Complet list of 1i5j hssp file
Complete list of 1i5j.hssp file
HSSP HOMOLOGY DERIVED SECONDARY STRUCTURE OF PROTEINS , VERSION 2.0 2011
PDBID 1I5J
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 2014-04-30
HEADER LIPID TRANSPORT 27-FEB-01 1I5J
COMPND MOL_ID: 1; MOLECULE: APOLIPOPROTEIN CII; CHAIN: A; SYNONYM: APOC-II; E
SOURCE MOL_ID: 1; ORGANISM_SCIENTIFIC: HOMO SAPIENS; ORGANISM_COMMON: HUMAN;
AUTHOR C.A.MACRAILD,D.M.HATTERS,G.J.HOWLETT,P.R.GOOLEY
DBREF 1I5J A 1 79 UNP P02655 APOC2_HUMAN 1 79
SEQLENGTH 67
NCHAIN 1 chain(s) in 1I5J data set
NALIGN 41
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 : APOC2_HUMAN 1.00 1.00 1 67 35 101 67 0 0 101 P02655 Apolipoprotein C-II OS=Homo sapiens GN=APOC2 PE=1 SV=1
2 : H2R605_PANTR 1.00 1.00 1 67 35 101 67 0 0 101 H2R605 Uncharacterized protein OS=Pan troglodytes GN=APOC2 PE=4 SV=1
3 : K7ER74_HUMAN 1.00 1.00 1 67 112 178 67 0 0 178 K7ER74 Protein APOC4-APOC2 OS=Homo sapiens GN=APOC4-APOC2 PE=4 SV=1
4 : H2NZ65_PONAB 0.94 1.00 1 67 35 101 67 0 0 101 H2NZ65 Uncharacterized protein OS=Pongo abelii GN=APOC2 PE=4 SV=1
5 : APOC2_COLGU 0.91 1.00 1 67 35 101 67 0 0 101 P0DKU5 Apolipoprotein C-II OS=Colobus guereza GN=APOC2 PE=3 SV=1
6 : APOC2_PAPHA 0.91 1.00 1 67 35 101 67 0 0 101 P0DKY1 Apolipoprotein C-II OS=Papio hamadryas GN=APOC2 PE=3 SV=1
7 : A2V9Y5_MACFA 0.90 1.00 1 67 35 101 67 0 0 101 A2V9Y5 Putative uncharacterized protein OS=Macaca fascicularis PE=4 SV=1
8 : APOC2_MACFA 0.90 1.00 1 67 35 101 67 0 0 101 P18658 Apolipoprotein C-II OS=Macaca fascicularis GN=APOC2 PE=1 SV=2
9 : G7NMB2_MACMU 0.90 1.00 1 67 35 101 67 0 0 101 G7NMB2 Uncharacterized protein OS=Macaca mulatta GN=APOC2 PE=4 SV=1
10 : G7PXV6_MACFA 0.90 1.00 1 67 35 101 67 0 0 101 G7PXV6 Putative uncharacterized protein OS=Macaca fascicularis GN=EGM_09851 PE=4 SV=1
11 : APOC2_CALMO 0.81 0.99 1 67 35 101 67 0 0 101 P0DKV9 Apolipoprotein C-II OS=Callicebus moloch GN=APOC2 PE=3 SV=1
12 : APOC2_AOTNA 0.79 0.99 1 67 35 101 67 0 0 101 P0DKV7 Apolipoprotein C-II OS=Aotus nancymaae GN=APOC2 PE=3 SV=1
13 : APOC2_SAIBB 0.78 0.99 1 67 35 101 67 0 0 101 P0DKW0 Apolipoprotein C-II OS=Saimiri boliviensis boliviensis GN=APOC2 PE=3 SV=1
14 : I3MTK2_SPETR 0.76 0.92 1 66 32 97 66 0 0 97 I3MTK2 Uncharacterized protein OS=Spermophilus tridecemlineatus GN=APOC2 PE=4 SV=1
