Complet list of 1zae hssp file
Complete list of 1zae.hssp file
HSSP HOMOLOGY DERIVED SECONDARY STRUCTURE OF PROTEINS , VERSION 2.0 2011
PDBID 1ZAE
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 DNA BINDING PROTEIN 06-APR-05 1ZAE
COMPND MOL_ID: 1; MOLECULE: EARLY PROTEIN GP16.7; CHAIN: A, B; FRAGMENT: C-TE
SOURCE MOL_ID: 1; ORGANISM_SCIENTIFIC: BACILLUS PHAGE PHI29; ORGANISM_TAXID:
AUTHOR J.L.ASENSIO,A.ALBERT,D.MUNOZ-ESPIN,C.GONZALEZ,J.HERMOSO, L.VILLAR,J.JI
DBREF 1ZAE A 63 130 UNP P16517 VG167_BPPH2 63 130
DBREF 1ZAE B 63 130 UNP P16517 VG167_BPPH2 63 130
SEQLENGTH 70
NCHAIN 2 chain(s) in 1ZAE data set
KCHAIN 1 chain(s) used here ; chains(s) : A
NALIGN 6
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 : B3VMQ4_BPPH2 0.99 1.00 2 70 62 130 69 0 0 130 B3VMQ4 Hypothetical early protein OS=Bacillus phage phi29 GN=16.7 PE=4 SV=1
2 : VG167_BPPH2 2C5R 0.99 1.00 2 70 62 130 69 0 0 130 P16517 Early protein GP16.7 OS=Bacillus phage phi29 GN=16.7 PE=1 SV=1
3 : VG167_BPPH5 0.91 1.00 2 70 62 130 69 0 0 130 P15853 Early protein GP16.7 OS=Bacillus phage phi15 GN=16.7 PE=3 SV=1
4 : VG167_BPPZA 0.90 1.00 2 70 62 130 69 0 0 130 P08386 Early protein GP16.7 OS=Bacillus phage PZA GN=16.7 PE=3 SV=1
5 : B7SSP1_BPNF 0.59 0.84 2 70 62 130 69 0 0 130 B7SSP1 DNA replication organizer OS=Bacillus phage Nf GN=16.7 PE=4 SV=1
6 : M4WNK5_9CAUD 0.34 0.58 8 69 83 144 62 0 0 144 M4WNK5 DNA replication organizer OS=Bacillus phage MG-B1 GN=mgb1_042 PE=4 SV=1
## ALIGNMENTS 1 - 6
SeqNo PDBNo AA STRUCTURE BP1 BP2 ACC NOCC VAR ....:....1....:....2....:....3....:....4....:....5....:....6....:....7
1 61 A H 0 0 88 1 0
2 62 A M - 0 0 195 6 26 IIVVI
3 63 A D - 0 0 41 6 0 DDDDD
4 64 A K + 0 0 43 6 56 KKKKN
5 65 A T + 0 0 102 6 81 TTSSN
6 66 A V - 0 0 92 6 20 VVVVI
7 67 A N - 0 0 107 6 56 NNNNQ
8 68 A L - 0 0 41 7 5 LLMMLL
9 69 A S > - 0 0 39 7 47 SSSSST
10 70 A A H > S+ 0 0 80 7 88 AAAAHV
11 71 A C H > S+ 0 0 6 7 108 CCCCVE
12 72 A E H > S+ 0 0 0 7 31 EEEEEQ
13 73 A V H X S+ 0 0 72 7 100 VVIISE
14 74 A A H X S+ 0 0 44 7 71 AAAASE
15 75 A V H X S+ 0 0 0 7 51 VVVVVA
16 76 A L H X S+ 0 0 18 7 27 LLLLLI
17 77 A D H X S+ 0 0 74 7 0 DDDDDD
18 78 A L H X S+ 0 0 38 7 0 LLLLLL
19 79 A Y H <>S+ 0 0 0 7 0 YYYYYY
20 80 A E H ><5S+ 0 0 86 7 13 EEEEDE
21 81 A Q H 3<5S+ 0 0 144 7 63 QQQQER
22 82 A S T 3<5S- 0 0 4 7 47 SSSSSN
23 83 A N T < 5S+ 0 0 104 7 0 NNNNNN
24 84 A I < - 0 0 0 7 0 IIIIII
25 85 A R - 0 0 52 7 0 RRRRRR
26 86 A I - 0 0 3 7 27 IIIIIL
27 87 A P >> - 0 0 0 7 0 PPPPPP
28 88 A S H >> S+ 0 0 0 7 89 SSSSVI
29 89 A D H 3> S+ 0 0 14 7 0 DDDDDD
30 90 A I H <> S+ 0 0 7 7 0 IIIIII
31 91 A I H X S+ 0 0 28 7 19 DDDDDE
34 94 A L H 3X S+ 0 0 4 7 5 LLMMLL
35 95 A V H 3< S+ 0 0 22 7 101 VVVVHS
36 96 A N H << S+ 0 0 110 7 81 NNNNHY
37 97 A Q H < S- 0 0 92 7 84 QQQQKS
38 98 A R < - 0 0 91 7 68 RRRRKN
39 99 A L - 0 0 44 7 75 LLLLLN
40 100 A Q S S+ 0 0 163 7 100 QQQQSV
41 101 A S S > S- 0 0 21 7 55 SSSTTT
42 102 A E H > S+ 0 0 43 7 79 EEEEEY
43 103 A Q H > S+ 0 0 75 7 58 QQQQKH
44 104 A E H > S+ 0 0 57 7 59 EEDDES
45 105 A V H X S+ 0 0 0 7 51 VVVVVA
46 106 A L H X S+ 0 0 4 7 33 LLLLMV
47 107 A N H X S+ 0 0 92 7 71 NNNNEA
