Complet list of 1wco hssp file
Complete list of 1wco.hssp file
HSSP HOMOLOGY DERIVED SECONDARY STRUCTURE OF PROTEINS , VERSION 2.0 2011
PDBID 1WCO
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 2014-05-11
HEADER PEPTIDE/ANTIBIOTIC 19-NOV-04 1WCO
COMPND MOL_ID: 1; MOLECULE: NISIN Z; CHAIN: N; MOL_ID: 2; MOLECULE: NAG-MUB-A
SOURCE MOL_ID: 1; ORGANISM_SCIENTIFIC: LACTOCOCCUS LACTIS; ORGANISM_TAXID: 13
AUTHOR S.-T.D.HSU,E.BREUKINK,E.TISCHENKO,M.A.G.LUTTERS,B.DE KRUIJFF, R.KAPTEI
DBREF 1WCO L 1 7 PDB 1WCO 1WCO 1 7
DBREF 1WCO N 1 34 UNP P29559 LANZ_LACLA 24 57
SEQLENGTH 34
NCHAIN 1 chain(s) in 1WCO data set
NALIGN 38
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 : A8CZX4_LACLL 0.76 0.76 1 34 20 53 34 0 0 53 A8CZX4 Nisin Z (Fragment) OS=Lactococcus lactis subsp. lactis PE=4 SV=1
2 : D2BR10_LACLK 0.76 0.76 1 34 17 50 34 0 0 50 D2BR10 Nisin, C-terminal OS=Lactococcus lactis subsp. lactis (strain KF147) GN=nisX PE=4 SV=1
3 : H5SXJ3_LACLL 0.76 0.76 1 34 24 57 34 0 0 57 H5SXJ3 GTNG_0265 lantibiotic antimicrobial peptinisin Ade OS=Lactococcus lactis subsp. lactis IO-1 GN=nisA PE=4 SV=1
4 : LANZ_LACLL 1WCO 0.76 0.76 1 34 24 57 34 0 0 57 P29559 Lantibiotic nisin-Z OS=Lactococcus lactis subsp. lactis GN=nisZ PE=1 SV=1
5 : Q7BB86_9LACT 0.76 0.76 1 34 24 57 34 0 0 57 Q7BB86 NisZ OS=Lactococcus lactis GN=nisZ PE=4 SV=1
6 : Q7DH25_LACLL 0.76 0.76 1 34 24 57 34 0 0 57 Q7DH25 Nisin Z OS=Lactococcus lactis subsp. lactis GN=nisZ PE=4 SV=1
7 : A3FEQ5_9LACT 0.74 0.76 1 34 20 53 34 0 0 53 A3FEQ5 Nisin (Fragment) OS=Lactococcus lactis PE=4 SV=1
8 : A7UGI5_9LACT 0.74 0.76 1 34 24 57 34 0 0 57 A7UGI5 Nisin F (Fragment) OS=Lactococcus lactis PE=4 SV=1
9 : F2HKA4_LACLV 0.74 0.76 1 34 24 57 34 0 0 57 F2HKA4 Nisin NisinA OS=Lactococcus lactis subsp. lactis (strain CV56) GN=nisA PE=4 SV=1
10 : LANN_LACLL 0.74 0.76 1 34 24 57 34 0 0 57 P13068 Lantibiotic nisin-A OS=Lactococcus lactis subsp. lactis GN=spaN PE=1 SV=1
11 : Q45RP0_LACLL 0.74 0.76 1 34 24 57 34 0 0 57 Q45RP0 Lantibiotic nisin A (Precursor) OS=Lactococcus lactis subsp. lactis GN=nis PE=4 SV=1
12 : Q7B8R0_9LACT 0.74 0.76 1 34 24 57 34 0 0 57 Q7B8R0 Nisin OS=Lactococcus lactis GN=nisA PE=4 SV=1
13 : T2C912_9LACT 0.74 0.76 1 34 24 57 34 0 0 57 T2C912 Nisin variant OS=Lactococcus lactis PE=4 SV=1
14 : I4DSZ9_LACLL 0.71 0.74 1 34 24 57 34 0 0 57 I4DSZ9 Nisin Z OS=Lactococcus lactis subsp. lactis GN=nisz PE=4 SV=1
15 : T2C9F0_LACLL 0.71 0.76 1 34 24 57 34 0 0 57 T2C9F0 Nisin variant OS=Lactococcus lactis subsp. lactis PE=4 SV=1
16 : Q76HP8_9LACT 0.68 0.74 1 34 24 57 34 0 0 57 Q76HP8 Nisin Q OS=Lactococcus lactis GN=nisQ PE=4 SV=1
17 : V5NTA4_9LACT 0.68 0.71 1 34 24 57 34 0 0 57 V5NTA4 NisA-NAI mutant OS=Lactococcus lactis GN=nisA PE=4 SV=1