15 : U3CZH0_CALJA 0.75 0.97 1 67 35 101 67 0 0 101 U3CZH0 Apolipoprotein C-II OS=Callithrix jacchus GN=APOC2 PE=4 SV=1
16 : V9GYJ8_HUMAN 0.73 0.75 1 67 35 87 67 1 14 87 V9GYJ8 Apolipoprotein C-II OS=Homo sapiens GN=APOC2 PE=4 SV=1
17 : L9L886_TUPCH 0.72 1.00 1 67 35 101 67 0 0 101 L9L886 Apolipoprotein C-II OS=Tupaia chinensis GN=TREES_T100011512 PE=4 SV=1
18 : APOC2_BOVIN 0.70 0.94 1 67 35 101 67 0 0 101 P19034 Apolipoprotein C-II OS=Bos taurus GN=APOC2 PE=1 SV=2
19 : APOC2_TUPGL 0.70 1.00 1 67 35 101 67 0 0 101 Q9BG58 Apolipoprotein C-II OS=Tupaia glis GN=APOC2 PE=2 SV=1
20 : D2HPB4_AILME 0.70 0.91 1 67 35 101 67 0 0 101 D2HPB4 Putative uncharacterized protein (Fragment) OS=Ailuropoda melanoleuca GN=PANDA_013607 PE=4 SV=1
21 : F7A1W7_HORSE 0.70 0.89 1 66 35 100 66 0 0 101 F7A1W7 Uncharacterized protein OS=Equus caballus GN=APOC2 PE=4 SV=1
22 : M3Y458_MUSPF 0.69 0.96 1 67 35 101 67 0 0 101 M3Y458 Uncharacterized protein OS=Mustela putorius furo GN=APOC2 PE=4 SV=1
23 : G3HPD1_CRIGR 0.68 0.97 1 66 35 100 66 0 0 100 G3HPD1 Apolipoprotein C-II OS=Cricetulus griseus GN=I79_012641 PE=4 SV=1
24 : G3V8D4_RAT 0.68 0.91 1 66 32 97 66 0 0 97 G3V8D4 Apolipoprotein C-II (Predicted) OS=Rattus norvegicus GN=Apoc2 PE=4 SV=1
25 : APOC2_CAVPO 0.67 0.95 8 67 41 100 60 0 0 100 P27916 Apolipoprotein C-II OS=Cavia porcellus GN=APOC2 PE=2 SV=1
26 : G5CBM3_HETGA 0.67 0.91 2 67 36 101 66 0 0 101 G5CBM3 Apolipoprotein C-II OS=Heterocephalus glaber GN=GW7_18157 PE=4 SV=1
27 : H0VEB5_CAVPO 0.67 0.95 8 67 38 97 60 0 0 97 H0VEB5 Uncharacterized protein OS=Cavia porcellus GN=Apoc2 PE=4 SV=1
28 : L8ID36_9CETA 0.67 0.94 1 67 35 101 67 0 0 101 L8ID36 Apolipoprotein C-II OS=Bos mutus GN=M91_05709 PE=4 SV=1
29 : S7MRF2_MYOBR 0.67 0.96 1 67 35 101 67 0 0 101 S7MRF2 Apolipoprotein C-II OS=Myotis brandtii GN=D623_10006035 PE=4 SV=1
30 : D3Y264_PIG 0.66 0.94 1 67 35 101 67 0 0 101 D3Y264 Apolipoprotein C-II OS=Sus scrofa GN=APOC2 PE=4 SV=1
31 : APOC2_CANFA 0.64 0.92 1 66 35 100 66 0 0 101 P12278 Apolipoprotein C-II OS=Canis familiaris GN=APOC2 PE=1 SV=1
32 : APOC2_MOUSE 0.64 0.86 1 66 32 97 66 0 0 97 Q05020 Apolipoprotein C-II OS=Mus musculus GN=Apoc2 PE=2 SV=1
33 : J9NWJ6_CANFA 0.64 0.92 1 66 90 155 66 0 0 156 J9NWJ6 Apolipoprotein C-II OS=Canis familiaris GN=APOC2 PE=4 SV=1
