Complet list of 3gb1 hssp file
Complete list of 3gb1.hssp file
HSSP HOMOLOGY DERIVED SECONDARY STRUCTURE OF PROTEINS , VERSION 2.0 2011
PDBID 3GB1
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 2013-09-29
HEADER IMMUNOGLOBULIN BINDING PROTEIN 1999-06-23 3GB1
COMPND PROTEIN (B1 DOMAIN OF STREPTOCOCCAL PROTEIN G)
SOURCE Streptococcus sp. 'group G'
AUTHOR Clore, G.M.
SEQLENGTH 56
NCHAIN 1 chain(s) in 3GB1 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 : C5WHI8_STRDG 1.00 1.00 2 56 303 357 55 0 0 523 C5WHI8 Immunoglobulin G-binding protein OS=Streptococcus dysgalactiae subsp. equisimilis (strain GGS_124) GN=spg PE=3 SV=1
2 : F5U588_STREQ 1.00 1.00 2 56 19 73 55 0 0 239 F5U588 Putative immunoglobulin G-binding protein G (Fragment) OS=Streptococcus dysgalactiae subsp. equisimilis SK1249 GN=HMPREF9964_0770 PE=4 SV=1
3 : F9NHM5_STREQ 1.00 1.00 2 56 202 256 55 0 0 422 F9NHM5 Immunoglobulin G-binding protein G OS=Streptococcus dysgalactiae subsp. equisimilis SK1250 GN=spg PE=4 SV=1
4 : K4Q980_STREQ 1.00 1.00 2 56 303 357 55 0 0 523 K4Q980 Immunoglobulin G-binding protein G OS=Streptococcus dysgalactiae subsp. equisimilis AC-2713 GN=spg PE=3 SV=1
5 : Q53291_PEPMA2ZW0 1.00 1.00 2 56 330 384 55 0 0 455 Q53291 Protein LG (Fragment) OS=Peptostreptococcus magnus PE=1 SV=1
6 : SPG1_STRSG 2RPV 1.00 1.00 2 56 228 282 55 0 0 448 P06654 Immunoglobulin G-binding protein G OS=Streptococcus sp. group G GN=spg PE=1 SV=1
7 : SPG2_STRSG 1ZXH 1.00 1.00 2 56 303 357 55 0 0 593 P19909 Immunoglobulin G-binding protein G OS=Streptococcus sp. group G GN=spg PE=1 SV=1
8 : E8QBR8_STRED 0.98 1.00 2 56 228 282 55 0 0 448 E8QBR8 IgG binding protein Zag OS=Streptococcus dysgalactiae subsp. equisimilis (strain ATCC 12394 / D166B) GN=SDE12394_07285 PE=3 SV=1
9 : M4YXE4_STREQ 0.98 1.00 2 56 240 294 55 0 0 460 M4YXE4 Immunoglobulin G-binding protein OS=Streptococcus dysgalactiae subsp. equisimilis RE378 GN=spg PE=3 SV=1
10 : Q54181_STRSG 0.96 1.00 2 56 61 115 55 0 0 185 Q54181 Protein G' OS=Streptococcus sp. group G GN=Protein G'gene PE=4 SV=1
11 : E7Q004_STRDY 0.87 0.93 2 56 364 418 55 0 0 519 E7Q004 Ig, alpha2-macroglobulin and albumin binding protein Zag OS=Streptococcus dysgalactiae subsp. dysgalactiae ATCC 27957 GN=SDD27957_06725 PE=3 SV=1
12 : Q53337_9STRE 0.87 0.93 2 56 3 57 55 0 0 60 Q53337 Protein G IgG Fc binding domain OS=Streptococcus sp. CMCC 32138 GN=PGFB PE=4 SV=1
13 : Q53974_STRDY 0.87 0.93 2 56 258 312 55 0 0 413 Q53974 Mag protein (Precursor) OS=Streptococcus dysgalactiae GN=mag PE=3 SV=1
14 : Q53975_STRDY 0.87 0.93 2 56 504 558 55 0 0 664 Q53975 Streptococcal surface protein (Precursor) OS=Streptococcus dysgalactiae GN=mig PE=3 SV=1
15 : Q93EM8_STRDY 0.85 0.91 2 56 504 558 55 0 0 669 Q93EM8 Mig (Precursor) OS=Streptococcus dysgalactiae PE=3 SV=1
