Complet list of 1xv3 hssp file
Complete list of 1xv3.hssp file
HSSP HOMOLOGY DERIVED SECONDARY STRUCTURE OF PROTEINS , VERSION 2.0 2011
PDBID 1XV3
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 2014-05-13
HEADER ANTIBIOTIC 27-OCT-04 1XV3
COMPND MOL_ID: 1; MOLECULE: PENAEIDIN-4D; CHAIN: A; SYNONYM: PEN-4D; ENGINEER
SOURCE MOL_ID: 1; SYNTHETIC: YES; OTHER_DETAILS: THE MOLECULE HAS BEEN SYNTHE
AUTHOR B.J.CUTHBERTSON,Y.YANG,E.E.BULLESBACH,E.BACHERE,P.S.GROSS, A.AUMELAS
DBREF 1XV3 A 1 47 UNP Q962A7 PEN4D_LITSE 20 66
SEQLENGTH 47
NCHAIN 1 chain(s) in 1XV3 data set
NALIGN 37
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 : PEN4D_LITSE 1XV3 1.00 1.00 1 47 20 66 47 0 0 67 Q962A7 Penaeidin-4d OS=Litopenaeus setiferus PE=1 SV=1
2 : PEN4A_LITVA 0.98 0.98 1 46 20 65 46 0 0 67 Q95NT0 Penaeidin-4a OS=Litopenaeus vannamei PE=3 SV=1
3 : PEN4C_LITVA 0.98 0.98 2 46 21 65 45 0 0 67 Q963C3 Penaeidin-4c OS=Litopenaeus vannamei PE=3 SV=1
4 : Q3HNH4_LITVA 0.98 0.98 1 46 20 65 46 0 0 67 Q3HNH4 PEN4-1 OS=Litopenaeus vannamei GN=PEN4-1 PE=4 SV=1
5 : Q56H80_LITSH 0.98 0.98 1 47 20 66 47 0 0 67 Q56H80 Antimicrobial peptide PEN4-1 OS=Litopenaeus schmitti GN=PEN4-1 PE=4 SV=1
6 : Q3HM08_LITVA 0.96 0.98 1 46 20 65 46 0 0 67 Q3HM08 Antimicrobial peptide PEN4-3 OS=Litopenaeus vannamei GN=PEN4-3 PE=4 SV=1
7 : A4UMS2_FARSU 0.46 0.67 3 47 24 70 48 3 4 73 A4UMS2 Penaeidin OS=Farfantepenaeus subtilis PE=4 SV=1
8 : PEN3C_LITVA 0.46 0.60 3 47 24 75 52 4 7 81 P81060 Penaeidin-3c OS=Litopenaeus vannamei PE=1 SV=1
9 : PEN3J_LITVA 0.46 0.60 3 47 24 75 52 4 7 81 Q963D9 Penaeidin-3j OS=Litopenaeus vannamei PE=3 SV=1
10 : Q3HM09_LITVA 0.46 0.60 3 47 24 75 52 4 7 81 Q3HM09 Antimicrobial peptide PEN3-11 OS=Litopenaeus vannamei GN=PEN3-11 PE=4 SV=1
11 : B0FLD4_FENPE 0.45 0.58 3 47 24 76 53 4 8 82 B0FLD4 Pen3-o OS=Fenneropenaeus penicillatus PE=4 SV=1
12 : B0FLD5_FENPE 0.45 0.58 3 47 24 76 53 4 8 82 B0FLD5 Pen3-p OS=Fenneropenaeus penicillatus PE=4 SV=1
13 : PEN3A_LITVA 1UEO 0.45 0.58 3 47 24 76 53 4 8 82 P81058 Penaeidin-3a OS=Litopenaeus vannamei PE=1 SV=1
14 : PEN3B_LITVA 0.45 0.58 3 47 24 76 53 4 8 82 P81059 Penaeidin-3b OS=Litopenaeus vannamei PE=1 SV=1
15 : PEN3D_LITVA 0.45 0.58 3 47 24 76 53 4 8 82 Q963D0 Penaeidin-3d OS=Litopenaeus vannamei PE=3 SV=1
16 : PEN3E_LITVA 0.45 0.58 3 47 24 76 53 4 8 82 Q963C9 Penaeidin-3e OS=Litopenaeus vannamei PE=3 SV=1
17 : PEN3F_LITVA 0.45 0.58 3 47 24 76 53 4 8 82 Q963C8 Penaeidin-3f OS=Litopenaeus vannamei PE=3 SV=1
18 : PEN3G_LITVA 0.45 0.58 3 47 24 76 53 4 8 82 Q963C7 Penaeidin-3g OS=Litopenaeus vannamei PE=3 SV=1
