Complet list of 1tv0 hssp file
Complete list of 1tv0.hssp file
HSSP HOMOLOGY DERIVED SECONDARY STRUCTURE OF PROTEINS , VERSION 2.0 2011
PDBID 1TV0
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 2014-05-10
HEADER ANTIMICROBIAL PROTEIN 25-JUN-04 1TV0
COMPND MOL_ID: 1; MOLECULE: CRYPTDIN-4; CHAIN: A; ENGINEERED: YES
SOURCE MOL_ID: 1; ORGANISM_SCIENTIFIC: MUS MUSCULUS; ORGANISM_COMMON: HOUSE M
AUTHOR W.JING,H.N.HUNTER,H.TANABE,A.J.OUELLETTE,H.J.VOGEL
DBREF 1TV0 A 1 32 UNP P28311 DEF4_MOUSE 61 92
SEQLENGTH 32
NCHAIN 1 chain(s) in 1TV0 data set
NALIGN 20
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 : DEFA4_MOUSE 2LEY 1.00 1.00 1 32 61 92 32 0 0 92 P28311 Alpha-defensin 4 OS=Mus musculus GN=Defa4 PE=1 SV=4
2 : DFA20_MOUSE 0.66 0.88 1 32 61 92 32 0 0 95 Q45VN2 Alpha-defensin 20 OS=Mus musculus GN=Defa20 PE=2 SV=2
3 : Q8C1N9_MOUSE 0.66 0.88 1 32 61 92 32 0 0 95 Q8C1N9 Alpha-defensin 2 OS=Mus musculus GN=Defcr20 PE=4 SV=1
4 : Q8C1P0_MOUSE 0.66 0.84 1 32 61 92 32 0 0 95 Q8C1P0 Putative uncharacterized protein OS=Mus musculus PE=4 SV=1
5 : DFA22_MOUSE 0.56 0.72 1 32 61 92 32 0 0 93 Q8C1N8 Alpha-defensin 22 OS=Mus musculus GN=Defa22 PE=2 SV=1
6 : W4VSN6_MOUSE 0.56 0.72 1 32 61 92 32 0 0 93 W4VSN6 Alpha-defensin 22 OS=Mus musculus GN=Defa22 PE=4 SV=1
7 : D3Z0J0_MOUSE 0.53 0.69 2 30 62 93 32 1 3 93 D3Z0J0 Protein Gm15315 OS=Mus musculus GN=Gm15315 PE=4 SV=1
8 : DEFA5_MOUSE 0.53 0.69 2 30 62 93 32 1 3 93 P28312 Alpha-defensin 5 OS=Mus musculus GN=Defa5 PE=1 SV=2
9 : DFA21_MOUSE 0.53 0.72 1 32 61 92 32 0 0 93 Q8C1P2 Alpha-defensin 21 OS=Mus musculus GN=Defa21 PE=3 SV=1
10 : E9QLQ1_MOUSE 0.53 0.69 2 30 62 93 32 1 3 93 E9QLQ1 Protein Gm10104 OS=Mus musculus GN=Gm10104 PE=4 SV=1
11 : H0XSF6_OTOGA 0.53 0.62 2 30 70 101 32 1 3 101 H0XSF6 Uncharacterized protein OS=Otolemur garnettii GN=DEFA6 PE=4 SV=1
12 : K9J724_MOUSE 0.53 0.69 2 30 62 93 32 1 3 93 K9J724 Protein Gm14850 OS=Mus musculus GN=Gm21498 PE=4 SV=1
13 : L7N230_MOUSE 0.53 0.69 2 30 62 93 32 1 3 93 L7N230 Alpha-defensin 5 OS=Mus musculus GN=Defa5 PE=4 SV=1
14 : Q0VDM0_MOUSE 0.53 0.69 2 30 60 91 32 1 3 91 Q0VDM0 Defcr5 protein (Fragment) OS=Mus musculus GN=Defa5 PE=2 SV=1
15 : D3YX02_MOUSE 0.50 0.66 2 30 62 93 32 1 3 93 D3YX02 Protein Gm15293 OS=Mus musculus GN=Gm15293 PE=4 SV=1
16 : DEFA3_MOUSE 0.48 0.64 1 30 61 93 33 1 3 93 P28310 Alpha-defensin 3 OS=Mus musculus GN=Defa3 PE=1 SV=2
