Complet list of 1by6 hssp file
Complete list of 1by6.hssp file
HSSP HOMOLOGY DERIVED SECONDARY STRUCTURE OF PROTEINS , VERSION 2.0 2011
PDBID 1BY6
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 SIGNALING PROTEIN 03-DEC-99 1BY6
COMPND MOL_ID: 1; MOLECULE: APOLIPOPROTEIN C-II; CHAIN: A; FRAGMENT: RESIDUES
SOURCE MOL_ID: 1; SYNTHETIC: YES; OTHER_DETAILS: THIS PEPTIDE WAS CHEMICALLY
AUTHOR R.STORJOHANN,A.ROZEK,J.T.SPARROW,R.J.CUSHLEY
DBREF 1BY6 A 44 79 UNP P02655 APOC2_HUMAN 66 101
SEQLENGTH 36
NCHAIN 1 chain(s) in 1BY6 data set
NALIGN 42
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 : A2V9Y5_MACFA 1.00 1.00 1 36 66 101 36 0 0 101 A2V9Y5 Putative uncharacterized protein OS=Macaca fascicularis PE=4 SV=1
2 : APOC2_COLGU 1.00 1.00 1 36 66 101 36 0 0 101 P0DKU5 Apolipoprotein C-II OS=Colobus guereza GN=APOC2 PE=3 SV=1
3 : APOC2_HUMAN 1.00 1.00 1 36 66 101 36 0 0 101 P02655 Apolipoprotein C-II OS=Homo sapiens GN=APOC2 PE=1 SV=1
4 : APOC2_MACFA 1.00 1.00 1 36 66 101 36 0 0 101 P18658 Apolipoprotein C-II OS=Macaca fascicularis GN=APOC2 PE=1 SV=2
5 : APOC2_PAPHA 1.00 1.00 1 36 66 101 36 0 0 101 P0DKY1 Apolipoprotein C-II OS=Papio hamadryas GN=APOC2 PE=3 SV=1
6 : G7NMB2_MACMU 1.00 1.00 1 36 66 101 36 0 0 101 G7NMB2 Uncharacterized protein OS=Macaca mulatta GN=APOC2 PE=4 SV=1
7 : G7PXV6_MACFA 1.00 1.00 1 36 66 101 36 0 0 101 G7PXV6 Putative uncharacterized protein OS=Macaca fascicularis GN=EGM_09851 PE=4 SV=1
8 : H2R605_PANTR 1.00 1.00 1 36 66 101 36 0 0 101 H2R605 Uncharacterized protein OS=Pan troglodytes GN=APOC2 PE=4 SV=1
9 : K7ER74_HUMAN 1.00 1.00 1 36 143 178 36 0 0 178 K7ER74 Protein APOC4-APOC2 OS=Homo sapiens GN=APOC4-APOC2 PE=4 SV=1
10 : V9GYJ8_HUMAN 1.00 1.00 9 36 60 87 28 0 0 87 V9GYJ8 Apolipoprotein C-II OS=Homo sapiens GN=APOC2 PE=4 SV=1
11 : H2NZ65_PONAB 0.97 1.00 1 36 66 101 36 0 0 101 H2NZ65 Uncharacterized protein OS=Pongo abelii GN=APOC2 PE=4 SV=1
12 : APOC2_AOTNA 0.86 1.00 1 36 66 101 36 0 0 101 P0DKV7 Apolipoprotein C-II OS=Aotus nancymaae GN=APOC2 PE=3 SV=1
13 : APOC2_ATEGE 0.86 1.00 8 36 1 29 29 0 0 29 P0DKV8 Apolipoprotein C-II (Fragment) OS=Ateles geoffroyi GN=APOC2 PE=3 SV=1
14 : APOC2_CALMO 0.86 1.00 1 36 66 101 36 0 0 101 P0DKV9 Apolipoprotein C-II OS=Callicebus moloch GN=APOC2 PE=3 SV=1
15 : APOC2_SAIBB 0.86 1.00 1 36 66 101 36 0 0 101 P0DKW0 Apolipoprotein C-II OS=Saimiri boliviensis boliviensis GN=APOC2 PE=3 SV=1
16 : U3CZH0_CALJA 0.81 1.00 1 36 66 101 36 0 0 101 U3CZH0 Apolipoprotein C-II OS=Callithrix jacchus GN=APOC2 PE=4 SV=1
17 : G3HPD1_CRIGR 0.77 1.00 1 35 66 100 35 0 0 100 G3HPD1 Apolipoprotein C-II OS=Cricetulus griseus GN=I79_012641 PE=4 SV=1
18 : G3V8D4_RAT 0.77 1.00 1 35 63 97 35 0 0 97 G3V8D4 Apolipoprotein C-II (Predicted) OS=Rattus norvegicus GN=Apoc2 PE=4 SV=1
19 : I3MTK2_SPETR 0.76 1.00 2 35 64 97 34 0 0 97 I3MTK2 Uncharacterized protein OS=Spermophilus tridecemlineatus GN=APOC2 PE=4 SV=1