19 : Q3HM10_LITVA 0.45 0.66 3 47 24 69 47 2 3 72 Q3HM10 Antimicrobial peptide PEN2-4 OS=Litopenaeus vannamei GN=PEN2-4 PE=4 SV=1
20 : Q3HNH3_LITVA 0.45 0.58 3 47 24 76 53 4 8 82 Q3HNH3 PEN3-1 OS=Litopenaeus vannamei GN=PEN3-1 PE=4 SV=1
21 : Q56H83_FARPA 0.44 0.71 3 47 24 70 48 3 4 73 Q56H83 Antimicrobial peptide PEN2-2 OS=Farfantepenaeus paulensis GN=PEN2-2 PE=4 SV=1
22 : PEN2A_LITVA 0.43 0.66 3 47 24 69 47 2 3 72 P81057 Penaeidin-2a OS=Litopenaeus vannamei PE=1 SV=1
23 : PEN2B_LITVA 0.43 0.66 3 47 24 69 47 2 3 72 Q963C4 Penaeidin-2b OS=Litopenaeus vannamei PE=3 SV=1
24 : PEN3H_LITVA 0.43 0.57 3 47 24 76 53 4 8 82 Q963C6 Penaeidin-3h OS=Litopenaeus vannamei PE=3 SV=1
25 : PEN3I_LITVA 0.43 0.57 3 47 24 76 53 4 8 82 Q963C5 Penaeidin-3i OS=Litopenaeus vannamei PE=3 SV=1
26 : Q3HNH5_LITVA 0.43 0.66 3 47 24 69 47 2 3 72 Q3HNH5 PEN2-1 OS=Litopenaeus vannamei GN=PEN2-1 PE=4 SV=1
27 : Q56H84_FARPA 0.43 0.69 2 47 23 70 49 3 4 73 Q56H84 Antimicrobial peptide PEN2-1 OS=Farfantepenaeus paulensis GN=PEN2-1 PE=4 SV=1
28 : Q6V4W5_LITST 0.42 0.62 3 47 24 69 48 3 5 72 Q6V4W5 Antimicrobial peptide penaeidin 2 OS=Litopenaeus stylirostris GN=pen2 PE=4 SV=1
29 : A4UMS5_FARBR 0.40 0.68 1 47 20 68 50 2 4 71 A4UMS5 Penaeidin OS=Farfantepenaeus brasiliensis PE=4 SV=1
30 : B8Y3W3_LITSH 0.40 0.58 3 47 24 69 48 4 5 75 B8Y3W3 Penaeidin 3-2 OS=Litopenaeus schmitti GN=PEN3-2 PE=4 SV=1
31 : PEN1_LITVA 0.40 0.64 3 47 3 48 47 2 3 50 P81056 Penaeidin-1 OS=Litopenaeus vannamei PE=1 SV=1
32 : B8Y3W2_LITSH 0.39 0.57 2 47 23 69 49 4 5 75 B8Y3W2 Penaeidin 3-1 OS=Litopenaeus schmitti GN=PEN3-1 PE=4 SV=1
33 : PEN3K_LITSE 0.39 0.57 2 47 23 69 49 4 5 75 Q962B2 Penaeidin-3k OS=Litopenaeus setiferus PE=3 SV=1
34 : PEN3L_LITSE 0.39 0.55 2 47 23 69 49 4 5 75 Q962A8 Penaeidin-3l OS=Litopenaeus setiferus PE=3 SV=1
35 : PEN3M_LITSE 0.39 0.57 2 47 23 69 49 4 5 75 Q962B1 Penaeidin-3m OS=Litopenaeus setiferus PE=3 SV=1
36 : Q4U5R1_LITST 0.39 0.53 3 46 24 72 49 4 5 79 Q4U5R1 PEN 3-2 OS=Litopenaeus stylirostris PE=4 SV=1
37 : Q3Y6N7_FENCH 0.38 0.46 1 45 26 74 50 4 6 79 Q3Y6N7 Penaeidin 5-1 OS=Fenneropenaeus chinensis GN=pen5-1 PE=4 SV=1
## ALIGNMENTS 1 - 37
SeqNo PDBNo AA STRUCTURE BP1 BP2 ACC NOCC VAR ....:....1....:....2....:....3....:....4....:....5....:....6....:....7
1 1 A H 0 0 229 8 0 HH HHH H H
2 2 A S - 0 0 118 14 77 SSSSSS K R KKKK T
3 3 A S - 0 0 113 38 26 SSSSSSSGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
4 4 A G - 0 0 73 38 26 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGPGPPPPGP
5 5 A Y + 0 0 177 38 0 YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY
6 6 A T + 0 0 117 38 5 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTP
7 7 A R + 0 0 190 38 46 RRRRRRRRRRRRRRRRRRGRRGGRRGRGRRGRRRRGR
8 8 A P - 0 0 104 38 0 PPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPp
9 9 A L - 0 0 182 38 39 LLLLLLFIVVVIIVIIIIIIFIIIIIFIFIIIIIIVg
10 10 A R - 0 0 238 38 59 RPPPPPSPPPPPPPPPPPPPSPPPPPSPPLPLLLLVS
11 11 A K - 0 0 150 38 18 KKKKKKRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR
12 12 A P - 0 0 103 38 0 PPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPP
13 13 A S - 0 0 117 38 75 SSSSSSPPPPPPPPPPPPPPPPPPPPPPPYPYYYYFI
14 14 A R - 0 0 147 38 90 RRRRRRffffppppppppppfpppppfpYvpvvvvvg
15 15 A P - 0 0 101 38 42 PPPPPPgppppppppppprpgrrpprgpGprpppppp
16 16 A I + 0 0 164 38 60 IIIIIIIVLLVLLLLLLLPLIPPLLPIPLFPVVVVII
17 17 A F - 0 0 182 38 95 FFFFFFypppppppppppPpyPPppPyLqVPVVVVgT
18 18 A I - 0 0 132 31 27 IIIIIIviiiiiiiiiiiLivFLiiFv.v.L....v.
19 19 A R - 0 0 80 33 80 RRRRRRRGGDGGGGGGGSRGRRRGGRRGR.R....VR
20 20 A P - 0 0 74 38 30 PPPPPPPpppppppppppPpPPPppPPPPsLsssssp
21 21 A I S S+ 0 0 145 29 85 IIIIII.nnnnnnnnnnn.n...nn....nVnnnnnp
22 22 A G S > S+ 0 0 7 38 56 GGGGGGVGGGGGGGGGGGVGAVVGGVAVAAVAAVAVS
23 23 A a T 3 S+ 0 0 5 38 4 CCCCCCCCCCCCCCCCCCCCCCCCRCCCCCCCCCCCC
24 24 A D T 3 S+ 0 0 92 37 78 DDDDDDNpppplppppppNpNNNppNNNNp.ptttpA
25 25 A V <> + 0 0 65 38 74 VVVVVVAsssssssssssAsAAAssAAHAsAsssssG
26 26 A b T 4 S+ 0 0 27 38 0 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
27 27 A Y T 4 S+ 0 0 181 38 92 YYYYYYYRRRRRRRRRRRYRYYYRRYYYYRYRRRRRR
28 28 A G T 4 S+ 0 0 84 38 66 GGGGGGRGGGGGGGGGGGRGSRRGGRSRRGRGGGGGI
29 29 A I S < S- 0 0 35 38 21 IIIIIILIIIIIIIIIIILIILLIILILLILIIIIII
30 30 A P > - 0 0 77 38 54 PPPPPPSSSSSSSSSSSSSSSSSSSSSASTSTTTTTT
31 31 A S H > S+ 0 0 92 38 86 SSSSSSYFFFFFFFFFFFVFFVVFFVFFYTVTTTTTL
32 32 A S H > S+ 0 0 84 38 40 SSSSSASSSSSSSSSSSSSSSSSSSSSPSTSTTTTLD
33 33 A T H > S+ 0 0 55 38 64 TTTTTTDQQQQQQQQQQQDQDDDQQDDDAQDQQQQQD
34 34 A A H X S+ 0 0 14 38 0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
35 35 A R H X S+ 0 0 163 38 38 RRRRRRLRRRRRRRRRRRRRLRRRRRLRLRRRRRRRI
36 36 A L H X>S+ 0 0 101 38 85 LLLLLLNSSSSSSSSSSSNSNNNSSNNNNSNSSSSSA
37 37 A a I <>S+ 0 0 4 38 1 CCCCCCCCCCCCCCCCCCCCCCCYCCCCCCCCCCCCC
38 38 A c I <5S+ 0 0 40 38 0 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
39 39 A F I <5S+ 0 0 163 38 89 FFFFFFTSSSSSSSSSSSISTIISSITSTTITTTTSR
40 40 A R I <5S+ 0 0 186 38 14 RRRRRRRRRRRRRRRRRRRRRKKRRKRRKRKRRRRRR
41 41 A Y I