Complet list of 1dw4 hssp file
Complete list of 1dw4.hssp file
HSSP HOMOLOGY DERIVED SECONDARY STRUCTURE OF PROTEINS , VERSION 2.0 2011
PDBID 1DW4
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 2014-04-12
HEADER TOXIN 24-JAN-00 1DW4
COMPND MOL_ID: 1; MOLECULE: OMEGA-CONOTOXIN MVIIA; CHAIN: A; ENGINEERED: YES;
SOURCE MOL_ID: 1; SYNTHETIC: YES; OTHER_DETAILS: THIS PEPTIDE WAS CHEMICALLY
AUTHOR R.A.ATKINSON,B.KIEFFER,A.DEJAEGERE,F.SIROCKIN,J.-F.LEFEVRE
DBREF 1DW4 A 1 25 UNP P05484 CXO7A_CONMA 1 25
SEQLENGTH 25
NCHAIN 1 chain(s) in 1DW4 data set
NALIGN 46
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 : CO17A_CONMA 1TT3 1.00 1.00 1 25 46 70 25 0 0 71 P05484 Omega-conotoxin MVIIA OS=Conus magus PE=1 SV=2
2 : CM7G_CONCN 0.84 0.84 1 25 1 25 25 0 0 26 P0DKQ5 Omega-conotoxin-like CnVIIG OS=Conus consors PE=1 SV=1
3 : S6CQ14_CONCN 0.84 0.84 1 25 46 70 25 0 0 71 S6CQ14 O superfamily CnVIIB OS=Conus consors PE=3 SV=1
4 : CO6C_CONCT 0.81 0.85 1 25 1 26 26 1 1 26 P58919 Omega-conotoxin CVIC OS=Conus catus PE=1 SV=1
5 : CO164_CONAH 0.80 0.84 1 25 46 70 25 0 0 71 P0C8V8 Omega-conotoxin-like Ac6.4 OS=Conus achatinus PE=1 SV=1
6 : Q9N633_CONCT 0.80 0.84 1 25 41 65 25 0 0 66 Q9N633 Four-loop conotoxin (Fragment) OS=Conus catus PE=3 SV=1
7 : Q9NCW3_CONCT 0.80 0.84 1 25 41 65 25 0 0 66 Q9NCW3 Four-loop conotoxin (Fragment) OS=Conus catus PE=3 SV=1
8 : Q9NCW5_CONCT 0.80 0.84 1 25 41 65 25 0 0 66 Q9NCW5 Four-loop conotoxin (Fragment) OS=Conus catus PE=3 SV=1
9 : Q9NCW6_CONCT 0.80 0.84 1 25 41 65 25 0 0 66 Q9NCW6 Four-loop conotoxin (Fragment) OS=Conus catus PE=3 SV=1
10 : CM7E_CONCN 0.76 0.84 1 25 1 25 25 0 0 26 P0DKQ3 Omega-conotoxin-like CnVIIE OS=Conus consors PE=1 SV=1
11 : CM7F_CONCN 0.76 0.84 1 25 1 25 25 0 0 26 P0DKQ4 Omega-conotoxin-like CnVIIF OS=Conus consors PE=1 SV=1
12 : CO6B_CONCT 0.76 0.84 1 25 1 25 25 0 0 25 P58918 Omega-conotoxin CVIB OS=Conus catus PE=1 SV=1
13 : CO7B_CONMA 0.76 0.76 1 25 1 25 25 0 0 25 P05485 Omega-conotoxin MVIIB OS=Conus magus PE=1 SV=1
14 : Q9NCW4_CONCT 0.76 0.84 1 25 41 65 25 0 0 66 Q9NCW4 Four-loop conotoxin (Fragment) OS=Conus catus PE=3 SV=1
15 : S6CPX8_CONCN 0.76 0.84 1 25 46 70 25 0 0 71 S6CPX8 O superfamily CnVIID OS=Conus consors PE=3 SV=1
16 : S6CQC0_CONCN 0.76 0.84 1 25 46 70 25 0 0 71 S6CQC0 O superfamily CnVIIC OS=Conus consors PE=3 SV=1
17 : CO166_CONST 0.73 0.81 1 25 46 71 26 1 1 72 P0C831 Omega-conotoxin-like S6.6 OS=Conus striatus PE=2 SV=1