17 : DFA25_MOUSE 0.48 0.64 1 29 60 92 33 2 4 92 Q5G864 Alpha-defensin 25 OS=Mus musculus GN=Defa25 PE=2 SV=1
18 : G3U1H0_LOXAF 0.48 0.64 1 30 62 94 33 1 3 94 G3U1H0 Uncharacterized protein OS=Loxodonta africana GN=LOC100655647 PE=4 SV=1
19 : Q499K8_MOUSE 0.48 0.65 1 28 59 89 31 1 3 89 Q499K8 Defcr3 protein (Fragment) OS=Mus musculus GN=Defcr3 PE=2 SV=1
20 : K7N7D8_MOUSE 0.47 0.62 1 29 34 65 32 1 3 66 K7N7D8 Protein Gm15299 OS=Mus musculus GN=Gm15299 PE=4 SV=1
## ALIGNMENTS 1 - 20
SeqNo PDBNo AA STRUCTURE BP1 BP2 ACC NOCC VAR ....:....1....:....2....:....3....:....4....:....5....:....6....:....7
1 1 A G 0 0 114 13 27 GDDDDD D DDNDD
2 2 A L + 0 0 146 21 0 LLLLLLLLLLLLLLLLLLLL
3 3 A L + 0 0 78 21 37 LIIIIIIIIISIIIIVITVI
4 4 A a - 0 0 20 21 0 CCCCCCCCCCCCCCCCCCCC
5 5 A Y E -A 28 0A 136 21 25 YYYYLLYYLYYYYYYYYYYY
6 6 A b E -A 27 0A 58 21 0 CCCCCCCCCCCCCCCCCCCC
7 7 A R E -A 26 0A 92 21 0 RRRRRRRRRRRRRRRRRRRR
8 8 A K E S-A 25 0A 115 21 83 KKKKKKIINIRIIIIKTSKT
9 9 A G S S- 0 0 57 21 71 GGGGRRRRRRGRRRRRRVRR
10 10 A H - 0 0 132 21 69 HGGGRRGGRGSGGGGGGRGG
11 11 A c - 0 0 15 21 0 CCCCCCCCCCCCCCCCCCCC
12 12 A K S S- 0 0 160 21 52 KNNNNNKKNKPKKKKKKRKK
13 13 A R S S+ 0 0 182 21 17 RRRRRRRRRRRRRRRRRIRR
14 14 A G - 0 0 27 21 81 GGGGGGRRGRPRRRRRRSRR
15 15 A E E +B 28 0A 115 21 0 EEEEEEEEEEEEEEEEEEEE
16 16 A R E -B 27 0A 113 21 64 RQQQLLRRLRRRRRCRRRRR
17 17 A V + 0 0 109 21 48 VVVVFFVVFVTVVVVMLVML
18 18 A R S S+ 0 0 156 21 76 RYYYYYFFYFYFFFFNNSNN
19 19 A G S S- 0 0 34 21 0 GGGGGGGGGGGGGGGGGGGG
20 20 A T - 0 0 92 21 17 TTTTTTTTTTTTTTTTTFTT
21 21 A b S S- 0 0 57 21 0 CCCCCCccCccccccccccc
22 22 A G S S- 0 0 33 21 106 GSSSAAffAfgffffhhghh
23 23 A I S S+ 0 0 176 21 78 IGGGGGLLGLLLLLLLLILL
24 24 A R S S+ 0 0 169 21 88 RRRRPPTTPTRTTTTMMAMM
25 25 A F E -A 8 0A 89 21 14 FLLLFFFFFFYFFFFYyYYY
26 26 A L E -A 7 0A 22 21 55 LLLLLLVVLVTVVVVTlLTT
27 27 A Y E -AB 6 16A 60 21 52 YFFLRRFFRFLFFFFLWFLL
28 28 A c E +AB 5 15A 4 21 0 CCCCCCCCCCCCCCCCCCCC
29 29 A a - 0 0 15 20 0 CCCCCCCCCCCCCCCCCC C
30 30 A P - 0 0 41 18 67 PRRRRRSSRSRSSSSR R
31 31 A R 0 0 252 8 0 RRRRRR R
32 32 A R 0 0 272 8 0 RRRRRR R
## 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 15 0 0 0 0 0 0 0 0 0 0 8 77 13 0 0 0.687 22 0.72
2 2 A 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 21 0 0 0.000 0 1.00
3 3 A 10 10 71 0 0 0 0 0 0 0 5 5 0 0 0 0 0 0 0 0 21 0 0 0.978 32 0.62
4 4 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 21 0 0 0.000 0 1.00