34 : M3WNX1_FELCA 0.64 0.88 1 66 35 100 66 0 0 101 M3WNX1 Uncharacterized protein OS=Felis catus GN=APOC2 PE=4 SV=1
35 : Q3UJG0_MOUSE 0.64 0.86 1 66 32 97 66 0 0 97 Q3UJG0 Apoc2 protein OS=Mus musculus GN=Apoc2 PE=4 SV=1
36 : W5PIA1_SHEEP 0.64 0.96 1 67 124 190 67 0 0 190 W5PIA1 Uncharacterized protein OS=Ovis aries GN=APOC2 PE=4 SV=1
37 : L5M6T0_MYODS 0.63 0.88 1 67 35 101 67 0 0 101 L5M6T0 Apolipoprotein C-II OS=Myotis davidii GN=MDA_GLEAN10005802 PE=4 SV=1
38 : G3TW86_LOXAF 0.58 0.85 1 67 35 101 67 0 0 101 G3TW86 Uncharacterized protein OS=Loxodonta africana GN=APOC2 PE=4 SV=1
39 : F6PKW1_ORNAN 0.48 0.81 1 67 37 103 67 0 0 103 F6PKW1 Uncharacterized protein (Fragment) OS=Ornithorhynchus anatinus GN=APOC2 PE=4 SV=1
40 : F6PLB0_ORNAN 0.48 0.81 1 67 31 97 67 0 0 97 F6PLB0 Uncharacterized protein OS=Ornithorhynchus anatinus GN=APOC2 PE=4 SV=1
41 : G3VHQ0_SARHA 0.46 0.84 1 67 34 100 67 0 0 100 G3VHQ0 Uncharacterized protein OS=Sarcophilus harrisii GN=APOC2 PE=4 SV=1
## ALIGNMENTS 1 - 41
SeqNo PDBNo AA STRUCTURE BP1 BP2 ACC NOCC VAR ....:....1....:....2....:....3....:....4....:....5....:....6....:....7
1 13 A T 0 0 148 39 43 TTTAAAAAAAAAAPATAAATPAAA ATAAAATAATTTTG
2 14 A F > + 0 0 171 40 7 FFFFLLLLLLLLLLLFLLLLLLLL M LLLLLLLLLLFLLL
3 15 A L H >> S+ 0 0 151 40 3 LLLLLLLLLLLLLLLLLLLLLLFL L LFLLLLLLLFLLLL
4 16 A T H 3> S+ 0 0 59 40 51 TTTTTSSSSSTTTATTATAGTTGD T TSTTGTSGTSTSSS
5 17 A Q H 3> S+ 0 0 106 40 54 QQQQQQRRRRQQQQQQQQQQKQKT Q QQKQTQKTKQWRRR
6 18 A V H X S+ 0 0 62 42 82 SSSSSSSSSSSSSSSSSLSYLYSFSFSLLYYLYYLLLRVVF
12 24 A S H 3X S+ 0 0 57 42 42 SSSSSSSSSSSSGSSSSGSGSSSSTSTGGGSSSGSGGRGGA
13 25 A Y H 3< S+ 0 0 208 42 0 YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY
14 26 A W H S+ 0 0 43 42 13 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAVVA
18 30 A K H X S+ 0 0 130 42 19 KKKKKKKKKKKKKKKKKKKKKRKKKKKKKKRKRKKKKKSSK
19 31 A T H >X S+ 0 0 83 42 49 TTTAAAAAAAAAAAATAAASTSAAAAAATASESAEANTTTA
20 32 A A H 3X S+ 0 0 63 42 33 AAAAAAAAAAAAAAAAAAAAAAAAAAAAATAVAAVAATTTK
21 33 A A H 3< S+ 0 0 45 42 6 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAV
22 34 A Q H S+ 0 0 77 42 44 QQQQQQQQQQSSSQSQQQQQQQQGQQQQQQEKEQKHQERRQ
23 35 A N I <>S+ 0 0 57 42 59 NNNNKKKKKKNKSGSNDKDGDEEEGGGKDDDDDDDKDGEEE
24 36 A L I <5S+ 0 0 115 42 0 LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL
25 37 A Y I 45S- 0 0 184 42 6 YYYYYYYYYYYYYYYDYYYYYYYYYYYYYYYYYYYYYYYYY
26 38 A E I <5S+ 0 0 109 42 58 EEEEQEEEEEQQQEQLQKQEKEQQNENKMRKQKKQKMQEEE
27 39 A K I - 0 0 38 41 11 DDDDDDDDDDDDDDD.DDDDDDDDDDDDDDDDDDDDDNNND
35 47 A E T 3 S+ 0 0 119 41 9 EEEEEEEEEEEEEEE.EEEEEEEEEREEEEEEEEEEKEEEE
36 48 A K T 3 S+ 0 0 189 41 20 KKKKKKKKKKKKKKK.KKRKKKKKTKTKNKKKKKKKKKKKN
37 49 A L S < S+ 0 0 95 41 26 LLLLLLLLLLLLLIL.IIIIIILLIIIIFIILIILIIIIIL
38 50 A R S S+ 0 0 84 41 8 RRRRRRRRRRRRRRR.RRRRRRRRRRRRRRRRRRRRRGRRR
39 51 A D S S+ 0 0 66 41 7 DDDDDDDDDDDDDDD.DDDDDDDDDDDDDDDDDDDDEDDDH
40 52 A L S > S+ 0 0 113 41 38 LLLLLLLLLLMMMLM.MIMMMLMMIMIIMMIMIMMIVMAAI
41 53 A Y T >4 S+ 0 0 138 41 0 YYYYYYYYYYYYYYY.YYYYYYYYYYYYYYYYYYYYYYYYY
42 54 A S T 34 S+ 0 0 9 41 22 SSSSSSSSSSSSSSS.SSSSSTSSSSSTISSSSSSSSTSSG
43 55 A K T 34 S+ 0 0 142 42 8 KKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKTKKEKKKK
44 56 A S S << S- 0 0 98 42 20 SSSSSSSSSSSSSGSSSSSSSSSSGSGSNSSSSSSSSCSSG
45 57 A T S S- 0 0 113 42 31 TTTTTTTTTTTTTSTTTTTTTTSSSSSTTTTSTTSTTTTTS
46 58 A A S >S+ 0 0 31 42 13 AAATAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAASAAE
47 59 A A T 5S+ 0 0 24 42 0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
48 60 A M T 5S+ 0 0 97 42 39 MMMMMMMMMMMMVMVMVVVVVVMMIIIVVVVMVVMVVAMMM
49 61 A S T 5S+ 0 0 73 42 46 SSSSSSSSSSSSSSSSTTTSSSSTSRSTTTSSSRSTSTTTT
50 62 A T T >>5S+ 0 0 96 42 8 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTITTTITTTTTTT
51 63 A Y H >> S+ 0 0 95 42 45 TTTTTTTTTTAAAAATAAAAAAAATTTAAAAAATAAALTTT
53 65 A G H <> S+ 0 0 41 42 6 GGGGGGGGGGGGGGGGGGGEEGGGGGGGGGGGGGGGGGGGG
54 66 A I H X S+ 0 0 77 42 3 TTTTTTTTTTTTTTTTTTTTTSTTTTTTTTTTTTTTTTTTT
57 69 A D H 3X S+ 0 0 52 42 0 DDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDD
58 70 A Q H 3< S+ 0 0 127 42 0 QQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQ
59 71 A V H <> S+ 0 0 65 42 29 VVVVVVVVVVVVVLLVLVLLFLLLIIIVVVLLLILVVIIII
60 72 A L H X>S+ 0 0 63 42 21 LLLLLLLLLLLLLLLLFFFLLLFLLLLFLLLLLLLFLVYYI
61 73 A S H <5S+ 0 0 49 42 53 SSSSSSSSSSSSSTSSSSSSSSTTTTTSSSSTSSTSHSHHH
62 74 A V H 45S+ 0 0 98 42 31 VVVVVVVVVVMMMLMVMVMMLMLLMIMMMLMLMMLIMILLM
63 75 A L H <5S+ 0 0 110 42 13 LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLVWWL
64 76 A K T <5S- 0 0 164 42 47 KKKKKKKKKKKKRKKKKSKKKKKKQQQSKTKRKSRSKKAAK
65 77 A G S