18 : CO7C_CONMA 1V4Q 0.73 0.81 1 25 3 28 26 1 1 29 P37300 Omega-conotoxin MVIIC (Fragment) OS=Conus magus PE=1 SV=1
19 : CO13_CONST 1FYG 0.72 0.84 1 25 46 70 25 0 0 71 Q9XZK2 Omega-conotoxin SO-3 OS=Conus striatus GN=SO3 PE=1 SV=1
20 : CO16A_CONCT 0.72 0.80 1 25 46 70 25 0 0 71 P58917 Omega-conotoxin CVIA OS=Conus catus PE=1 SV=1
21 : CO8_CONBU 0.72 0.80 1 25 25 49 25 0 0 50 P0CY66 Omega-conotoxin-like Bu8 (Fragment) OS=Conus bullatus PE=2 SV=1
22 : Q9N625_CONCT 0.72 0.80 1 25 41 65 25 0 0 66 Q9N625 Four-loop conotoxin (Fragment) OS=Conus catus PE=3 SV=1
23 : Q9N628_CONCT 0.72 0.80 1 25 41 65 25 0 0 66 Q9N628 Four-loop conotoxin (Fragment) OS=Conus catus PE=3 SV=1
24 : Q9N6N6_CONST 0.72 0.84 1 25 41 65 25 0 0 66 Q9N6N6 Four-loop conotoxin (Fragment) OS=Conus striatus PE=3 SV=1
25 : Q9NCU1_CONST 0.72 0.84 1 25 41 65 25 0 0 66 Q9NCU1 Four-loop conotoxin (Fragment) OS=Conus striatus PE=3 SV=1
26 : Q9NCV0_CONST 0.72 0.84 1 25 41 65 25 0 0 66 Q9NCV0 Four-loop conotoxin (Fragment) OS=Conus striatus PE=3 SV=1
27 : Q9NCV1_CONST 0.72 0.84 1 25 41 65 25 0 0 66 Q9NCV1 Four-loop conotoxin (Fragment) OS=Conus striatus PE=3 SV=1
28 : Q9NCV2_CONST 0.72 0.84 1 25 41 65 25 0 0 66 Q9NCV2 Four-loop conotoxin (Fragment) OS=Conus striatus PE=3 SV=1
29 : Q9NCV4_CONST 0.72 0.84 1 25 41 65 25 0 0 66 Q9NCV4 Four-loop conotoxin (Fragment) OS=Conus striatus PE=3 SV=1
30 : Q9NCV5_CONCT 0.72 0.84 1 25 41 65 25 0 0 66 Q9NCV5 Four-loop conotoxin (Fragment) OS=Conus catus PE=3 SV=1
31 : Q9NCW1_CONCT 0.72 0.80 1 25 41 65 25 0 0 66 Q9NCW1 Four-loop conotoxin (Fragment) OS=Conus catus PE=3 SV=1
32 : Q9NCW2_CONCT 0.72 0.80 1 25 41 65 25 0 0 66 Q9NCW2 Four-loop conotoxin (Fragment) OS=Conus catus PE=3 SV=1
33 : CO16D_CONCT 0.70 0.85 1 25 46 72 27 1 2 73 P58920 Omega-conotoxin CVID OS=Conus catus PE=1 SV=1
34 : CO7A_CONCN 0.70 0.78 1 25 1 27 27 1 2 28 P58916 Omega-conotoxin-like CnVIIH OS=Conus consors PE=1 SV=2
35 : S6CRD7_CONCN 0.70 0.78 1 25 46 72 27 1 2 73 S6CRD7 O superfamily CnVIIA OS=Conus consors PE=3 SV=1
36 : Q9NCV7_CONCT 0.68 0.84 1 25 41 65 25 0 0 66 Q9NCV7 Four-loop conotoxin (Fragment) OS=Conus catus PE=3 SV=1
37 : CO16B_CONST 1MVJ 0.65 0.73 1 25 46 71 26 1 1 72 P28881 Omega-conotoxin SVIB OS=Conus striatus PE=1 SV=2
38 : CO713_CONBU 0.64 0.76 1 25 25 49 25 0 0 50 P0CY71 Conotoxin Bu13 (Fragment) OS=Conus bullatus PE=2 SV=1
39 : CO71_CONBU 0.64 0.72 1 25 46 70 25 0 0 70 P0CY60 Omega-conotoxin-like Bu1 OS=Conus bullatus PE=2 SV=1
