Complet list of 1b8w hssp file
Complete list of 1b8w.hssp file
HSSP HOMOLOGY DERIVED SECONDARY STRUCTURE OF PROTEINS , VERSION 2.0 2011
PDBID 1B8W
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 2014-04-27
HEADER TOXIN 02-FEB-99 1B8W
COMPND MOL_ID: 1; MOLECULE: PROTEIN (DEFENSIN-LIKE PEPTIDE 1); CHAIN: A; OTHE
SOURCE MOL_ID: 1; ORGANISM_SCIENTIFIC: ORNITHORHYNCHUS ANATINUS; ORGANISM_COM
AUTHOR A.M.TORRES,X.WANG,J.I.FLETCHER,D.ALEWOOD,P.F.ALEWOOD, R.SMITH,R.J.SIMP
DBREF 1B8W A 1 42 UNP P82172 DLP1_ORNAN 1 42
SEQLENGTH 42
NCHAIN 1 chain(s) in 1B8W data set
NALIGN 3
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 : DLP1_ORNAN 1B8W 0.98 0.98 1 42 25 66 42 0 0 66 P82172 Defensin-like peptide 1 OS=Ornithorhynchus anatinus PE=1 SV=2
2 : F6UKT6_ORNAN 0.98 0.98 1 42 1 42 42 0 0 42 F6UKT6 Uncharacterized protein (Fragment) OS=Ornithorhynchus anatinus PE=4 SV=1
3 : DLPA_ORNAN 0.47 0.66 9 40 33 64 32 0 0 66 P0C8B2 Ornithorhynchus venom defensin-like peptide A OS=Ornithorhynchus anatinus PE=2 SV=1
## ALIGNMENTS 1 - 3
SeqNo PDBNo AA STRUCTURE BP1 BP2 ACC NOCC VAR ....:....1....:....2....:....3....:....4....:....5....:....6....:....7
1 1 A F 0 0 241 3 0 FF
2 2 A V - 0 0 103 3 0 VV
3 3 A Q - 0 0 101 3 0 QQ
4 4 A H + 0 0 184 3 0 HH
5 5 A R - 0 0 128 3 0 RR
6 6 A P - 0 0 113 3 0 PP
7 7 A R - 0 0 124 3 0 RR
8 8 A D - 0 0 12 3 0 DD
9 9 A a S > >S+ 0 0 0 4 0 CCC
10 10 A E G > 5S+ 0 0 153 4 84 EES
11 11 A S G 3 5S+ 0 0 86 4 122 SSY
12 12 A I G < 5S- 0 0 50 4 90 IIY
13 13 A N T < 5S+ 0 0 133 4 51 NND
14 14 A G < - 0 0 1 4 0 GGG
15 15 A V E -A 40 0A 25 4 0 VVV
16 16 A b E +A 39 0A 28 4 0 CCC
17 17 A R E -A 38 0A 104 4 0 RRR
18 18 A H E > -A 37 0A 110 4 71 HHD
19 19 A K T 3 S+ 0 0 133 4 0 KKK
20 20 A D T 3 S+ 0 0 140 4 84 DDS
21 21 A T < - 0 0 44 4 84 TTD
22 22 A V S S+ 0 0 138 4 0 VVV
23 23 A N S S+ 0 0 139 4 0 NNN
24 24 A c S S- 0 0 24 4 0 CCC
25 25 A R - 0 0 157 4 45 RRK
26 26 A E B -B 40 0A 74 4 129 EEY
27 27 A I > - 0 0 33 4 0 III
28 28 A F T 3 S+ 0 0 173 4 129 FFA
29 29 A L T 3 S+ 0 0 118 4 19 LLF
30 30 A A < - 0 0 4 4 71 AAT
31 31 A D - 0 0 73 4 129 DDY
32 32 A b - 0 0 12 4 0 CCC
33 33 A Y S S+ 0 0 159 4 129 YYE
34 34 A N S S- 0 0 111 4 0 NNN
35 35 A D S S+ 0 0 156 4 90 DDP
36 36 A G S S+ 0 0 22 4 68 EEN
37 37 A Q E -A 18 0A 53 4 0 QQQ
38 38 A K E -A 17 0A 26 4 45 KKR
39 39 A a E -A 16 0A 0 4 0 CCC
40 40 A c E -AB 15 26A 2 4 0 CCC
41 41 A R 0 0 128 3 0 RR
42 42 A K 0 0 153 3 0 KK
## 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 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0.000 0 1.00
2 2 A 100 0 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
3 3 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 3 0 0 0.000 0 1.00
4 4 A 0 0 0 0 0 0 0 0 0 0 0 0 0 100 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 0 0 100 0 0 0 0 0 3 0 0 0.000 0 1.00
6 6 A 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 3 0 0 0.000 0 1.00
