Complet list of 1wn4 hssp file
Complete list of 1wn4.hssp file
HSSP HOMOLOGY DERIVED SECONDARY STRUCTURE OF PROTEINS , VERSION 2.0 2011
PDBID 1WN4
THRESHOLD according to: t(L)=(290.15 * L ** -0.562) + 5
REFERENCE Sander C., Schneider R. : Database of homology-derived protein structures. Proteins, 9:56-68 (1991).
CONTACT Maintained at http://www.cmbi.ru.nl/ by Maarten L. Hekkelman
DATE file generated on 2014-05-12
HEADER PLANT PROTEIN 27-JUL-04 1WN4
COMPND MOL_ID: 1; MOLECULE: VONTR PROTEIN; CHAIN: A; FRAGMENT: N-TERMINAL REP
SOURCE MOL_ID: 1; SYNTHETIC: YES; OTHER_DETAILS: THIS IS A SYNTHETIC PEPTIDE
AUTHOR J.L.DUTTON,R.F.RENDA,C.WAINE,R.J.CLARK,N.L.DALY, C.V.JENNINGS,M.A.ANDE
DBREF 1WN4 A 1 28 PDB 1WN4 1WN4 1 28
SEQLENGTH 28
NCHAIN 1 chain(s) in 1WN4 data set
NALIGN 9
NOTATION : ID: EMBL/SWISSPROT identifier of the aligned (homologous) protein
NOTATION : STRID: if the 3-D structure of the aligned protein is known, then STRID is the Protein Data Bank identifier as taken
NOTATION : from the database reference or DR-line of the EMBL/SWISSPROT entry
NOTATION : %IDE: percentage of residue identity of the alignment
NOTATION : %SIM (%WSIM): (weighted) similarity of the alignment
NOTATION : IFIR/ILAS: first and last residue of the alignment in the test sequence
NOTATION : JFIR/JLAS: first and last residue of the alignment in the alignend protein
NOTATION : LALI: length of the alignment excluding insertions and deletions
NOTATION : NGAP: number of insertions and deletions in the alignment
NOTATION : LGAP: total length of all insertions and deletions
NOTATION : LSEQ2: length of the entire sequence of the aligned protein
NOTATION : ACCNUM: SwissProt accession number
NOTATION : PROTEIN: one-line description of aligned protein
NOTATION : SeqNo,PDBNo,AA,STRUCTURE,BP1,BP2,ACC: sequential and PDB residue numbers, amino acid (lower case = Cys), secondary
NOTATION : structure, bridge partners, solvent exposure as in DSSP (Kabsch and Sander, Biopolymers 22, 2577-2637(1983)
NOTATION : VAR: sequence variability on a scale of 0-100 as derived from the NALIGN alignments
NOTATION : pair of lower case characters (AvaK) in the alignend sequence bracket a point of insertion in this sequence
NOTATION : dots (....) in the alignend sequence indicate points of deletion in this sequence
NOTATION : SEQUENCE PROFILE: relative frequency of an amino acid type at each position. Asx and Glx are in their
NOTATION : acid/amide form in proportion to their database frequencies
NOTATION : NOCC: number of aligned sequences spanning this position (including the test sequence)
NOTATION : NDEL: number of sequences with a deletion in the test protein at this position
NOTATION : NINS: number of sequences with an insertion in the test protein at this position
NOTATION : ENTROPY: entropy measure of sequence variability at this position
NOTATION : RELENT: relative entropy, i.e. entropy normalized to the range 0-100
NOTATION : WEIGHT: conservation weight
## PROTEINS : identifier and alignment statistics
NR. ID STRID %IDE %WSIM IFIR ILAS JFIR JLAS LALI NGAP LGAP LSEQ2 ACCNUM PROTEIN
1 : B6E615_VIOOD 1.00 1.00 1 28 150 177 28 0 0 207 B6E615 Cycloviolacin O8 OS=Viola odorata PE=4 SV=1
2 : M9T7B1_VIOOD 1.00 1.00 1 28 45 72 28 0 0 102 M9T7B1 Cyclotide C (Fragment) OS=Viola odorata GN=vocC PE=2 SV=1
3 : VARA_VIOOD 1WN4 1.00 1.00 1 28 150 177 28 0 0 207 Q5USN7 Varv peptide A/Kalata-B1 OS=Viola odorata GN=Vok1 PE=1 SV=1
4 : B5B3Z3_9ROSI 0.96 1.00 1 28 96 123 28 0 0 153 B5B3Z3 Cyclotide 6b OS=Viola baoshanensis PE=2 SV=1
5 : B5B3Z6_9ROSI 0.96 1.00 1 28 150 177 28 0 0 207 B5B3Z6 Cyclotide 7b OS=Viola baoshanensis PE=2 SV=1
6 : B5B3Z7_9ROSI 0.96 1.00 1 28 150 177 28 0 0 207 B5B3Z7 Cyclotide 7c OS=Viola baoshanensis PE=2 SV=1
7 : A5YRZ3_9ROSI 0.86 0.93 1 28 96 123 28 0 0 153 A5YRZ3 Cyclotide 6 OS=Viola baoshanensis PE=2 SV=1
8 : B5B3Z5_9ROSI 0.86 0.93 1 28 96 123 28 0 0 153 B5B3Z5 Cyclotide 6d OS=Viola baoshanensis PE=2 SV=1
9 : A5YRZ4_9ROSI 0.79 0.93 1 28 150 177 28 0 0 207 A5YRZ4 Cyclotide 7 OS=Viola baoshanensis PE=2 SV=1
## ALIGNMENTS 1 - 9
SeqNo PDBNo AA STRUCTURE BP1 BP2 ACC NOCC VAR ....:....1....:....2....:....3....:....4....:....5....:....6....:....7
1 1 A A 0 0 108 10 29 AAAAAAAAS
2 2 A L > + 0 0 111 10 0 LLLLLLLLL
3 3 A E T 3 + 0 0 62 10 98 EEEEEEVVV
4 4 A T T 3 S+ 0 0 125 10 31 TTTTTTTTS
5 5 A Q S < S+ 0 0 151 10 46 QQQQQQEEE
6 6 A K S > S- 0 0 106 10 0 KKKKKKKKK
7 7 A P T 3 S+ 0 0 97 10 63 PPPPPPSSS
8 8 A N T 3> S+ 0 0 84 10 0 NNNNNNNNN
9 9 A H H <> + 0 0 56 10 92 HHHHHHAAA
10 10 A L H > S+ 0 0 67 10 0 LLLLLLLLL
11 11 A L H > S+ 0 0 107 10 0 LLLLLLLLL
12 12 A E H X S+ 0 0 61 10 0 EEEEEEEEE
13 13 A E H X S+ 0 0 96 10 0 EEEEEEEEE
14 14 A A H X S+ 0 0 62 10 0 AAAAAAAAA
15 15 A L H >X S+ 0 0 111 10 0 LLLLLLLLL
16 16 A V H 3X S+ 0 0 64 10 13 VVVIIIVVV
17 17 A A H 3< S+ 0 0 29 10 0 AAAAAAAAA
18 18 A F H