40 : Q9N6F7_CONCT 0.64 0.88 1 25 41 65 25 0 0 66 Q9N6F7 Four-loop conotoxin (Fragment) OS=Conus catus PE=3 SV=1
41 : Q9NCV6_CONCT 0.64 0.72 1 25 41 65 25 0 0 66 Q9NCV6 Four-loop conotoxin (Fragment) OS=Conus catus PE=3 SV=1
42 : CO7D_CONMA 0.56 0.80 1 25 4 28 25 0 0 29 Q26350 Omega-conotoxin MVIID (Fragment) OS=Conus magus PE=1 SV=1
43 : Q9N6F8_CONCT 0.56 0.80 1 25 41 65 25 0 0 66 Q9N6F8 Four-loop conotoxin (Fragment) OS=Conus catus PE=3 SV=1
44 : Q9NCV9_CONCT 0.56 0.80 1 25 41 65 25 0 0 66 Q9NCV9 Four-loop conotoxin (Fragment) OS=Conus catus PE=3 SV=1
45 : Q9NCW0_CONCT 0.56 0.80 1 25 41 65 25 0 0 66 Q9NCW0 Four-loop conotoxin (Fragment) OS=Conus catus PE=3 SV=1
46 : Q9NCV8_CONCT 0.54 0.79 2 25 42 65 24 0 0 66 Q9NCV8 Four-loop conotoxin (Fragment) OS=Conus catus PE=3 SV=1
## ALIGNMENTS 1 - 46
SeqNo PDBNo AA STRUCTURE BP1 BP2 ACC NOCC VAR ....:....1....:....2....:....3....:....4....:....5....:....6....:....7
1 1 A a 0 0 122 46 0 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
2 2 A K B -a 15 0A 102 47 25 KKKKKKKKKKKKKKKKKKKKKKKKKKKKKQKKKKKQKKKQKQQQQQ
3 3 A G > - 0 0 41 47 40 GGGGGGGGGGGGGGGGGGASRSSAAAAAAGSSSGGGLGGGSGGGGG
4 4 A K T 3 S+ 0 0 145 47 68 KKKKKKKKKTKKKKKTKKATKTTAAAAAARTTKKKRKPPRTRRRRR
5 5 A G T 3 S+ 0 0 54 47 0 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
6 6 A A S < S- 0 0 33 47 48 AAAQAAAAAKAAAAAKAAKASAAKKKKKKAAAAAAAQAAAAAAAAA
7 7 A K - 0 0 148 47 39 KSSSSSSSSPSSSSSPPPPSSSSSSSPPSSSSKPPSSSKSSSSSSS
8 8 A b - 0 0 20 47 0 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
9 9 A S - 0 0 59 47 68 SRRSSRRRRSSRHRSSRRSRRRRSSSSSSRRRSTTRRILRRRRRRR
10 10 A R S S- 0 0 151 47 23 RRRKRRRRRRRKRRRRKKRRRRRRRRRRRRRRKRRKKRKKRKKKKK
11 11 A L S S+ 0 0 105 47 56 LTTLTTTTTITTTTTITTITTTTIIIIIITTTLLLTTITTTTTTTT
12 12 A M S S- 0 0 107 47 79 MSSMMSSSSAMMSSMAMMASSSSAAAAAASPSMMMSSAMMSMMMMM
13 13 A Y + 0 0 181 47 0 YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY
14 14 A D + 0 0 59 47 32 DDDDNDDDDNNDDGNNDDNDDDDNNNNNNDDDDDDDDNDNDNNNNN
15 15 A c B -a 2 0A 15 47 0 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
16 16 A a S S+ 0 0 79 47 0 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
17 17 A T S S+ 0 0 111 47 55 TTTTTTTTTTSRTTSTSSTTTTTTTTTTTTTTSHHTSKKSTSSSSS
18 18 A G S S- 0 0 47 47 16 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGYYGGGGGGG
19 19 A S - 0 0 53 47 0 SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
20 20 A b + 0 0 24 47 0 CCCcCCCCCCCCCCCCccCCCCCCCCCCCCCCcccCcCCCCCCCCC
21 21 A R B > -B 24 0B 165 47 52 RRRrNRRRRRNRNRNRrrRRRRRRRRRRRRRRtssRrRSRDNNNNN