7 7 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 3 0 0 0.000 0 1.00
8 8 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 3 0 0 0.000 0 1.00
9 9 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 4 0 0 0.000 0 1.00
10 10 A 0 0 0 0 0 0 0 0 0 0 25 0 0 0 0 0 0 75 0 0 4 0 0 0.562 18 0.16
11 11 A 0 0 0 0 0 0 25 0 0 0 75 0 0 0 0 0 0 0 0 0 4 0 0 0.562 18 -0.23
12 12 A 0 0 75 0 0 0 25 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0.562 18 0.09
13 13 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 75 25 4 0 0 0.562 18 0.48
14 14 A 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0.000 0 1.00
15 15 A 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0.000 0 1.00
16 16 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 4 0 0 0.000 0 1.00
17 17 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 4 0 0 0.000 0 1.00
18 18 A 0 0 0 0 0 0 0 0 0 0 0 0 0 75 0 0 0 0 0 25 4 0 0 0.562 18 0.29
19 19 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 4 0 0 0.000 0 1.00
20 20 A 0 0 0 0 0 0 0 0 0 0 25 0 0 0 0 0 0 0 0 75 4 0 0 0.562 18 0.16
21 21 A 0 0 0 0 0 0 0 0 0 0 0 75 0 0 0 0 0 0 0 25 4 0 0 0.562 18 0.16
22 22 A 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0.000 0 1.00
23 23 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 4 0 0 0.000 0 1.00
24 24 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 4 0 0 0.000 0 1.00
25 25 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 75 25 0 0 0 0 4 0 0 0.562 18 0.55
26 26 A 0 0 0 0 0 0 25 0 0 0 0 0 0 0 0 0 0 75 0 0 4 0 0 0.562 18 -0.29
27 27 A 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0.000 0 1.00
28 28 A 0 0 0 0 75 0 0 0 25 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0.562 18 -0.29
29 29 A 0 75 0 0 25 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0.562 18 0.81
30 30 A 0 0 0 0 0 0 0 0 75 0 0 25 0 0 0 0 0 0 0 0 4 0 0 0.562 18 0.29
31 31 A 0 0 0 0 0 0 25 0 0 0 0 0 0 0 0 0 0 0 0 75 4 0 0 0.562 18 -0.29
32 32 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 4 0 0 0.000 0 1.00
33 33 A 0 0 0 0 0 0 75 0 0 0 0 0 0 0 0 0 0 25 0 0 4 0 0 0.562 18 -0.29
34 34 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 4 0 0 0.000 0 1.00
35 35 A 0 0 0 0 0 0 0 0 0 25 0 0 0 0 0 0 0 0 0 75 4 0 0 0.562 18 0.09
36 36 A 0 0 0 0 0 0 0 25 0 0 0 0 0 0 0 0 0 50 25 0 4 0 0 1.040 34 0.31
37 37 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 4 0 0 0.000 0 1.00
38 38 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 25 75 0 0 0 0 4 0 0 0.562 18 0.55
39 39 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 4 0 0 0.000 0 1.00
40 40 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 4 0 0 0.000 0 1.00
41 41 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 3 0 0 0.000 0 1.00
42 42 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
## INSERTION LIST
AliNo IPOS JPOS Len Sequence
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