18 : V5NTN6_9LACT 0.68 0.71 1 34 24 57 34 0 0 57 V5NTN6 NisA-AAK mutant OS=Lactococcus lactis GN=nisA PE=4 SV=1
19 : V5NST0_9LACT 0.65 0.71 1 34 24 57 34 0 0 57 V5NST0 NisA-SAA mutant OS=Lactococcus lactis GN=nisA PE=4 SV=1
20 : V5NT69_9LACT 0.65 0.74 1 34 24 57 34 0 0 57 V5NT69 NisA-SLS mutant OS=Lactococcus lactis GN=nisA PE=4 SV=1
21 : V5NV19_9LACT 0.65 0.68 1 34 24 57 34 0 0 57 V5NV19 NisA-AAA mutant OS=Lactococcus lactis GN=nisA PE=4 SV=1
22 : LANNU_STRUB 0.54 0.57 1 28 25 52 28 0 0 55 Q2QBT0 Lantibiotic nisin-U OS=Streptococcus uberis GN=nsuA PE=1 SV=1
23 : D2CGP4_STRAG 0.50 0.57 1 28 25 52 28 0 0 55 D2CGP4 NsuA2 OS=Streptococcus agalactiae GN=nsuA2 PE=4 SV=1
24 : D2CGP6_STRPO 0.50 0.57 1 28 25 52 28 0 0 55 D2CGP6 NsuA2 OS=Streptococcus porcinus GN=nsuA2 PE=4 SV=1
25 : E7S5A3_STRAG 0.50 0.57 1 28 25 52 28 0 0 55 E7S5A3 Lantibiotic nisin-Z OS=Streptococcus agalactiae ATCC 13813 GN=nisZ PE=4 SV=1
26 : F5X6X4_STRPX 0.50 0.57 1 28 25 52 28 0 0 55 F5X6X4 Nisin U lantibiotic OS=Streptococcus pasteurianus (strain ATCC 43144 / JCM 5346 / CDC 1723-81) GN=nsuA PE=4 SV=1
27 : F8Y197_STRAG 0.50 0.57 1 28 25 52 28 0 0 55 F8Y197 Putative nisin OS=Streptococcus agalactiae FSL S3-026 GN=FSLSAGS3026_07300 PE=4 SV=1
28 : S0MAG4_9ENTE 0.50 0.59 1 34 24 57 34 0 0 58 S0MAG4 Uncharacterized protein OS=Enterococcus moraviensis ATCC BAA-383 GN=I586_02329 PE=4 SV=1
29 : S0MP14_9ENTE 0.50 0.59 1 34 24 57 34 0 0 58 S0MP14 Uncharacterized protein OS=Enterococcus moraviensis ATCC BAA-383 GN=I586_02327 PE=4 SV=1
30 : S8P9W3_STRAG 0.50 0.57 1 28 25 52 28 0 0 55 S8P9W3 Lantibiotic nisin-A OS=Streptococcus agalactiae MRI Z1-216 GN=SAG0164_11305 PE=4 SV=1
31 : S8PZH5_STRAG 0.50 0.57 1 28 25 52 28 0 0 55 S8PZH5 Lantibiotic nisin-A OS=Streptococcus agalactiae MRI Z1-213 GN=SAG0161_01695 PE=4 SV=1
32 : S8QN57_STRAG 0.50 0.57 1 28 25 52 28 0 0 55 S8QN57 Lantibiotic nisin-A OS=Streptococcus agalactiae MRI Z1-214 GN=SAG0162_11380 PE=4 SV=1
33 : S8UN76_STRAG 0.50 0.57 1 28 25 52 28 0 0 55 S8UN76 Lantibiotic nisin-A OS=Streptococcus agalactiae GB00548 GN=SAG0327_08720 PE=4 SV=1
34 : S9A987_STRAG 0.50 0.57 1 28 25 52 28 0 0 55 S9A987 Lantibiotic nisin-A OS=Streptococcus agalactiae GB00922 GN=SAG0359_03500 PE=4 SV=1
35 : S9ABJ1_STRAG 0.50 0.57 1 28 25 52 28 0 0 55 S9ABJ1 Lantibiotic nisin-A OS=Streptococcus agalactiae GB00984 GN=SAG0375_01295 PE=4 SV=1
36 : S9CV27_STRAG 0.50 0.57 1 28 25 52 28 0 0 55 S9CV27 Lantibiotic nisin-A OS=Streptococcus agalactiae FSL S3-586 GN=SAG0014_10220 PE=4 SV=1
37 : S9MQW8_STRAG 0.50 0.57 1 28 25 52 28 0 0 55 S9MQW8 Lantibiotic nisin-A OS=Streptococcus agalactiae MRI Z1-217 GN=SAG0165_10545 PE=4 SV=1
38 : T1ZKD9_STRIT 0.50 0.71 1 34 24 57 34 0 0 57 T1ZKD9 Uncharacterized protein OS=Streptococcus intermedius C270 GN=SII_0990 PE=4 SV=1