22 22 A S T 3 S- 0 0 82 47 59 SSSRRSSSSSRSRSRSRRSSNSSSSSSSSSSSVKKSSNRSRRRRRR
23 23 A G T 3 S+ 0 0 25 47 0 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
24 24 A K B < B 21 0B 93 47 27 KKKKKRRRRKKRKRKKKKKRKRRKKKKKKRRRRRRRKKRRRRRRRR
25 25 A c 0 0 2 47 0 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
## 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 0 0 0 0 0 100 0 0 0 0 0 0 0 46 0 0 0.000 0 1.00
2 2 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 83 17 0 0 0 47 0 0 0.456 15 0.75
3 3 A 0 2 0 0 0 0 0 66 15 0 15 0 0 0 2 0 0 0 0 0 47 0 0 1.006 33 0.60
4 4 A 0 0 0 0 0 0 0 0 15 4 0 17 0 0 17 47 0 0 0 0 47 0 0 1.376 45 0.31
5 5 A 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 47 0 0 0.000 0 1.00
6 6 A 0 0 0 0 0 0 0 0 74 0 2 0 0 0 0 19 4 0 0 0 47 0 0 0.752 25 0.51
7 7 A 0 0 0 0 0 0 0 0 0 19 72 0 0 0 0 9 0 0 0 0 47 0 0 0.760 25 0.60
8 8 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 47 0 0 0.000 0 1.00
9 9 A 0 2 2 0 0 0 0 0 0 0 34 4 0 2 55 0 0 0 0 0 47 0 0 1.074 35 0.31
10 10 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 70 30 0 0 0 0 47 0 0 0.609 20 0.76
11 11 A 0 13 21 0 0 0 0 0 0 0 0 66 0 0 0 0 0 0 0 0 47 0 0 0.867 28 0.44
12 12 A 0 0 0 40 0 0 0 0 21 2 36 0 0 0 0 0 0 0 0 0 47 0 0 1.145 38 0.20
13 13 A 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 47 0 0 0.000 0 1.00
14 14 A 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 40 57 47 0 0 0.766 25 0.68
15 15 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 47 0 0 0.000 0 1.00
16 16 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 47 0 0 0.000 0 1.00
17 17 A 0 0 0 0 0 0 0 0 0 0 26 64 0 4 2 4 0 0 0 0 47 0 0 0.986 32 0.45
18 18 A 0 0 0 0 0 0 4 96 0 0 0 0 0 0 0 0 0 0 0 0 47 0 0 0.176 5 0.84
19 19 A 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 47 0 0 0.000 0 1.00
20 20 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 47 0 7 0.000 0 1.00
21 21 A 0 0 0 0 0 0 0 0 0 0 6 2 0 0 70 0 0 0 19 2 47 0 0 0.904 30 0.47
22 22 A 2 0 0 0 0 0 0 0 0 0 60 0 0 0 30 4 0 0 4 0 47 0 0 1.020 34 0.40
23 23 A 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 47 0 0 0.000 0 1.00
24 24 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 51 49 0 0 0 0 47 0 0 0.693 23 0.73
25 25 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 47 0 0 0.000 0 1.00
## INSERTION LIST
AliNo IPOS JPOS Len Sequence
4 21 21 1 cSr
17 21 66 1 cGr
18 21 23 1 cGr
33 21 66 2 cSGt
34 21 21 2 cSSs
35 21 66 2 cSSs
37 21 66 1 cGr
//