Complet list of 1osx hssp file
Complete list of 1osx.hssp file
HSSP HOMOLOGY DERIVED SECONDARY STRUCTURE OF PROTEINS , VERSION 2.0 2011
PDBID 1OSX
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 2014-05-05
HEADER IMMUNE SYSTEM 20-MAR-03 1OSX
COMPND MOL_ID: 1; MOLECULE: TUMOR NECROSIS FACTOR RECEPTOR SUPERFAMILY MEMBER
SOURCE MOL_ID: 1; ORGANISM_SCIENTIFIC: HOMO SAPIENS; ORGANISM_COMMON: HUMAN;
AUTHOR N.C.GORDON,B.PAN,S.G.HYMOWITZ,J.P.YIN,R.F.KELLEY, A.G.COCHRAN,M.YAN,V.
DBREF 1OSX A 1 61 UNP Q96RJ3 TR13C_HUMAN 1 61
SEQLENGTH 26
NCHAIN 1 chain(s) in 1OSX data set
NALIGN 31
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 : C8ZLJ6_HUMAN 1.00 1.00 1 26 17 42 26 0 0 184 C8ZLJ6 BAFF receptor OS=Homo sapiens GN=TNFRSF13C PE=4 SV=1
2 : F7ECK1_MACMU 1.00 1.00 1 26 17 42 26 0 0 184 F7ECK1 Uncharacterized protein OS=Macaca mulatta GN=TNFRSF13C PE=4 SV=1
3 : G1S0G7_NOMLE 1.00 1.00 1 26 17 42 26 0 0 184 G1S0G7 Uncharacterized protein OS=Nomascus leucogenys GN=TNFRSF13C PE=4 SV=1
4 : G3R8S3_GORGO 1.00 1.00 1 26 17 42 26 0 0 184 G3R8S3 Uncharacterized protein OS=Gorilla gorilla gorilla GN=101141773 PE=4 SV=1
5 : Q5H8V1_HUMAN 1.00 1.00 1 26 17 42 26 0 0 184 Q5H8V1 BAFF receptor OS=Homo sapiens GN=TNFRSF13C PE=2 SV=1
6 : S6FW99_HUMAN 1.00 1.00 1 26 17 42 26 0 0 184 S6FW99 Tumor necrosis factor receptor superfamily, member 13C OS=Homo sapiens GN=TNFRSF13C PE=4 SV=1
7 : TR13C_HUMAN 1P0T 1.00 1.00 1 26 17 42 26 0 0 184 Q96RJ3 Tumor necrosis factor receptor superfamily member 13C OS=Homo sapiens GN=TNFRSF13C PE=1 SV=1
8 : H2P4K9_PONAB 0.96 1.00 1 26 1 26 26 0 0 168 H2P4K9 Uncharacterized protein (Fragment) OS=Pongo abelii GN=TNFRSF13C PE=4 SV=1
9 : G3IBR9_CRIGR 0.80 0.84 1 25 3 27 25 0 0 162 G3IBR9 Tumor necrosis factor receptor superfamily member 13C OS=Cricetulus griseus GN=I79_021096 PE=4 SV=1
10 : F1PL17_CANFA 0.76 0.84 1 25 18 42 25 0 0 187 F1PL17 Uncharacterized protein (Fragment) OS=Canis familiaris GN=TNFRSF13C PE=4 SV=2
11 : F2YU84_HORSE 0.76 0.80 1 25 17 41 25 0 0 183 F2YU84 B cell-activating factor receptor OS=Equus caballus PE=2 SV=1
12 : G5BPQ7_HETGA 0.76 0.88 1 25 23 47 25 0 0 182 G5BPQ7 Tumor necrosis factor receptor superfamily member 13C OS=Heterocephalus glaber GN=GW7_19445 PE=4 SV=1
13 : H0W812_CAVPO 0.76 0.84 1 25 17 41 25 0 0 176 H0W812 Uncharacterized protein OS=Cavia porcellus GN=TNFRSF13C PE=4 SV=1
14 : F6VS44_HORSE 0.72 0.76 1 25 20 43 25 1 1 171 F6VS44 Uncharacterized protein (Fragment) OS=Equus caballus GN=TNFRSF13C PE=4 SV=1
15 : G1LRZ9_AILME 0.72 0.84 1 25 19 43 25 0 0 166 G1LRZ9 Uncharacterized protein (Fragment) OS=Ailuropoda melanoleuca GN=TNFRSF13C PE=4 SV=1
16 : G3U9C5_LOXAF 0.72 0.80 1 25 17 41 25 0 0 182 G3U9C5 Uncharacterized protein OS=Loxodonta africana GN=TNFRSF13C PE=4 SV=1
17 : H9KVT2_CALJA 0.72 0.84 1 25 17 41 25 0 0 186 H9KVT2 Uncharacterized protein OS=Callithrix jacchus GN=TNFRSF13C PE=4 SV=1