20 : L9L886_TUPCH 0.75 1.00 1 36 66 101 36 0 0 101 L9L886 Apolipoprotein C-II OS=Tupaia chinensis GN=TREES_T100011512 PE=4 SV=1
21 : APOC2_CANFA 0.74 1.00 1 35 66 100 35 0 0 101 P12278 Apolipoprotein C-II OS=Canis familiaris GN=APOC2 PE=1 SV=1
22 : APOC2_MOUSE 0.74 1.00 1 35 63 97 35 0 0 97 Q05020 Apolipoprotein C-II OS=Mus musculus GN=Apoc2 PE=2 SV=1
23 : J9NWJ6_CANFA 0.74 1.00 1 35 121 155 35 0 0 156 J9NWJ6 Apolipoprotein C-II OS=Canis familiaris GN=APOC2 PE=4 SV=1
24 : Q3UJG0_MOUSE 0.74 1.00 1 35 63 97 35 0 0 97 Q3UJG0 Apoc2 protein OS=Mus musculus GN=Apoc2 PE=4 SV=1
25 : APOC2_BOVIN 0.72 0.94 1 36 66 101 36 0 0 101 P19034 Apolipoprotein C-II OS=Bos taurus GN=APOC2 PE=1 SV=2
26 : APOC2_TUPGL 0.72 1.00 1 36 66 101 36 0 0 101 Q9BG58 Apolipoprotein C-II OS=Tupaia glis GN=APOC2 PE=2 SV=1
27 : D2HPB4_AILME 0.72 0.97 1 36 66 101 36 0 0 101 D2HPB4 Putative uncharacterized protein (Fragment) OS=Ailuropoda melanoleuca GN=PANDA_013607 PE=4 SV=1
28 : M3Y458_MUSPF 0.72 1.00 1 36 66 101 36 0 0 101 M3Y458 Uncharacterized protein OS=Mustela putorius furo GN=APOC2 PE=4 SV=1
29 : F7A1W7_HORSE 0.71 0.94 1 35 66 100 35 0 0 101 F7A1W7 Uncharacterized protein OS=Equus caballus GN=APOC2 PE=4 SV=1
30 : D3Y264_PIG 0.69 0.94 1 36 66 101 36 0 0 101 D3Y264 Apolipoprotein C-II OS=Sus scrofa GN=APOC2 PE=4 SV=1
31 : S7MRF2_MYOBR 0.69 0.97 1 36 66 101 36 0 0 101 S7MRF2 Apolipoprotein C-II OS=Myotis brandtii GN=D623_10006035 PE=4 SV=1
32 : W5PIA1_SHEEP 0.69 0.97 1 36 155 190 36 0 0 190 W5PIA1 Uncharacterized protein OS=Ovis aries GN=APOC2 PE=4 SV=1
33 : L5M6T0_MYODS 0.67 0.89 1 36 66 101 36 0 0 101 L5M6T0 Apolipoprotein C-II OS=Myotis davidii GN=MDA_GLEAN10005802 PE=4 SV=1
34 : L8ID36_9CETA 0.67 0.94 1 36 66 101 36 0 0 101 L8ID36 Apolipoprotein C-II OS=Bos mutus GN=M91_05709 PE=4 SV=1
35 : M3WNX1_FELCA 0.66 0.89 1 35 66 100 35 0 0 101 M3WNX1 Uncharacterized protein OS=Felis catus GN=APOC2 PE=4 SV=1
36 : APOC2_CAVPO 0.64 0.94 1 36 65 100 36 0 0 100 P27916 Apolipoprotein C-II OS=Cavia porcellus GN=APOC2 PE=2 SV=1
37 : G5CBM3_HETGA 0.64 0.94 1 36 66 101 36 0 0 101 G5CBM3 Apolipoprotein C-II OS=Heterocephalus glaber GN=GW7_18157 PE=4 SV=1
38 : H0VEB5_CAVPO 0.64 0.94 1 36 62 97 36 0 0 97 H0VEB5 Uncharacterized protein OS=Cavia porcellus GN=Apoc2 PE=4 SV=1
39 : F6PKW1_ORNAN 0.58 0.86 1 36 68 103 36 0 0 103 F6PKW1 Uncharacterized protein (Fragment) OS=Ornithorhynchus anatinus GN=APOC2 PE=4 SV=1
40 : F6PLB0_ORNAN 0.58 0.86 1 36 62 97 36 0 0 97 F6PLB0 Uncharacterized protein OS=Ornithorhynchus anatinus GN=APOC2 PE=4 SV=1
41 : G3VHQ0_SARHA 0.57 0.94 2 36 66 100 35 0 0 100 G3VHQ0 Uncharacterized protein OS=Sarcophilus harrisii GN=APOC2 PE=4 SV=1
42 : G3TW86_LOXAF 0.56 0.89 1 36 66 101 36 0 0 101 G3TW86 Uncharacterized protein OS=Loxodonta africana GN=APOC2 PE=4 SV=1
## ALIGNMENTS 1 - 42
SeqNo PDBNo AA STRUCTURE BP1 BP2 ACC NOCC VAR ....:....1....:....2....:....3....:....4....:....5....:....6....:....7
