Complet list of 1i2u hssp file
Complete list of 1i2u.hssp file
HSSP HOMOLOGY DERIVED SECONDARY STRUCTURE OF PROTEINS , VERSION 2.0 2011
PDBID 1I2U
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 ANTIFUNGAL PROTEIN 12-FEB-01 1I2U
COMPND MOL_ID: 1; MOLECULE: DEFENSIN HELIOMICIN; CHAIN: A; ENGINEERED: YES
SOURCE MOL_ID: 1; ORGANISM_SCIENTIFIC: HELIOTHIS VIRESCENS; ORGANISM_COMMON:
AUTHOR M.LAMBERTY,A.CAILLE,C.LANDON,S.TASSIN-MOINDROT,C.HETRU, P.BULET,F.VOVE
DBREF 1I2U A 1 44 UNP P81544 DEFN_HELVI 1 44
SEQLENGTH 44
NCHAIN 1 chain(s) in 1I2U data set
NALIGN 16
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 : D3G9G5_HELVI 1.00 1.00 1 44 30 73 44 0 0 73 D3G9G5 Heliomicin OS=Heliothis virescens PE=4 SV=1
2 : DEFN_HELVI 1I2U 1.00 1.00 1 44 1 44 44 0 0 44 P81544 Defensin heliomicin OS=Heliothis virescens PE=1 SV=1
3 : E5D602_HELAM 1.00 1.00 1 44 30 73 44 0 0 73 E5D602 Galiomicin OS=Helicoverpa armigera GN=Gali PE=4 SV=1
4 : S5TR00_HELZE 0.98 0.98 1 44 25 68 44 0 0 68 S5TR00 Galiomicin (Fragment) OS=Helicoverpa zea GN=gali PE=4 SV=1
5 : DEFN_ARCDE 1P00 0.95 1.00 1 44 1 44 44 0 0 44 P84156 Defensin ARD1 OS=Archaeoprepona demophon PE=1 SV=1
6 : DEF2_GALME 0.93 0.95 1 43 1 43 43 0 0 44 P85215 Defensin-like peptide OS=Galleria mellonella PE=1 SV=1
7 : DEF1_GALME 0.91 0.93 1 43 30 72 43 0 0 72 P85213 Defensin OS=Galleria mellonella PE=1 SV=2
8 : E5LBK2_MANSE 0.89 0.98 1 44 27 70 44 0 0 70 E5LBK2 Defensin 2 OS=Manduca sexta PE=4 SV=1
9 : V9MG79_COTVE 0.89 0.95 1 44 30 73 44 0 0 73 V9MG79 Defensin 3 OS=Cotesia vestalis GN=def-3 PE=4 SV=1
10 : R4IXW7_BEMTA 0.86 0.89 1 44 30 73 44 0 0 75 R4IXW7 Defensin OS=Bemisia tabaci GN=Def PE=4 SV=1
11 : V9MMW2_COTVE 0.82 0.90 4 43 33 72 40 0 0 73 V9MMW2 Defensin 2 OS=Cotesia vestalis GN=def-2 PE=4 SV=1
12 : R4H5E1_MESEU 0.47 0.56 1 43 13 53 43 2 2 72 R4H5E1 Sodium channel toxin 17 (Fragment) OS=Mesobuthus eupeus PE=2 SV=1
13 : E4VP32_MESEU 0.44 0.53 1 43 27 67 45 3 6 86 E4VP32 Venom sodium channel toxin-5 OS=Mesobuthus eupeus PE=3 SV=1
14 : F1CIV8_HOTJU 0.42 0.56 1 43 27 67 43 2 2 86 F1CIV8 Beta-buthitoxin-Hj2a OS=Hottentotta judaicus PE=3 SV=1
15 : SCAS_MESMA 0.42 0.53 1 43 26 66 43 2 2 85 Q9UAC9 Beta-toxin BmKAS OS=Mesobuthus martensii PE=1 SV=1
16 : I6MRK9_CAERE 0.40 0.62 1 44 17 54 45 3 8 54 I6MRK9 Mycin-7 (Precursor) OS=Caenorhabditis remanei PE=2 SV=1
## ALIGNMENTS 1 - 16
SeqNo PDBNo AA STRUCTURE BP1 BP2 ACC NOCC VAR ....:....1....:....2....:....3....:....4....:....5....:....6....:....7
1 1 A D 0 0 127 16 22 DDDDDDDDDD DDNDG
2 2 A K E -A 42 0A 97 16 21 KKKKKKTKKV KKKKK
3 3 A L E +A 41 0A 84 16 62 LLLLLLLLLL YYAYF
4 4 A I E - 0 0A 25 17 74 IIIIIIIIIIITTTTK
5 5 A G E S-A 40 0A 9 17 0 GGGGGGGGGGGGGGGG
6 6 A S E -Ab 39 14A 20 17 49 SSSSSSSSSSSCCCCP
7 7 A a + 0 0 5 17 94 CCCCCCCCCCCKEKKC
8 8 A V S S- 0 0 81 16 0 VVVVVVVVVVVVVVV.