48 108 A Y H X S+ 0 0 56 7 3 YYYYYF
49 109 A I H X S+ 0 0 6 7 10 IIIIVI
50 110 A E H X S+ 0 0 37 7 0 EEEEEE
51 111 A T H >X S+ 0 0 91 7 88 TTTTNM
52 112 A Q H 3X S+ 0 0 41 7 0 QQQQQQ
53 113 A R H 3X S+ 0 0 4 7 0 RRRRRR
54 114 A T H X S+ 0 0 86 7 63 LLLLLA
59 119 A E H 3< S+ 0 0 19 7 31 EEEEEQ
60 120 A N H 3< S+ 0 0 0 7 79 NNNNNF
61 121 A Q H << S+ 0 0 125 7 86 QQQQTT
62 122 A K S < S- 0 0 50 7 67 KKKKKV
63 123 A K + 0 0 114 7 51 KKKKKT
64 124 A L - 0 0 4 7 7 LLLLLM
65 125 A Y - 0 0 116 7 71 YYYYYT
66 126 A R - 0 0 88 7 37 RRRRKK
67 127 A G S S+ 0 0 36 7 0 GGGGGG
68 128 A S S S+ 0 0 33 7 99 SSSSVM
69 129 A L 0 0 131 7 27 LLLLLI
70 130 A K 0 0 153 6 0 KKKKK
## 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 61 A 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 1 0 0 0.000 0 1.00
2 62 A 33 0 50 17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 0 1.011 33 0.74
3 63 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 6 0 0 0.000 0 1.00
4 64 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 83 0 0 17 0 6 0 0 0.451 15 0.43
5 65 A 0 0 0 0 0 0 0 0 0 0 33 50 0 0 0 0 0 0 17 0 6 0 0 1.011 33 0.18
6 66 A 83 0 17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 0 0.451 15 0.79
7 67 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 17 0 83 0 6 0 0 0.451 15 0.43
8 68 A 0 71 0 29 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 0.598 19 0.94
9 69 A 0 0 0 0 0 0 0 0 0 0 86 14 0 0 0 0 0 0 0 0 7 0 0 0.410 13 0.52
10 70 A 14 0 0 0 0 0 0 0 71 0 0 0 0 14 0 0 0 0 0 0 7 0 0 0.796 26 0.12
11 71 A 14 0 0 0 0 0 0 0 0 0 0 0 71 0 0 0 0 14 0 0 7 0 0 0.796 26 -0.08
12 72 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 14 86 0 0 7 0 0 0.410 13 0.68
13 73 A 43 0 29 0 0 0 0 0 0 0 14 0 0 0 0 0 0 14 0 0 7 0 0 1.277 42 -0.01
14 74 A 0 0 0 0 0 0 0 0 71 0 14 0 0 0 0 0 0 14 0 0 7 0 0 0.796 26 0.29
15 75 A 86 0 0 0 0 0 0 0 14 0 0 0 0 0 0 0 0 0 0 0 7 0 0 0.410 13 0.48
16 76 A 0 86 14 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 0.410 13 0.72
17 77 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 7 0 0 0.000 0 1.00
18 78 A 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 0.000 0 1.00
19 79 A 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 0.000 0 1.00
20 80 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 86 0 14 7 0 0 0.410 13 0.86
21 81 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 14 0 71 14 0 0 7 0 0 0.796 26 0.37
22 82 A 0 0 0 0 0 0 0 0 0 0 86 0 0 0 0 0 0 0 14 0 7 0 0 0.410 13 0.52
23 83 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 7 0 0 0.000 0 1.00
24 84 A 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 0.000 0 1.00
25 85 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 7 0 0 0.000 0 1.00
26 86 A 0 14 86 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 0.410 13 0.72
27 87 A 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 7 0 0 0.000 0 1.00
28 88 A 14 0 14 0 0 0 0 0 0 0 71 0 0 0 0 0 0 0 0 0 7 0 0 0.796 26 0.11
29 89 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 7 0 0 0.000 0 1.00
30 90 A 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 0.000 0 1.00
31 91 A 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 0.000 0 1.00