1 44 A A 0 0 152 39 53 AAAAAAAAA AT TATSS ATSTSAAGATTSTSATATAGG T
2 45 A V + 0 0 113 41 28 VVVVVVVVV VV VVVVVMVMMMMVVMMVVMVMVVVVVLLMV
3 46 A D + 0 0 146 41 11 DDDDDDDDD DD DDDDDDDDDDDDDDDDDDDDDDDDDNNDN
4 47 A E S S- 0 0 163 41 10 EEEEEEEEE EE EEEEEEEEEEEEEEEEEEEKEEEREEEEE
5 48 A K - 0 0 134 41 21 KKKKKKKKK KK KKKKKKKKKKKKRKKKKNKKKKTKTKKNK
6 49 A L S S- 0 0 110 41 27 LLLLLLLLL LL LLLLLIIILILIIIIIIFIIIIIIIIILI
7 50 A R - 0 0 174 41 9 RRRRRRRRR RR RRRRRRRRRRRRRRRRRRRRRRRRRRRRG
8 51 A D S S+ 0 0 98 42 7 DDDDDDDDD DDDDDDDDDDDDDDDDDDDDDDEDDDDDDDHD
9 52 A L S > S+ 0 0 130 43 38 LLLLLLLLLLLMMMMMMMLMIMIMIMMLMMMIVIMIMIAAIM
10 53 A Y T 4 S+ 0 0 168 43 0 YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY
11 54 A S T 4 S+ 0 0 73 43 22 SSSSSSSSSSSSSSSSSSSSSSSSSSSTSSISSTSSSSSSGT
12 55 A K T 4 S+ 0 0 157 43 9 KKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKEKTKKKKKKK
13 56 A S S >X S+ 0 0 68 43 21 SSSSSSSSSSSSSSSSSSGSSSSSSSSSSSNSSSSGSGSSGC
14 57 A T T 34 S+ 0 0 79 43 32 TTTTTTTTTTTTTTTTSSSTTSTSTTTTTTTTTTTSSSTTST
15 58 A A T 34 S- 0 0 70 43 13 AAAAAAAAAATAAAAAAAAAAAAAAAAAAAAAAAAAAAAAES
16 59 A A T <4 + 0 0 45 43 0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
17 60 A M >< + 0 0 137 43 41 MMMMMMMMMMMMMMVVMMMVVMVMVVVVVVVVVVVIIIMMMA
18 61 A S T 3 S- 0 0 102 43 48 SSSSSSSSSSSSSSSSSTSTSSSSTTSSSTTTSTRSRSTTTT
19 62 A T T 3 S+ 0 0 83 43 9 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTITTTTITTTTTTT
20 63 A Y < + 0 0 132 43 0 YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY
21 64 A T S S- 0 0 110 43 46 TTTTTTTTTTTAAAAAAAAAAAAAAAAAAAAAAATTTTTTTL
22 65 A G S S- 0 0 52 43 6 GGGGGGGGGGGGGGGGGGGGGGGGGGEGEGGGGGGGGGGGGG
23 66 A I S S+ 0 0 134 43 0 IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
24 67 A F + 0 0 88 43 16 FFFFFFFFFFFLLLFLFFFFFFFFIFFFLFFIFILLFLLLLL
25 68 A T - 0 0 71 43 4 TTTTTTTTTTTTTTTTTTTTTTTTTTTSTTTTTTTTTTTTTT
26 69 A D S > S+ 0 0 110 43 0 DDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDD
27 70 A Q G > S+ 0 0 125 43 0 QQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQ
28 71 A V G 3 S+ 0 0 115 43 29 VVVVVVVVVVVVVVVLLLLLLLLLVLLLFVVVVVIIIIIIII
29 72 A L G < S+ 0 0 121 43 21 LLLLLLLLLLLLLLLLFLLFLLLLFFLLLLLFLFLLLLYYIV
30 73 A S S < S+ 0 0 74 43 52 SSSSSSSSSSSSSSSSTTTSSTSTSSSSSSSSHSSTTTHHHS
31 74 A V > + 0 0 106 43 32 VVVVVVVVVVVMMMMMLLLMMLMLVMMMLLMIMMMMIMLLMI
32 75 A L G > S+ 0 0 116 43 12 LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLWWLV
33 76 A K G 3 S+ 0 0 199 43 49 KKKKKKKKKKKKKKRKKKKKKRKRSKKKKTKSKSSQQQAAKK
34 77 A G G < S- 0 0 61 43 0 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
35 78 A E < 0 0 177 43 32 EEEEEEEEEEEEEEEEEEEEDEDEKEEDDDEEGKDKDKDDEE
36 79 A E 0 0 179 34 36 EEEEEEEEEEEEEEEE Q DQQQ HEDED QQQQQQE
## 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 44 A 0 0 0 0 0 0 0 8 49 0 15 28 0 0 0 0 0 0 0 0 39 0 0 1.193 39 0.47
2 45 A 71 5 0 24 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 41 0 0 0.736 24 0.72
