Complet list of 2ajo hssp file
Complete list of 2ajo.hssp file
HSSP HOMOLOGY DERIVED SECONDARY STRUCTURE OF PROTEINS , VERSION 2.0 2011
PDBID 2AJO
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 2014-05-14
HEADER MEMBRANE PROTEIN 02-AUG-05 2AJO
COMPND MOL_ID: 1; MOLECULE: NONSTRUCTURAL PROTEIN 5A; CHAIN: A; FRAGMENT: BVD
SOURCE MOL_ID: 1; SYNTHETIC: YES; OTHER_DETAILS: THE PEPTIDE WAS CHEMICALLY S
AUTHOR N.SAPAY,R.MONTSERRET,C.CHIPOT,V.BRASS,D.MORADPOUR,G.DELEAGE, F.PENIN
DBREF 2AJO A 1 28 UNP Q96662 POLG_BVDVC 2693 2720
SEQLENGTH 28
NCHAIN 1 chain(s) in 2AJO data set
NALIGN 24
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 : C1J954_BVDV 0.93 1.00 1 28 1 28 28 0 0 496 C1J954 Nonstructrual protein 5A (Fragment) OS=Bovine viral diarrhea virus PE=4 SV=1
2 : C1J955_BVDV 0.93 1.00 1 28 1 28 28 0 0 496 C1J955 Nonstructrual protein 5A (Fragment) OS=Bovine viral diarrhea virus PE=4 SV=1
3 : C1J941_BVDV 0.89 1.00 1 28 1 28 28 0 0 496 C1J941 Nonstructrual protein 5A (Fragment) OS=Bovine viral diarrhea virus PE=4 SV=1
4 : C1J942_BVDV 0.89 1.00 1 28 1 28 28 0 0 496 C1J942 Nonstructrual protein 5A (Fragment) OS=Bovine viral diarrhea virus PE=4 SV=1
5 : C1J947_BVDV 0.89 1.00 1 28 1 28 28 0 0 496 C1J947 Nonstructrual protein 5A (Fragment) OS=Bovine viral diarrhea virus PE=4 SV=1
6 : C1J948_BVDV 0.89 1.00 1 28 1 28 28 0 0 496 C1J948 Nonstructrual protein 5A (Fragment) OS=Bovine viral diarrhea virus PE=4 SV=1
7 : C1J949_BVDV 0.89 1.00 1 28 1 28 28 0 0 496 C1J949 Nonstructrual protein 5A (Fragment) OS=Bovine viral diarrhea virus PE=4 SV=1
8 : C1J951_BVDV 0.89 1.00 1 28 1 28 28 0 0 496 C1J951 Nonstructrual protein 5A (Fragment) OS=Bovine viral diarrhea virus PE=4 SV=1
9 : C1J953_BVDV 0.89 1.00 1 28 1 28 28 0 0 496 C1J953 Nonstructrual protein 5A (Fragment) OS=Bovine viral diarrhea virus PE=4 SV=1
10 : C1J956_BVDV 0.89 1.00 1 28 1 28 28 0 0 496 C1J956 Nonstructrual protein 5A (Fragment) OS=Bovine viral diarrhea virus PE=4 SV=1
11 : Q91N47_BVDV 0.89 1.00 1 28 1095 1122 28 0 0 1158 Q91N47 Polyprotein (Fragment) OS=Bovine viral diarrhea virus PE=4 SV=1
12 : Q9IHZ2_BVDV 0.89 1.00 1 28 367 394 28 0 0 424 Q9IHZ2 Polyprotein (Fragment) OS=Bovine viral diarrhea virus-1 strain NCP821 PE=4 SV=1
13 : C1J937_BVDV 0.86 1.00 1 28 1 28 28 0 0 496 C1J937 Nonstructrual protein 5A (Fragment) OS=Bovine viral diarrhea virus PE=4 SV=1
14 : C1J938_BVDV 0.86 1.00 1 28 1 28 28 0 0 496 C1J938 Nonstructrual protein 5A (Fragment) OS=Bovine viral diarrhea virus PE=4 SV=1
15 : C1J943_BVDV 0.86 1.00 1 28 1 28 28 0 0 496 C1J943 Nonstructrual protein 5A (Fragment) OS=Bovine viral diarrhea virus PE=4 SV=1
16 : C1J945_BVDV 0.86 1.00 1 28 1 28 28 0 0 496 C1J945 Nonstructrual protein 5A (Fragment) OS=Bovine viral diarrhea virus PE=4 SV=1
17 : C1J952_BVDV 0.86 1.00 1 28 1 28 28 0 0 496 C1J952 Nonstructrual protein 5A (Fragment) OS=Bovine viral diarrhea virus PE=4 SV=1
18 : Q91N48_BVDV 0.86 1.00 1 28 1095 1122 28 0 0 1159 Q91N48 Polyprotein (Fragment) OS=Bovine viral diarrhea virus PE=4 SV=1
19 : C1J944_BVDV 0.82 1.00 1 28 1 28 28 0 0 496 C1J944 Nonstructrual protein 5A (Fragment) OS=Bovine viral diarrhea virus PE=4 SV=1
20 : C1J946_BVDV 0.82 0.89 1 28 1 28 28 0 0 496 C1J946 Nonstructrual protein 5A (Fragment) OS=Bovine viral diarrhea virus PE=4 SV=1
21 : C1J950_BVDV 0.82 1.00 1 28 1 28 28 0 0 496 C1J950 Nonstructrual protein 5A (Fragment) OS=Bovine viral diarrhea virus PE=4 SV=1
22 : C1J957_BVDV 0.82 1.00 1 28 1 28 28 0 0 496 C1J957 Nonstructrual protein 5A (Fragment) OS=Bovine viral diarrhea virus PE=4 SV=1
23 : C1J939_BVDV 0.79 0.89 1 28 1 28 28 0 0 496 C1J939 Nonstructrual protein 5A (Fragment) OS=Bovine viral diarrhea virus PE=4 SV=1
24 : C1J940_BVDV 0.79 1.00 1 28 1 28 28 0 0 496 C1J940 Nonstructrual protein 5A (Fragment) OS=Bovine viral diarrhea virus PE=4 SV=1