18 : L5K9E1_PTEAL 0.72 0.84 1 25 17 41 25 0 0 104 L5K9E1 Tumor necrosis factor receptor superfamily member 13C OS=Pteropus alecto GN=PAL_GLEAN10007214 PE=4 SV=1
19 : M3YY53_MUSPF 0.72 0.84 1 25 20 44 25 0 0 187 M3YY53 Uncharacterized protein OS=Mustela putorius furo GN=TNFRSF13C PE=4 SV=1
20 : U3DPW7_CALJA 0.72 0.84 1 25 17 41 25 0 0 185 U3DPW7 Tumor necrosis factor receptor superfamily member 13C OS=Callithrix jacchus GN=TNFRSF13C PE=2 SV=1
21 : U3FID9_CALJA 0.72 0.84 1 25 17 41 25 0 0 186 U3FID9 Tumor necrosis factor receptor superfamily member 13C OS=Callithrix jacchus GN=TNFRSF13C PE=2 SV=1
22 : G1T4W9_RABIT 0.68 0.80 1 25 20 44 25 0 0 181 G1T4W9 Uncharacterized protein (Fragment) OS=Oryctolagus cuniculus GN=TNFRSF13C PE=4 SV=1
23 : M3WQA3_FELCA 0.68 0.68 1 25 17 41 25 0 0 183 M3WQA3 Uncharacterized protein (Fragment) OS=Felis catus GN=TNFRSF13C PE=4 SV=1
24 : S9XLJ2_9CETA 0.68 0.92 1 25 22 46 25 0 0 110 S9XLJ2 BAFF receptor isoform 3-like protein OS=Camelus ferus GN=CB1_000168017 PE=4 SV=1
25 : F1MJD0_BOVIN 0.67 0.88 1 24 17 40 24 0 0 129 F1MJD0 Uncharacterized protein OS=Bos taurus GN=TNFRSF13C PE=4 SV=2
26 : H0XRB7_OTOGA 0.64 0.80 1 25 20 44 25 0 0 185 H0XRB7 Uncharacterized protein (Fragment) OS=Otolemur garnettii GN=TNFRSF13C PE=4 SV=1
27 : Q3SXS6_MOUSE 0.60 0.80 1 25 20 44 25 0 0 175 Q3SXS6 BAFF receptor OS=Mus musculus GN=Tnfrsf13c PE=2 SV=1
28 : Q3SXS7_MOUSE 0.60 0.80 1 25 20 44 25 0 0 164 Q3SXS7 Tnfrsf13c protein OS=Mus musculus GN=Tnfrsf13c PE=2 SV=1
29 : Q3U106_MOUSE 0.60 0.80 1 25 20 44 25 0 0 200 Q3U106 Tumor necrosis factor receptor superfamily member 13C OS=Mus musculus GN=Tnfrsf13c PE=2 SV=1
30 : Q8R4W8_MOUSE 0.60 0.80 1 25 20 44 25 0 0 175 Q8R4W8 TRAF3 binding protein OS=Mus musculus GN=Tnfrsf13c PE=2 SV=1
31 : TR13C_MOUSE 0.60 0.80 1 25 20 44 25 0 0 175 Q9D8D0 Tumor necrosis factor receptor superfamily member 13C OS=Mus musculus GN=Tnfrsf13c PE=2 SV=1
## ALIGNMENTS 1 - 31
SeqNo PDBNo AA STRUCTURE BP1 BP2 ACC NOCC VAR ....:....1....:....2....:....3....:....4....:....5....:....6....:....7
1 17 A T 0 0 186 32 0 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
2 18 A P - 0 0 124 32 69 PPPPPPPPPRQRRQQLPQQPPSKQQSQQQQQ
3 19 A a - 0 0 28 32 0 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
4 20 A V B > -A 7 0A 76 32 65 VVVVVVVIVVAIVAVGVVVVVVVLLYNNNNN
5 21 A P T 3 S+ 0 0 137 32 53 PPPPPPPPQQPQQPQQPQQPPQVQQPQQQQQ
6 22 A A T 3 S+ 0 0 74 32 45 AAAAAAAATAAATAAATAATTADTTATTTTT
7 23 A E E < S-AB 4 18A 73 32 33 EEEEEEEELEQEEQEEEQQEEQKQQQEEEEE
8 24 A b E - B 0 17A 67 32 0 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
9 25 A F E - B 0 16A 107 32 1 FFFFFFFFFFFFFFFFYFFYYFFFFFFFFFF
10 26 A D E > - B 0 15A 38 32 0 DDDDDDDDDDDDDDDDDDDDDDDDDDDDDDD
11 27 A L T 5S+ 0 0 110 32 77 LLLLLLLLPPPHHPPLLPPLLPPVPPPPPPP
12 28 A L T 5S+ 0 0 156 32 0 LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL
13 29 A V T 5S- 0 0 78 32 13 VVVVVVVVVVVVVVVLVVVVVTVVVLVVVVV
14 30 A R T 5S+ 0 0 186 32 0 RRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR
15 31 A H E -B 7 0A 58 32 50 AAAAAAAAAAAASAAADAADDADAADSSSSS
19 35 A b T 3 S+ 0 0 47 31 0 CCCCCCCCCCCCC.CCCCCCCCCCCCCCCCC
20 36 A G T 3 S- 0 0 57 32 84 GGGGGGGGNKHSRHKRRKNRRYRSSEEEEEE
21 37 A L S < S+ 0 0 125 32 0 LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL
22 38 A L S S- 0 0 110 32 10 LLLLLLLLLLLLLLFFLFFLLLLLLFFFFFF
23 39 A R S S- 0 0 224 32 26 RRRRRRRRRWRRRRRRRRRRRHRRRRHHHHH
24 40 A T S S- 0 0 118 32 31 TTTTTTTTTTTTTTTTRTTRRITTTTTTTTT
25 41 A P 0 0 116 31 24 PPPPPPPPPPPAPPSPSPPSSPPP PPPPPP
26 42 A R 0 0 286 9 0 RRRRRRRR
## 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 17 A 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 32 0 0 0.000 0 1.00
2 18 A 0 3 0 0 0 0 0 0 0 41 6 0 0 0 9 3 38 0 0 0 32 0 0 1.346 44 0.31
3 19 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 32 0 0 0.000 0 1.00
4 20 A 59 6 6 0 0 0 3 3 6 0 0 0 0 0 0 0 0 0 16 0 32 0 0 1.336 44 0.34
5 21 A 3 0 0 0 0 0 0 0 0 47 0 0 0 0 0 0 50 0 0 0 32 0 0 0.810 27 0.46
6 22 A 0 0 0 0 0 0 0 0 59 0 0 38 0 0 0 0 0 0 0 3 32 0 0 0.786 26 0.55
7 23 A 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 3 25 69 0 0 32 0 0 0.821 27 0.66
8 24 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 32 0 0 0.000 0 1.00
9 25 A 0 0 0 0 91 0 9 0 0 0 0 0 0 0 0 0 0 0 0 0 32 0 0 0.311 10 0.98
10 26 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 32 0 0 0.000 0 1.00
11 27 A 3 41 0 0 0 0 0 0 0 50 0 0 0 6 0 0 0 0 0 0 32 0 0 0.994 33 0.22
12 28 A 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 32 0 0 0.000 0 1.00
13 29 A 91 6 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 0 32 0 0 0.371 12 0.87
14 30 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 32 0 0 0.000 0 1.00
15 31 A 3 3 0 0 0 0 0 0 0 0 0 0 0 41 0 19 0 0 34 0 32 0 0 1.263 42 0.32
16 32 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 32 0 0 0.000 0 1.00
17 33 A 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 32 0 0 0.000 0 1.00
18 34 A 0 0 0 0 0 0 0 0 66 0 19 0 0 0 0 0 0 0 0 16 32 1 0 0.880 29 0.50
19 35 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 31 0 0 0.000 0 1.00
20 36 A 0 0 0 0 0 0 3 28 0 0 9 0 0 6 19 9 0 19 6 0 32 0 0 1.883 62 0.15
21 37 A 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 32 0 0 0.000 0 1.00
22 38 A 0 69 0 0 31 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 32 0 0 0.621 20 0.89
23 39 A 0 0 0 0 0 3 0 0 0 0 0 0 0 19 78 0 0 0 0 0 32 0 0 0.615 20 0.73
24 40 A 0 0 3 0 0 0 0 0 0 0 0 88 0 0 9 0 0 0 0 0 32 0 0 0.447 14 0.69
25 41 A 0 0 0 0 0 0 0 0 3 84 13 0 0 0 0 0 0 0 0 0 31 0 0 0.523 17 0.75
26 42 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 9 0 0 0.000 0 1.00
## INSERTION LIST
AliNo IPOS JPOS Len Sequence
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