16 : C0MA37_STRE4 0.73 0.89 2 56 300 354 55 0 0 429 C0MA37 Ig, alpha2-macroglobulin and albumin binding protein Eag OS=Streptococcus equi subsp. equi (strain 4047) GN=SEQ_0721 PE=3 SV=1
17 : C0MCK9_STRS7 0.73 0.89 2 56 300 354 55 0 0 429 C0MCK9 Ig, alpha2-macroglobulin and albumin binding protein Zag (Precursor) OS=Streptococcus equi subsp. zooepidemicus (strain H70) GN=SZO_13070 PE=3 SV=1
18 : F8INR7_STREC 0.73 0.89 2 56 300 354 55 0 0 429 F8INR7 Cell surface protein OS=Streptococcus equi subsp. zooepidemicus (strain ATCC 35246 / C74-63) GN=SeseC_00850 PE=3 SV=1
19 : Q56212_STRSZ 0.73 0.89 2 56 300 354 55 0 0 429 Q56212 Cell surface protein (Precursor) OS=Streptococcus equi subsp. zooepidemicus PE=3 SV=1
20 : B4U242_STREM 0.71 0.89 2 56 316 370 55 0 0 445 B4U242 IgG binding protein Zag OS=Streptococcus equi subsp. zooepidemicus (strain MGCS10565) GN=zag PE=3 SV=1
21 : Q76K19_STRSZ 0.71 0.89 2 56 304 358 55 0 0 433 Q76K19 Cell surface protein OS=Streptococcus equi subsp. zooepidemicus GN=zag PE=3 SV=2
22 : K9E8M0_9LACT 0.55 0.66 14 56 458 501 44 1 1 598 K9E8M0 YSIRK family Gram-positive signal peptide (Fragment) OS=Alloiococcus otitis ATCC 51267 GN=HMPREF9698_01324 PE=4 SV=1
23 : K9EBI3_9LACT 0.44 0.58 3 56 192 246 55 1 1 562 K9EBI3 Uncharacterized protein (Fragment) OS=Alloiococcus otitis ATCC 51267 GN=HMPREF9698_00508 PE=4 SV=1
24 : E4KPW8_9LACT 0.41 0.61 2 56 43 98 56 1 1 100 E4KPW8 B domain protein OS=Eremococcus coleocola ACS-139-V-Col8 GN=HMPREF9257_1607 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 M 0 0 132 1 0
2 2 A T E -A 19 0A 91 23 0 TTTTTTTTTTTTTTTTTTTTT T
3 3 A Y E -A 18 0A 9 24 0 YYYYYYYYYYYYYYYYYYYYY YY
4 4 A K E -Ab 17 51A 77 24 52 KKKKKKKKKKKKKKKRRRRRR YK
5 5 A L E -Ab 16 52A 0 24 4 LLLLLLLLLLLLLLLLLLLLL FL
6 6 A I E -Ab 15 53A 51 24 32 IIIIIIIIIVVVVVVVVVVVV AV
7 7 A L E +Ab 14 54A 10 24 49 LLLLLLLLLIIIIIIIIIIII QV
8 8 A N E +Ab 13 55A 71 24 53 NNNNNNNNNNNNNNNKKKKKK RN
9 9 A G - 0 0 2 24 28 GGGGGGGGGGGGGGGGGGGGG TS
10 10 A K S S+ 0 0 151 24 74 KKKKKKKKKKKKKKKVVAVVV KE
11 11 A T S S+ 0 0 138 24 33 TTTTTTTTTTTTTTTTTTTTT GD
12 12 A L + 0 0 69 24 59 LLLLLLLLLLLLLLLFFFFFF KA
13 13 A K E +A 8 0A 149 24 70 KKKKKKKKKKKKKKKSSSSSS NQ
14 14 A G E -A 7 0A 36 25 22 GGGGGGGGGGGGGGGGGGGGGGGI
15 15 A E E +A 6 0A 129 25 45 EEEEEEEQQEEEEEEEEEEEEAAT
16 16 A T E -A 5 0A 47 25 15 TTTTTTTTTTTTTTTTTTTTTTTS
17 17 A T E +A 4 0A 87 25 51 TTTTTTTTTTTTTTTASAAAATTE
18 18 A T E -A 3 0A 42 25 49 TTTTTTTTTTTTTTTTTTTTTVVY
19 19 A E E +A 2 0A 163 25 57 EEEEEEEEEEKKKKKKKKKKKKKT
20 20 A A - 0 0 12 25 4 AAAAAAAAAAATAAAAAAAAAAAA
21 21 A V S S- 0 0 126 25 54 VVVVVVVVVVVVVVVVVVVVVSKS
22 22 A D S > S- 0 0 63 25 42 DDDDDDDDDDDDDDDDDDDDDSSS
23 23 A A H > S+ 0 0 21 25 21 AAAAAAAAAAAAAAVAAAAAAAAV
24 24 A A H > S+ 0 0 53 25 48 AAAAAAAAAAEEEEEAAAAAAEEE
