TTHHHHHHHH RRQAAAAAAAAA BLMLMMMMMMMM
11047 (1mol A 9)		GPFTQNLGKFA SHHHHHHHHHH 0QAAAAAAAAA MMMMMMMMMMM
5236 (1vhh 154)		RDRSK __GGG RRQAA PAKLM
7256 (1ceo 106)		FEDPNQQ TT_HHHH ABGQAAA MMMMLMM

[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)