32 92 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 7 0 0 0.000 0 1.00
33 93 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 14 0 86 7 0 0 0.410 13 0.80
34 94 A 0 71 0 29 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 0.598 19 0.94
35 95 A 71 0 0 0 0 0 0 0 0 0 14 0 0 14 0 0 0 0 0 0 7 0 0 0.796 26 -0.02
36 96 A 0 0 0 0 0 0 14 0 0 0 0 0 0 14 0 0 0 0 71 0 7 0 0 0.796 26 0.18
37 97 A 0 0 0 0 0 0 0 0 0 0 14 0 0 0 0 14 71 0 0 0 7 0 0 0.796 26 0.15
38 98 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 71 14 0 0 14 0 7 0 0 0.796 26 0.32
39 99 A 0 86 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 14 0 7 0 0 0.410 13 0.24
40 100 A 14 0 0 0 0 0 0 0 0 0 14 0 0 0 0 0 71 0 0 0 7 0 0 0.796 26 -0.00
41 101 A 0 0 0 0 0 0 0 0 0 0 57 43 0 0 0 0 0 0 0 0 7 0 0 0.683 22 0.45
42 102 A 0 0 0 0 0 0 14 0 0 0 0 0 0 0 0 0 0 86 0 0 7 0 0 0.410 13 0.20
43 103 A 0 0 0 0 0 0 0 0 0 0 0 0 0 14 0 14 71 0 0 0 7 0 0 0.796 26 0.41
44 104 A 0 0 0 0 0 0 0 0 0 0 14 0 0 0 0 0 0 57 0 29 7 0 0 0.956 31 0.41
45 105 A 86 0 0 0 0 0 0 0 14 0 0 0 0 0 0 0 0 0 0 0 7 0 0 0.410 13 0.48
46 106 A 14 71 0 14 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 0.796 26 0.67
47 107 A 0 0 0 0 0 0 0 0 14 0 0 0 0 0 0 0 0 14 71 0 7 0 0 0.796 26 0.28
48 108 A 0 0 0 0 14 0 86 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 0.410 13 0.96
49 109 A 14 0 86 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 0.410 13 0.89
50 110 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 7 0 0 0.000 0 1.00
51 111 A 0 0 0 14 0 0 0 0 0 0 0 71 0 0 0 0 0 0 14 0 7 0 0 0.796 26 0.11
52 112 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 7 0 0 0.000 0 1.00
53 113 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 7 0 0 0.000 0 1.00
54 114 A 0 0 0 0 0 0 0 0 0 0 0 71 0 0 0 14 0 0 14 0 7 0 0 0.796 26 0.23
55 115 A 14 0 0 0 14 0 71 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 0.796 26 0.36
56 116 A 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 0.000 0 1.00
57 117 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 7 0 0 0.000 0 1.00
58 118 A 0 86 0 0 0 0 0 0 14 0 0 0 0 0 0 0 0 0 0 0 7 0 0 0.410 13 0.36
59 119 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 14 86 0 0 7 0 0 0.410 13 0.68
60 120 A 0 0 0 0 14 0 0 0 0 0 0 0 0 0 0 0 0 0 86 0 7 0 0 0.410 13 0.20
61 121 A 0 0 0 0 0 0 0 0 0 0 0 29 0 0 0 0 71 0 0 0 7 0 0 0.598 19 0.13
62 122 A 14 0 0 0 0 0 0 0 0 0 0 0 0 0 0 86 0 0 0 0 7 0 0 0.410 13 0.32
63 123 A 0 0 0 0 0 0 0 0 0 0 0 14 0 0 0 86 0 0 0 0 7 0 0 0.410 13 0.48
64 124 A 0 86 0 14 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 0.410 13 0.92
65 125 A 0 0 0 0 0 0 86 0 0 0 0 14 0 0 0 0 0 0 0 0 7 0 0 0.410 13 0.28
66 126 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 71 29 0 0 0 0 7 0 0 0.598 19 0.62
67 127 A 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 0.000 0 1.00
68 128 A 14 0 0 14 0 0 0 0 0 0 71 0 0 0 0 0 0 0 0 0 7 0 0 0.796 26 0.01
69 129 A 0 86 14 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 0.410 13 0.72
70 130 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 6 0 0 0.000 0 1.00
## INSERTION LIST
AliNo IPOS JPOS Len Sequence
//