25 25 A T H > S+ 0 0 40 25 50 TTTTTTTTTTTTTTTTTTTTTQEL
26 26 A A H X>S+ 0 0 0 25 0 AAAAAAAAAAAAAAAAAAAAAAAA
27 27 A E H X5S+ 0 0 108 25 12 EEEEEEEEEEEEEEEEEEEEEEEG
28 28 A K H X5S+ 0 0 150 25 57 KKKKKKKKKKKKKKKQQQQQQKTQ
29 29 A V H X5S+ 0 0 64 25 92 VVVVVVVVVVAAAAATTAATTYYY
30 30 A F H X5S+ 0 0 4 25 0 FFFFFFFFFFFFFFFFFFFFFFFF
31 31 A K H XS+ 0 0 0 25 28 AAAAAAAAAAAAAAAAAAAAAVAV
35 35 A N H ><5S+ 0 0 96 25 0 NNNNNNNNNNNNNNNNNNNNNNNN
36 36 A D H 3<5S+ 0 0 122 25 25 DDDDDDDDDDEDEEEDDDDDDEEN
37 37 A N T 3<5S- 0 0 71 25 0 NNNNNNNNNNNNNNNNNNNNNNNN
38 38 A G T < 5 + 0 0 52 25 9 GGGGGGGGGGGGGGGGGGGGGgdg
39 39 A V < + 0 0 5 25 47 VVVVVVVVVVVVVVVVVVVIIggg
40 40 A D + 0 0 106 25 44 DDDDDDDDDDDDDDDTTTTTTDDD
41 41 A G S S- 0 0 34 25 65 GGGGGGGGGGGGGGGGGGGGGLLL
42 42 A E E -C 55 0A 151 25 48 EEEEEEEEEEVVVVVEEEEEEEKE
43 43 A W E +C 54 0A 84 25 0 WWWWWWWWWWWWWWWWWWWWWWWW
44 44 A T E -C 53 0A 79 25 65 TTTTTTTTTTTTTTTAAAAAASSS
45 45 A Y E -C 52 0A 75 25 0 YYYYYYYYYYYYYYYYYYYYYYYY
46 46 A D E >> -C 51 0A 71 25 0 DDDDDDDDDDDDDDDDDDDDDDDD
47 47 A D T 45S+ 0 0 113 25 62 DDDDDDDDDDDDDDDAAAATTEEP
48 48 A A T 45S+ 0 0 91 25 26 AAAAAAAAAAAAAAAAAAAAADEA
49 49 A T T 45S- 0 0 77 25 0 TTTTTTTTTTTTTTTTTTTTTTTT
50 50 A K T <5 + 0 0 61 25 26 KKKKKKKKKKKKKKKKKKKKKKKY
51 51 A T E < -bC 4 46A 21 25 0 TTTTTTTTTTTTTTTTTTTTTTTT
52 52 A F E -bC 5 45A 6 25 0 FFFFFFFFFFFFFFFFFFFFFFFF
53 53 A T E -bC 6 44A 35 25 0 TTTTTTTTTTTTTTTTTTTTTTTT
54 54 A V E -bC 7 43A 0 25 42 VVVVVVVVVVVVVVVVVVVVVAAA
55 55 A T E bC 8 42A 62 25 32 TTTTTTTTTTTTTTTTTTTTTIRT
56 56 A E 0 0 90 25 6 EEEEEEEEEEEEEEEEEEEEEEED
## 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 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0.000 0 1.00
2 2 A 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 23 0 0 0.000 0 1.00
3 3 A 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 24 0 0 0.000 0 1.00
4 4 A 0 0 0 0 0 0 4 0 0 0 0 0 0 0 25 71 0 0 0 0 24 0 0 0.723 24 0.47
5 5 A 0 96 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 24 0 0 0.173 5 0.96
6 6 A 54 0 42 0 0 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 24 0 0 0.829 27 0.67
7 7 A 4 42 50 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0 24 0 0 0.976 32 0.50
8 8 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 25 0 0 71 0 24 0 0 0.723 24 0.47
9 9 A 0 0 0 0 0 0 0 92 0 0 4 4 0 0 0 0 0 0 0 0 24 0 0 0.345 11 0.72
10 10 A 21 0 0 0 0 0 0 0 4 0 0 0 0 0 0 71 0 4 0 0 24 0 0 0.836 27 0.25
11 11 A 0 0 0 0 0 0 0 4 0 0 0 92 0 0 0 0 0 0 0 4 24 0 0 0.345 11 0.67
12 12 A 0 67 0 0 25 0 0 0 4 0 0 0 0 0 0 4 0 0 0 0 24 0 0 0.882 29 0.41
13 13 A 0 0 0 0 0 0 0 0 0 0 25 0 0 0 0 67 4 0 4 0 24 0 0 0.882 29 0.29
14 14 A 0 0 4 0 0 0 0 96 0 0 0 0 0 0 0 0 0 0 0 0 25 0 0 0.168 5 0.77
15 15 A 0 0 0 0 0 0 0 0 8 0 0 4 0 0 0 0 8 80 0 0 25 0 0 0.711 23 0.54