3 46 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 93 41 0 0 0.262 8 0.89
4 47 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 95 0 0 41 0 0 0.229 7 0.89
5 48 A 0 0 0 0 0 0 0 0 0 0 0 5 0 0 2 88 0 0 5 0 41 0 0 0.499 16 0.78
6 49 A 0 49 49 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 41 0 0 0.791 26 0.72
7 50 A 0 0 0 0 0 0 0 2 0 0 0 0 0 0 98 0 0 0 0 0 41 0 0 0.115 3 0.91
8 51 A 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 2 0 95 42 0 0 0.224 7 0.93
9 52 A 2 33 19 42 0 0 0 0 5 0 0 0 0 0 0 0 0 0 0 0 43 0 0 1.273 42 0.62
10 53 A 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 43 0 0 0.000 0 1.00
11 54 A 0 0 2 0 0 0 0 2 0 0 88 7 0 0 0 0 0 0 0 0 43 0 0 0.470 15 0.77
12 55 A 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 95 0 2 0 0 43 0 0 0.220 7 0.91
13 56 A 0 0 0 0 0 0 0 9 0 0 86 0 2 0 0 0 0 0 2 0 43 0 0 0.525 17 0.79
14 57 A 0 0 0 0 0 0 0 0 0 0 21 79 0 0 0 0 0 0 0 0 43 0 0 0.513 17 0.67
15 58 A 0 0 0 0 0 0 0 0 93 0 2 2 0 0 0 0 0 2 0 0 43 0 0 0.330 11 0.86
16 59 A 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 43 0 0 0.000 0 1.00
17 60 A 37 0 7 53 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 43 0 0 0.976 32 0.59
18 61 A 0 0 0 0 0 0 0 0 0 0 67 28 0 0 5 0 0 0 0 0 43 0 0 0.765 25 0.52
19 62 A 0 0 5 0 0 0 0 0 0 0 0 95 0 0 0 0 0 0 0 0 43 0 0 0.188 6 0.91
20 63 A 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 43 0 0 0.000 0 1.00
21 64 A 0 2 0 0 0 0 0 0 53 0 0 44 0 0 0 0 0 0 0 0 43 0 0 0.783 26 0.54
22 65 A 0 0 0 0 0 0 0 95 0 0 0 0 0 0 0 0 0 5 0 0 43 0 0 0.188 6 0.94
23 66 A 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 43 0 0 0.000 0 1.00
24 67 A 0 28 7 0 65 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 43 0 0 0.821 27 0.83
25 68 A 0 0 0 0 0 0 0 0 0 0 2 98 0 0 0 0 0 0 0 0 43 0 0 0.110 3 0.96
26 69 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 43 0 0 0.000 0 1.00
27 70 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 43 0 0 0.000 0 1.00
28 71 A 51 28 19 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 43 0 0 1.099 36 0.70
29 72 A 2 77 2 0 14 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 43 0 0 0.796 26 0.79
30 73 A 0 0 0 0 0 0 0 0 0 0 72 19 0 9 0 0 0 0 0 0 43 0 0 0.770 25 0.47
31 74 A 30 21 7 42 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 43 0 0 1.239 41 0.67
32 75 A 2 93 0 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 43 0 0 0.297 9 0.87
33 76 A 0 0 0 0 0 0 0 0 5 0 9 2 0 0 7 70 7 0 0 0 43 0 0 1.074 35 0.51
34 77 A 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 43 0 0 0.000 0 1.00
35 78 A 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 9 0 67 0 21 43 0 0 0.901 30 0.68
36 79 A 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 29 59 0 9 34 0 0 0.990 33 0.64
## INSERTION LIST
AliNo IPOS JPOS Len Sequence
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