## ALIGNMENTS 1 - 24
SeqNo PDBNo AA STRUCTURE BP1 BP2 ACC NOCC VAR ....:....1....:....2....:....3....:....4....:....5....:....6....:....7
1 1 A S 0 0 155 25 0 SSSSSSSSSSSSSSSSSSSSSSSS
2 2 A G - 0 0 67 25 0 GGGGGGGGGGGGGGGGGGGGGGGG
3 3 A N S S+ 0 0 133 25 0 NNNNNNNNNNNNNNNNNNNNNNNN
4 4 A Y + 0 0 146 25 0 YYYYYYYYYYYYYYYYYYYYYYYY
5 5 A V S S+ 0 0 97 25 2 IIIIIIIIIIIIIIIIIIIIIIII
6 6 A L S > S+ 0 0 129 25 0 LLLLLLLLLLLLLLLLLLLLLLLL
7 7 A D H > S+ 0 0 92 25 11 DDDDDDDDDDDEDEDDDDDDDEDE
8 8 A L H > S+ 0 0 97 25 1 LLLLLLLLLLLLLLLLMLLLLLLL
9 9 A I H >> S+ 0 0 123 25 2 IIIIIIIIIIIIIIIIIVIIIIII
10 10 A Y H 3X S+ 0 0 135 25 8 YYYYYYYYYYYYYYYYYYYCYYCY
11 11 A S H 3X S+ 0 0 71 25 37 GSSSSGSSSGSSGGSGSSGSGGSG
12 12 A L H X S+ 0 0 141 25 8 RRRRRRRRRRRRRRRRRRKRKRRR
19 19 A G H 3X S+ 0 0 31 25 31 GGGGGGGGGGGGGGGGGGGCGGHS
20 20 A L H 3< S+ 0 0 107 25 0 LLLLLLLLLLLLLLLLLLLLLLLL
21 21 A K H <> S+ 0 0 96 25 21 KKKKKKKKKKKKRKKRKKKRKRRK
22 22 A K H < S+ 0 0 115 25 6 KKKKKKKKKKKKKKKKKKKKKKRK
23 23 A I T < S+ 0 0 94 25 55 IVVVVMVVVIVMMIVMVVMTMMTM
24 24 A V T >4 S+ 0 0 81 25 32 VVIIIVIIIVIVVMIVIIMVMVVM
25 25 A L T 3< S+ 0 0 143 25 0 LLLLLLLLLLLLLLLLLLLLLLLL
26 26 A G T 3 S+ 0 0 48 25 0 GGGGGGGGGGGGGGGGGGGGGGGG
27 27 A W < 0 0 224 25 0 WWWWWWWWWWWWWWWWWWWWWWWW
28 28 A A 0 0 161 25 0 AAAAAAAAAAAAAAAAAAAAAAAA
## 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 0 100 0 0 0 0 0 0 0 0 0 25 0 0 0.000 0 1.00
2 2 A 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 25 0 0 0.000 0 1.00
3 3 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 25 0 0 0.000 0 1.00
4 4 A 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 25 0 0 0.000 0 1.00
5 5 A 4 0 96 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 25 0 0 0.168 5 0.98
6 6 A 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 25 0 0 0.000 0 1.00
7 7 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 16 0 84 25 0 0 0.440 14 0.89
8 8 A 0 96 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 25 0 0 0.168 5 0.99
9 9 A 4 0 96 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 25 0 0 0.168 5 0.98
10 10 A 0 0 0 0 0 0 92 0 0 0 0 0 8 0 0 0 0 0 0 0 25 0 0 0.279 9 0.91
11 11 A 0 0 0 0 0 0 0 40 0 0 60 0 0 0 0 0 0 0 0 0 25 0 0 0.673 22 0.62
12 12 A 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 25 0 0 0.000 0 1.00
13 13 A 0 0 0 0 0 0 0 0 0 0 0 0 0 96 0 0 4 0 0 0 25 0 0 0.168 5 0.95
14 14 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 96 0 0 0 0 25 0 0 0.168 5 0.96
15 15 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 25 0 0 0.000 0 1.00
16 16 A 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 25 0 0 0.000 0 1.00
17 17 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 25 0 0 0.000 0 1.00
18 18 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 92 8 0 0 0 0 25 0 0 0.279 9 0.91
19 19 A 0 0 0 0 0 0 0 88 0 0 4 0 4 4 0 0 0 0 0 0 25 0 0 0.499 16 0.68
20 20 A 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 25 0 0 0.000 0 1.00
21 21 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 20 80 0 0 0 0 25 0 0 0.500 16 0.79
22 22 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 96 0 0 0 0 25 0 0 0.168 5 0.93
23 23 A 44 0 16 32 0 0 0 0 0 0 0 8 0 0 0 0 0 0 0 0 25 0 0 1.221 40 0.44
24 24 A 44 0 40 16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 25 0 0 1.021 34 0.67
25 25 A 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 25 0 0 0.000 0 1.00
26 26 A 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 25 0 0 0.000 0 1.00
27 27 A 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 25 0 0 0.000 0 1.00
28 28 A 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 25 0 0 0.000 0 1.00
## INSERTION LIST
AliNo IPOS JPOS Len Sequence
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