## ALIGNMENTS 1 - 38
SeqNo PDBNo AA STRUCTURE BP1 BP2 ACC NOCC VAR ....:....1....:....2....:....3....:....4....:....5....:....6....:....7
1 1 N I 0 0 94 39 17 IIIIIIIIIIIIIIIIIIIIIIVVVVVIIVVVVVVVVV
2 2 N X - 0 0 73 38 0 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
3 3 N X + 0 0 41 38 0 SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
4 4 N I S S+ 0 0 150 39 84 IIIIIIIIIIIIIIVIIIIIIKKKKKKKKKKKKKKKKV
5 5 N X S S+ 0 0 78 38 11 SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSF
6 6 N L > - 0 0 144 39 1 LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLM
7 7 N C T 4 + 0 0 75 39 0 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
8 8 N X T >> S+ 0 0 49 38 0 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
9 9 N P H 3> S+ 0 0 79 39 0 PPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPP
10 10 N G H 3< S+ 0 0 16 39 0 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
11 11 N C H <4 S- 0 0 46 39 0 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
12 12 N K H < S+ 0 0 91 39 26 KKKKKKKKKKKKKKKKKKKKKKKKKKKVVKKKKKKKKV
13 13 N X S < S+ 0 0 33 38 0 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
14 14 N G S >> S- 0 0 5 39 0 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
15 15 N A T 34 S+ 0 0 107 39 73 AAAAAAAAAAAAAAAVAAAAAIIIIIIVVIIIIIIIIA
16 16 N L T 34 S- 0 0 104 39 4 LLLLLLLLLLLLVLVLLLLLLLLLLLLLLLLLLLLLLL
17 17 N M T <4 S- 0 0 84 39 0 MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM
18 18 N G S < S- 0 0 58 39 49 GGGGGGGGGGGGGGGGGGGGGTTTTTTGGTTTTTTTTG
19 19 N C - 0 0 58 39 3 CCCCCCCCCCCCCACCCCCCCCCCCCCCCCCCCCCCCC
20 20 N N + 0 0 61 39 68 NNNNNNNNNNNNNNNNNASSAPPPAAAAAAAAAAAAAN
21 21 N M + 0 0 175 39 49 MMMMMMMMMMMMMMMLAAALALLLIIILLIIIIIIIIL
22 22 N K + 0 0 150 39 26 KKKKKKKKKKKKKKKKIKASAKKKKKKKKKKKKKKKKQ
23 23 N X + 0 0 72 38 0 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
24 24 N A S S- 0 0 96 39 15 AAAAAAAAAAAAAAAAAAAAAAAAAAAIIAAAAAAAAA
25 25 N X S > S+ 0 0 60 38 0 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
26 26 N C T 3 S+ 0 0 88 39 0 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
27 27 N N T 3 S+ 0 0 116 39 72 NNNNNNHNHHHHNHNNHHHHHGGGGGGNNGGGGGGGGN
28 28 N C < + 0 0 59 39 0 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
29 29 N S + 0 0 94 25 20 SSSSSSSSSSSSSSSSSSSSS SS H
30 30 N I + 0 0 133 25 15 IIIIIIIVIIIIIIIVIIIII VV V
31 31 N H S S- 0 0 179 25 39 HHHHHHHHHHHHHHHHHHHHH GG H
32 32 N V S S- 0 0 129 25 13 VVVVVVVVVVVVVVVVVVVVV II I
33 33 N X 0 0 97 24 23 SSSSSSSSSSSSSSSSSSSSS GG S
34 34 N K 0 0 236 25 0 KKKKKKKKKKKKKKKKKKKKK KK K