9 9 A W S S+ 0 0 190 16 0 WWWWWWWWWWWWWWW.
10 10 A G S S+ 0 0 70 16 66 GGGGGGGGGGGCCCC.
11 11 A A S > S- 0 0 52 16 72 AAAAAAAAAGGVVVV.
12 12 A V T 3 S+ 0 0 146 16 36 VVVVVTTVTVVIIVI.
13 13 A N T 3 + 0 0 99 16 5 NNNNNNNDNNNNNNN.
14 14 A Y B < -b 6 0A 79 17 71 YYYYYYYYYYYNNNNY
15 15 A T > - 0 0 16 17 74 TTTTTTTTTTVEEAEs
16 16 A S T 3 S+ 0 0 108 13 0 SSSSSSSSSSS....s
17 17 A D T 3> S+ 0 0 105 17 66 DDDDNDDNNDNSSSSN
18 18 A b H <> S+ 0 0 9 17 0 CCCCCCCCCCCCCCCC
19 19 A N H > S+ 0 0 71 17 27 NNNNNNNNNLLNNNNN
20 20 A G H > S+ 0 0 19 17 51 GGGGAAAAAKDGGSSG
21 21 A E H X S+ 0 0 57 17 39 EEEEEEEEEEEEESEV
22 22 A c H ><>S+ 0 0 0 17 0 CCCCCCCCCCCCCCCC
23 23 A K H ><5S+ 0 0 127 17 20 KKKKKKKVKKKKKKKR
24 24 A R H 3<5S+ 0 0 198 17 63 RRRRRRRRRRRRRLID
25 25 A R T <<5S- 0 0 128 17 21 RRRRRRRRRRRRRRRE
26 26 A G T < 5S+ 0 0 68 17 0 GGGGGGGGGGGGGGGG
27 27 A Y < - 0 0 59 16 103 YYYYYYYFFYYG.GGH
28 28 A K S S- 0 0 128 16 73 KKKKKKKKKKKY.NYK
29 29 A G + 0 0 6 16 99 GGGGGGGGGGGY.YYS
30 30 A G E +C 42 0A 3 17 0 GGGGGGGGGGGGGGGG
31 31 A H E -C 41 0A 81 17 53 HHHHHHHHHHHYYYYH
32 32 A a E +C 40 0A 38 17 5 CCCCCCCCCCCCYCCC
33 33 A G + 0 0 52 16 74 GGGGGGGGGGG.gYYS
34 34 A S S S- 0 0 55 15 88 SSSSSSSSSSSYy..H
35 35 A F S S- 0 0 183 17 17 FFFFFFFFFAFFFFFW
36 36 A A S S- 0 0 72 17 98 AAAAAWLAWLAWWWWS
37 37 A N S S+ 0 0 99 17 62 NNNNNNNNNNNKKKKG
38 38 A V + 0 0 49 17 57 VVVVVVVVVVNLLLLA
39 39 A N E -A 6 0A 54 16 74 NNNNNNNNNNIAAAA.
