Complet list of 1yp8 hssp file
Complete list of 1yp8.hssp file
HSSP HOMOLOGY DERIVED SECONDARY STRUCTURE OF PROTEINS , VERSION 2.0 2011
PDBID 1YP8
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 2014-05-14
HEADER CELL CYCLE 30-JAN-05 1YP8
COMPND MOL_ID: 1; MOLECULE: TRICYCLON A; CHAIN: A
SOURCE MOL_ID: 1; ORGANISM_SCIENTIFIC: VIOLA TRICOLOR; ORGANISM_TAXID: 214053
AUTHOR J.P.MULVENNA,L.SANDO,D.J.CRAIK
DBREF 1YP8 A 1 33 PDB 1YP8 1YP8 1 33
SEQLENGTH 33
NCHAIN 1 chain(s) in 1YP8 data set
NALIGN 2
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 : B6E617_9ROSI 0.96 1.00 1 28 67 94 28 0 0 288 B6E617 Tricyclon A protein (Fragment) OS=Viola tricolor PE=4 SV=1
2 : TRIC_VIOAR 1YP8 0.96 1.00 1 28 79 106 28 0 0 204 P0C589 Pro-tricyclons OS=Viola arvensis PE=1 SV=1
## ALIGNMENTS 1 - 2
SeqNo PDBNo AA STRUCTURE BP1 BP2 ACC NOCC VAR ....:....1....:....2....:....3....:....4....:....5....:....6....:....7
1 1 A a 0 0 15 3 0 CC
2 2 A G + 0 0 91 3 0 GG
3 3 A E - 0 0 30 3 0 EE
4 4 A S + 0 0 91 3 0 SS
5 5 A b + 0 0 2 3 0 CC
6 6 A F S S+ 0 0 167 3 0 FF
7 7 A L S S- 0 0 154 3 0 LL
8 8 A G S S+ 0 0 36 3 0 GG
9 9 A T - 0 0 110 3 0 TT
10 10 A c - 0 0 33 3 0 CC
11 11 A Y S S+ 0 0 197 3 0 YY
12 12 A T S > S- 0 0 77 3 0 TT
13 13 A K T 3 S+ 0 0 185 3 0 KK
14 14 A G T 3 S+ 0 0 22 3 0 GG
15 15 A a E < -A 25 0A 8 3 0 CC
16 16 A S E -A 24 0A 75 3 0 SS
17 17 A b E -A 23 0A 44 3 0 CC
18 18 A G E >> -A 22 0A 21 3 0 GG
19 19 A E T 34 S+ 0 0 200 3 0 EE
20 20 A W T 34 S- 0 0 163 3 0 WW
21 21 A K T <4 S+ 0 0 101 3 0 KK
22 22 A L E < -A 18 0A 79 3 0 LL
23 23 A c E -A 17 0A 1 3 0 CC
24 24 A Y E -A 16 0A 70 3 0 YY
25 25 A G E +AB 15 32A 0 3 0 GG
26 26 A T E > + B 0 31A 68 3 0 TT
27 27 A N E > S- B 0 30A 65 3 0 NN
28 28 A G T 3 S- 0 0 85 3 59 SS
29 29 A G T < S+ 0 0 68 1 0
30 30 A T E < -B 27 0A 85 1 0
31 31 A I E +B 26 0A 119 1 0
32 32 A F E B 25 0A 85 1 0
33 33 A D 0 0 94 1 0
## SEQUENCE PROFILE AND ENTROPY
SeqNo PDBNo V L I M F W Y G A P S T C H R K Q E N D NOCC NDEL NINS ENTROPY RELENT WEIGHT
1 1 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 3 0 0 0.000 0 1.00
2 2 A 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0.000 0 1.00
3 3 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 3 0 0 0.000 0 1.00
4 4 A 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 3 0 0 0.000 0 1.00
5 5 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 3 0 0 0.000 0 1.00
6 6 A 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0.000 0 1.00
7 7 A 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0.000 0 1.00
8 8 A 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0.000 0 1.00
9 9 A 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 3 0 0 0.000 0 1.00
10 10 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 3 0 0 0.000 0 1.00
11 11 A 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0.000 0 1.00
12 12 A 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 3 0 0 0.000 0 1.00
13 13 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 3 0 0 0.000 0 1.00
14 14 A 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0.000 0 1.00
15 15 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 3 0 0 0.000 0 1.00
16 16 A 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 3 0 0 0.000 0 1.00
17 17 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 3 0 0 0.000 0 1.00
18 18 A 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0.000 0 1.00
19 19 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 3 0 0 0.000 0 1.00
20 20 A 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0.000 0 1.00
21 21 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 3 0 0 0.000 0 1.00
22 22 A 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0.000 0 1.00
23 23 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 3 0 0 0.000 0 1.00
24 24 A 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0.000 0 1.00
25 25 A 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0.000 0 1.00
26 26 A 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 3 0 0 0.000 0 1.00
27 27 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 3 0 0 0.000 0 1.00
28 28 A 0 0 0 0 0 0 0 33 0 0 67 0 0 0 0 0 0 0 0 0 3 0 0 0.637 21 0.40
29 29 A 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0.000 0 1.00
30 30 A 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 1 0 0 0.000 0 1.00
31 31 A 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0.000 0 1.00
32 32 A 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0.000 0 1.00
33 33 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 1 0 0 0.000 0 1.00
## INSERTION LIST
AliNo IPOS JPOS Len Sequence
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