I-sites 2

[Glycine alpha-C-cap (Schellman) 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
10201 (1pii 127)		RYYQADACLL HHTT_SEEEE AABR0R0000 MNOPABDCDD
11630 (1pii 126)		ARYYQADACLL HHHTT_SEEEE AAABR0R0000 MNOPABDCDD
12013 (1pbg A 64)		EEYGVNGIRISI HHTT__EEEEE_ AAB000000000 MNOPABDCDDDD
12014 (1pbg A 63)		AEEYGVNGIRIS HHHTT__EEEEE AAAB00000000 MMNOPABDCDDD
15006 (1ceo 33)		DIETIAEAGFDHVRL HHHHHHHHT__EEEE AAAAAAAB00R0000 XMMMMMNOPABDCDD
15333 (1ceo 34)		IETIAEAGFDHVRLP HHHHHHHT__EEEEE AAAAAAB00R00000 MMMMMNOPABDCDDD
15585 (1ceo 31)		EKDIETIAEAGFDHV HHHHHHHHHHT__EE QAAAAAAAAB00R00 KLMMMMMMNOPABDC
15901 (4xia A 37)		EAVHKLAELGAYGIT HHHHHHHHHT__EEE AAAAAAAAB00R000 MMMMMMMNOPABDCD
4227 (3pmg A 219)		IRID EEEE 0000 DDDE
7136 (2cmd 70)		ADVVLIS _SEEEE_ 0R00000 ABDCDFE
7312 (2dld A 228)		GVVIVNC TEEEEE_ R00000R PACDDFK
11015 (1bpl A 35)		HGITAVWIPPA TT__EEE____ B00R000000R OPABDCDDDFB
7135 (1mmo G 27)		KAAEMLK HHHHHHH AAAAAAA MMMMMMM
11054 (1dea A 49)		YKALVEMHKAG HHHHHHHHHTT AAAAAAAAABR MMMMMMMMNOP
3069 (2pgd 244)		ADG TTS QBR KLP
4034 (1mmo D 226)		ANGD HTT_ ABR0 NOPA
8020 (1hmt 46)		GDILTLKT TTEEEEEE 0RG00000 JACCDDDD
8032 (1lyl A 133)		GELSIHCT TEEEEEEE R0000R0R AACDDDFB
9013 (2tmd A 479)		GADKVIIAT __SEEEE__ R0R0000RR PABDCDDEH