I-sites 6

[Serine alpha N-cap (N-capping box), 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
13008 (1ubs B 38)		DPEFQAQFADLLK _HHHHHHHHHHHH GQAAAAAAAAAB0 MKLMMMMMMMMMM
15353 (1eft 143)		DPELLDLVEMEVRDL _TTHHHHHHHHHHHH RQAAAAAAAAAAAAA LMLMMMMMMMMMMMM
15001 (1sbp 12)		PTRELYEQYNKAFSA TTHHHHHHHHHHHHH QBQAAAAAAAAAAAA MMMMMMMMMMMMMMM
10554 (1fnc 212)		YKEEFEKMKE THHHHHHHHH RQAAAAAAAA KLMMMMMMMM
12005 (1frp A 36)		SLCTAVKAISTA HHHHHHHHHHHH AAAAAAAAAAAA MMMMMMMMMMMM
13010 (1ubs A 78)		PAQCFEMLALIRE HHHHHHHHHHHHH QAAAAAAAAAAAA KLMMMMMMMMMMM
15008 (2prd 157)		DRKAALEEVRACIAR _HHHHHHHHHHHHHH 0QAAAAAAAAAAAAA FKLMMMMMMMMMMMM
15015 (1gad O 250)		ATYEQIKAAVKAAAE __HHHHHHHHHHHHH 00QAAAAAAAAAAAB DFKLMMMMMMMMMMM
15074 (4xia A 63)		TAAEREKILGDFNQA _HHHHHHHHHHHHHH 0QAAAAAAAAAAAAA FKLMMMMMMMMMMMM
15286 (1hgx A 15)		YNQDDIQKRIRELAA E_HHHHHHHHHHHHH 00QAAAAAAAAAAAA DFKLMMMMMMMMMMM
7048 (1dts 65)		QLDYATV ___HHHH O00QAAB CDFKLMM
7124 (1oyc 162)		TKDEIKQ _HHHHHH 0QAAAAA FKLMMMM
8038 (1gln 203)		VIRAEEWL EEEEGGGG 0000QABQ CDDFKLMM
9021 (1lcp A 202)		IRPKSWIEE EEEHHHHHH R00QAAAAA DDFKLMMMN
9175 (1cel A 326)		LNDDYCTAE B_HHHHHHH R0QAAAAAA FKLMMMMMM
10095 (1lcp A 201)		FIRPKSWIEE EEEEHHHHHH 0R00QAAAAA DDDFKLMMMN
11012 (1dpg A 46)		RQALNDDEFKQ SS___HHHHHH RGR00QAAAAA BDFBLMLMMMM
12001 (1scm C 115)		ERLSDEDVDEII S___TTHHHHHT R000QAAAA9AB OCDFKLMMMMMM
12012 (1gky B 51)		NFVSVDEFKSMI EE__HHHHHHHH R000QAAAAAAA CDDFKLMMMMMM
7248 (1isc A 104)		ADFKAQF HHHHHHH AAAAAAA LMMMMMM
11390 (1ecl 142)		ITKNAIRQAFN _SHHHHHHHHH 00QHAAAAAAB CFKLMMMMMMM
13005 (1nal 1 112)		PFSFEEHCDHYRA ___HHHHHHHHHH 000QAAAAAAAAA CDFKLMMMMMMMN
13018 (1mla 138)		LDDASIAKACEEA __HHHHHHHHHHH G0QAAAAAAAAAA AFKLMMMMMMMMN
8150 (1inp 140)		EINIPQDI _____GGG R0000QAB CCDDFKLP
9029 (1cpt 250)		NYIDDKYIN SB__HHHHH G000QAAAA ACDFKLMMM