5 5 A 0 14 0 0 0 0 86 0 0 0 0 0 0 0 0 0 0 0 0 0 21 0 0 0.410 13 0.75
6 6 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 21 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 21 0 0 0.000 0 1.00
8 8 A 0 0 33 0 0 0 0 0 0 0 5 10 0 0 5 43 0 0 5 0 21 0 0 1.388 46 0.16
9 9 A 5 0 0 0 0 0 0 29 0 0 0 0 0 0 67 0 0 0 0 0 21 0 0 0.773 25 0.29
10 10 A 0 0 0 0 0 0 0 67 0 0 5 0 0 10 19 0 0 0 0 0 21 0 0 0.955 31 0.30
11 11 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 21 0 0 0.000 0 1.00
12 12 A 0 0 0 0 0 0 0 0 0 5 0 0 0 0 5 62 0 0 29 0 21 0 0 0.945 31 0.47
13 13 A 0 0 5 0 0 0 0 0 0 0 0 0 0 0 95 0 0 0 0 0 21 0 0 0.191 6 0.83
14 14 A 0 0 0 0 0 0 0 38 0 5 5 0 0 0 52 0 0 0 0 0 21 0 0 0.996 33 0.18
15 15 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 21 0 0 0.000 0 1.00
16 16 A 0 14 0 0 0 0 0 0 0 0 0 0 5 0 67 0 14 0 0 0 21 0 0 0.971 32 0.36
17 17 A 62 10 0 10 14 0 0 0 0 0 0 5 0 0 0 0 0 0 0 0 21 0 0 1.168 38 0.51
18 18 A 0 0 0 0 33 0 33 0 0 0 5 0 0 0 10 0 0 0 19 0 21 0 0 1.417 47 0.23
19 19 A 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 21 0 0 0.000 0 1.00
20 20 A 0 0 0 0 5 0 0 0 0 0 0 95 0 0 0 0 0 0 0 0 21 0 0 0.191 6 0.83
21 21 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 21 0 13 0.000 0 1.00
22 22 A 0 0 0 0 33 0 0 19 14 0 14 0 0 19 0 0 0 0 0 0 21 0 0 1.554 51 -0.06
23 23 A 0 57 14 0 0 0 0 29 0 0 0 0 0 0 0 0 0 0 0 0 21 0 0 0.956 31 0.21
24 24 A 0 0 0 19 0 0 0 0 5 14 0 33 0 0 29 0 0 0 0 0 21 0 0 1.463 48 0.11
25 25 A 0 14 0 0 57 0 29 0 0 0 0 0 0 0 0 0 0 0 0 0 21 0 1 0.956 31 0.86
26 26 A 33 48 0 0 0 0 0 0 0 0 0 19 0 0 0 0 0 0 0 0 21 0 0 1.035 34 0.44
27 27 A 0 24 0 0 48 5 10 0 0 0 0 0 0 0 14 0 0 0 0 0 21 0 0 1.342 44 0.48
28 28 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 21 0 0 0.000 0 1.00
29 29 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 20 0 0 0.000 0 1.00
30 30 A 0 0 0 0 0 0 0 0 0 11 39 0 0 0 50 0 0 0 0 0 18 0 0 0.958 31 0.32
31 31 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 8 0 0 0.000 0 1.00
32 32 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 8 0 0 0.000 0 1.00
## INSERTION LIST
AliNo IPOS JPOS Len Sequence
7 21 82 3 cRNLf
8 21 82 3 cRNLf
10 21 82 3 cRNLf
11 21 90 3 cTSGg
12 21 82 3 cRNLf
13 21 82 3 cRNLf
14 21 80 3 cRNLf
15 21 82 3 cRNLf
16 22 82 3 cRKGh
17 22 81 3 cRKGh
17 26 88 1 yMl
18 22 83 3 cKTKg
19 22 80 3 cRKGh
20 22 55 3 cRKGh
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