40 40 A b E -AC 5 32A 3 17 0 CCCCCCCCCCCCCCCC
41 41 A W E -AC 3 31A 80 17 11 WWWWWWWWWWWFFYFW
42 42 A c E -AC 2 30A 0 17 7 CCCGCCCCCCCCCCCC
43 43 A E 0 0 95 17 32 EEEEEEEEEEEQQEQD
44 44 A T 0 0 78 10 0 TTTTT TTT T
## 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 6 0 0 0 0 0 0 0 0 0 0 6 88 16 0 0 0.463 15 0.78
2 2 A 6 0 0 0 0 0 0 0 0 0 0 6 0 0 0 88 0 0 0 0 16 0 0 0.463 15 0.78
3 3 A 0 69 0 0 6 0 19 0 6 0 0 0 0 0 0 0 0 0 0 0 16 0 0 0.918 30 0.37
4 4 A 0 0 71 0 0 0 0 0 0 0 0 24 0 0 0 6 0 0 0 0 17 0 0 0.753 25 0.25
5 5 A 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 17 0 0 0.000 0 1.00
6 6 A 0 0 0 0 0 0 0 0 0 6 71 0 24 0 0 0 0 0 0 0 17 0 0 0.753 25 0.51
7 7 A 0 0 0 0 0 0 0 0 0 0 0 0 76 0 0 18 0 6 0 0 17 1 0 0.678 22 0.05
8 8 A 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 16 0 0 0.000 0 1.00
9 9 A 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 16 0 0 0.000 0 1.00
10 10 A 0 0 0 0 0 0 0 75 0 0 0 0 25 0 0 0 0 0 0 0 16 0 0 0.562 18 0.33
11 11 A 25 0 0 0 0 0 0 13 63 0 0 0 0 0 0 0 0 0 0 0 16 0 0 0.900 30 0.28
12 12 A 63 0 19 0 0 0 0 0 0 0 0 19 0 0 0 0 0 0 0 0 16 0 0 0.921 30 0.63
13 13 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 94 6 16 0 0 0.234 7 0.94
14 14 A 0 0 0 0 0 0 76 0 0 0 0 0 0 0 0 0 0 0 24 0 17 0 0 0.546 18 0.29
15 15 A 6 0 0 0 0 0 0 0 6 0 6 65 0 0 0 0 0 18 0 0 17 4 1 1.088 36 0.25
16 16 A 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 13 0 0 0.000 0 1.00
17 17 A 0 0 0 0 0 0 0 0 0 0 24 0 0 0 0 0 0 0 29 47 17 0 0 1.055 35 0.33
18 18 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 17 0 0 0.000 0 1.00
19 19 A 0 12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 88 0 17 0 0 0.362 12 0.73
20 20 A 0 0 0 0 0 0 0 47 29 0 12 0 0 0 0 6 0 0 0 6 17 0 0 1.300 43 0.49
21 21 A 6 0 0 0 0 0 0 0 0 0 6 0 0 0 0 0 0 88 0 0 17 0 0 0.444 14 0.61
22 22 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 17 0 0 0.000 0 1.00
23 23 A 6 0 0 0 0 0 0 0 0 0 0 0 0 0 6 88 0 0 0 0 17 0 0 0.444 14 0.79
24 24 A 0 6 6 0 0 0 0 0 0 0 0 0 0 0 82 0 0 0 0 6 17 0 0 0.660 22 0.37
25 25 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 94 0 0 6 0 0 17 0 0 0.224 7 0.79
26 26 A 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 17 1 0 0.000 0 1.00
27 27 A 0 0 0 0 13 0 63 19 0 0 0 0 0 6 0 0 0 0 0 0 16 0 0 1.041 34 -0.03
28 28 A 0 0 0 0 0 0 13 0 0 0 0 0 0 0 0 81 0 0 6 0 16 0 0 0.602 20 0.26
29 29 A 0 0 0 0 0 0 19 75 0 0 6 0 0 0 0 0 0 0 0 0 16 0 0 0.703 23 0.00
30 30 A 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 17 0 0 0.000 0 1.00
31 31 A 0 0 0 0 0 0 24 0 0 0 0 0 0 76 0 0 0 0 0 0 17 0 0 0.546 18 0.46
32 32 A 0 0 0 0 0 0 6 0 0 0 0 0 94 0 0 0 0 0 0 0 17 1 0 0.224 7 0.94
33 33 A 0 0 0 0 0 0 13 81 0 0 6 0 0 0 0 0 0 0 0 0 16 2 1 0.602 20 0.25
34 34 A 0 0 0 0 0 0 13 0 0 0 80 0 0 7 0 0 0 0 0 0 15 0 0 0.628 20 0.11
35 35 A 0 0 0 0 88 6 0 0 6 0 0 0 0 0 0 0 0 0 0 0 17 0 0 0.444 14 0.82
36 36 A 0 12 0 0 0 35 0 0 47 0 6 0 0 0 0 0 0 0 0 0 17 0 0 1.141 38 0.01
37 37 A 0 0 0 0 0 0 0 6 0 0 0 0 0 0 0 24 0 0 71 0 17 0 0 0.753 25 0.38
38 38 A 65 24 0 0 0 0 0 0 6 0 0 0 0 0 0 0 0 0 6 0 17 1 0 0.955 31 0.42
39 39 A 0 0 6 0 0 0 0 0 25 0 0 0 0 0 0 0 0 0 69 0 16 0 0 0.777 25 0.25
40 40 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 17 0 0 0.000 0 1.00
41 41 A 0 0 0 0 18 76 6 0 0 0 0 0 0 0 0 0 0 0 0 0 17 0 0 0.678 22 0.89
42 42 A 0 0 0 0 0 0 0 6 0 0 0 0 94 0 0 0 0 0 0 0 17 0 0 0.224 7 0.93
43 43 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 18 76 0 6 17 0 0 0.678 22 0.67
44 44 A 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 10 0 0 0.000 0 1.00
## INSERTION LIST
AliNo IPOS JPOS Len Sequence
13 30 56 2 gYCy
16 10 26 1 sDs
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