I-sites 5

[Amphipathic alpha helix]

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
11028 (1cpc B 5)		FAKVVSQADAR HHHHHHHHHTT AAAAAAAAAAB MMMMMMMMMNO
12046 (1frp A 37)		LCTAVKAISTAV HHHHHHHHHHHH AAAAAAAAAAAA MMMMMMMMMMMN
13160 (1hqa A 346)		DEAVQRALEFAKK HHHHHHHHHHHHH AAAAAAAAAAAAA MMMMMMMMMMMMN
15106 (1xaa 305)		VELARKVEDAVAKAL HHHHHHHHHHHHHHH QAAAAAAAAAAAAAA KLMMMMMMMMMMMMM
15205 (1xyz A 767)		TAFQVQANNYKELMK HHHHHHHHHHHHHHH AAAAAAAAAAAAAAA MMMMMMMMMMMMMMM
11176 (1dpe 453)		NKRVELYKQAQ HHHHHHHHHHH AAAAAAAAAAA LMMMMMMMMMM
10401 (1bdm B 244)		SAANAAIEHI HHHHHHHHHH AAAAAAAAAA MMMMMMMMMM
15548 (1rcf 151)		LTDDRIKSWVAQLKS GHHHHHHHHHHHHHH BQAAAAAAAAAAAAA MMMMMMMMMMMMMMM
13001 (2cyp 258)		FFKDSKAFEKLL HHHHHHHHHHHH AAAAAAAAAAAA MMMMMMMMMMMM
3023 (2adm A 173)		DFA GGH ABQ LMM
5032 (1itg 164)		QVRDQ HHTTT ABQAB MMMMP
3043 (1ptd 95)		INE HHH AAA MMM
4143 (2amg 336)		MYDW HHTS G000 MMNO
4026 (1sra 181)		KIHE HHHH AAAB MMMM
4058 (1eri A 144)		ERSH GGHH AAAA MMMM
4064 (1pvd A 122)		FTVF SSHH QHQA KLMM
6507 (1hgx A 18)		DDIQKR HHHHHH AAAAAA LMMMMM
8055 (1hgx A 18)		DDIQKRIR HHHHHHHH AAAAAAAA LMMMMMMM