## 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 N 36 0 64 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 39 0 0 0.653 21 0.82
2 2 N 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 38 0 0 0.000 0 1.00
3 3 N 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 38 0 0 0.000 0 1.00
4 4 N 5 0 54 0 0 0 0 0 0 0 0 0 0 0 0 41 0 0 0 0 39 0 0 0.851 28 0.15
5 5 N 0 0 0 0 3 0 0 0 0 0 97 0 0 0 0 0 0 0 0 0 38 0 0 0.122 4 0.88
6 6 N 0 97 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 39 0 0 0.119 3 0.99
7 7 N 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 39 0 0 0.000 0 1.00
8 8 N 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 38 0 0 0.000 0 1.00
9 9 N 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 39 0 0 0.000 0 1.00
10 10 N 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 39 0 0 0.000 0 1.00
11 11 N 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 39 0 0 0.000 0 1.00
12 12 N 8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 92 0 0 0 0 39 0 0 0.271 9 0.73
13 13 N 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 38 0 0 0.000 0 1.00
14 14 N 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 39 0 0 0.000 0 1.00
15 15 N 8 0 36 0 0 0 0 0 56 0 0 0 0 0 0 0 0 0 0 0 39 0 0 0.888 29 0.27
16 16 N 5 95 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 39 0 0 0.202 6 0.95
17 17 N 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 39 0 0 0.000 0 1.00
18 18 N 0 0 0 0 0 0 0 64 0 0 0 36 0 0 0 0 0 0 0 0 39 0 0 0.653 21 0.50
19 19 N 0 0 0 0 0 0 0 0 3 0 0 0 97 0 0 0 0 0 0 0 39 0 0 0.119 3 0.96
20 20 N 0 0 0 0 0 0 0 0 38 8 5 0 0 0 0 0 0 0 49 0 39 0 0 1.067 35 0.32
21 21 N 0 21 28 41 0 0 0 0 10 0 0 0 0 0 0 0 0 0 0 0 39 0 0 1.281 42 0.50
22 22 N 0 0 3 0 0 0 0 0 5 0 3 0 0 0 0 87 3 0 0 0 39 0 0 0.554 18 0.74
23 23 N 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 38 0 0 0.000 0 1.00
24 24 N 0 0 5 0 0 0 0 0 95 0 0 0 0 0 0 0 0 0 0 0 39 0 0 0.202 6 0.84
25 25 N 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 38 0 0 0.000 0 1.00
26 26 N 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 39 0 0 0.000 0 1.00
27 27 N 0 0 0 0 0 0 0 36 0 0 0 0 0 28 0 0 0 0 36 0 39 0 0 1.093 36 0.28
28 28 N 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 39 0 0 0.000 0 1.00
29 29 N 0 0 0 0 0 0 0 0 0 0 96 0 0 4 0 0 0 0 0 0 25 0 0 0.168 5 0.79
30 30 N 20 0 80 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 25 0 0 0.500 16 0.85
31 31 N 0 0 0 0 0 0 0 8 0 0 0 0 0 92 0 0 0 0 0 0 25 0 0 0.279 9 0.60
32 32 N 88 0 12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 25 0 0 0.367 12 0.87
33 33 N 0 0 0 0 0 0 0 8 0 0 92 0 0 0 0 0 0 0 0 0 24 0 0 0.287 9 0.76
34 34 N 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 25 0 0 0.000 0 1.00
## INSERTION LIST
AliNo IPOS JPOS Len Sequence
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