16 16 A 0 0 0 0 0 0 0 0 0 0 4 96 0 0 0 0 0 0 0 0 25 0 0 0.168 5 0.85
17 17 A 0 0 0 0 0 0 0 0 20 0 4 72 0 0 0 0 0 4 0 0 25 0 0 0.816 27 0.49
18 18 A 8 0 0 0 0 0 4 0 0 0 0 88 0 0 0 0 0 0 0 0 25 0 0 0.443 14 0.50
19 19 A 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0 52 0 44 0 0 25 0 0 0.830 27 0.43
20 20 A 0 0 0 0 0 0 0 0 96 0 0 4 0 0 0 0 0 0 0 0 25 0 0 0.168 5 0.95
21 21 A 88 0 0 0 0 0 0 0 0 0 8 0 0 0 0 4 0 0 0 0 25 0 0 0.443 14 0.46
22 22 A 0 0 0 0 0 0 0 0 0 0 12 0 0 0 0 0 0 0 0 88 25 0 0 0.367 12 0.58
23 23 A 8 0 0 0 0 0 0 0 92 0 0 0 0 0 0 0 0 0 0 0 25 0 0 0.279 9 0.79
24 24 A 0 0 0 0 0 0 0 0 68 0 0 0 0 0 0 0 0 32 0 0 25 0 0 0.627 20 0.52
25 25 A 0 4 0 0 0 0 0 0 0 0 0 88 0 0 0 0 4 4 0 0 25 0 0 0.499 16 0.50
26 26 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
27 27 A 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 0 0 96 0 0 25 0 0 0.168 5 0.87
28 28 A 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0 68 28 0 0 0 25 0 0 0.747 24 0.43
29 29 A 44 0 0 0 0 0 12 0 28 0 0 16 0 0 0 0 0 0 0 0 25 0 0 1.265 42 0.07
30 30 A 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 25 0 0 0.000 0 1.00
31 31 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 28 72 0 0 0 0 25 0 0 0.593 19 0.72
32 32 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 88 0 8 4 25 0 0 0.443 14 0.67
33 33 A 0 0 0 0 8 0 92 0 0 0 0 0 0 0 0 0 0 0 0 0 25 0 0 0.279 9 0.98
34 34 A 8 0 0 0 0 0 0 0 92 0 0 0 0 0 0 0 0 0 0 0 25 0 0 0.279 9 0.72
35 35 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
36 36 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 24 4 72 25 0 0 0.708 23 0.75
37 37 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
38 38 A 0 0 0 0 0 0 0 96 0 0 0 0 0 0 0 0 0 0 0 4 25 0 3 0.168 5 0.90
39 39 A 80 0 8 0 0 0 0 12 0 0 0 0 0 0 0 0 0 0 0 0 25 0 0 0.635 21 0.52
40 40 A 0 0 0 0 0 0 0 0 0 0 0 24 0 0 0 0 0 0 0 76 25 0 0 0.551 18 0.55
41 41 A 0 12 0 0 0 0 0 88 0 0 0 0 0 0 0 0 0 0 0 0 25 0 0 0.367 12 0.35
42 42 A 20 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 76 0 0 25 0 0 0.659 22 0.52
43 43 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
44 44 A 0 0 0 0 0 0 0 0 24 0 12 64 0 0 0 0 0 0 0 0 25 0 0 0.883 29 0.35
45 45 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
46 46 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 25 0 0 0.000 0 1.00
47 47 A 0 0 0 0 0 0 0 0 16 4 0 8 0 0 0 0 0 8 0 64 25 0 0 1.112 37 0.37
48 48 A 0 0 0 0 0 0 0 0 92 0 0 0 0 0 0 0 0 4 0 4 25 0 0 0.334 11 0.74
49 49 A 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 25 0 0 0.000 0 1.00
50 50 A 0 0 0 0 0 0 4 0 0 0 0 0 0 0 0 96 0 0 0 0 25 0 0 0.168 5 0.73
51 51 A 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 25 0 0 0.000 0 1.00
52 52 A 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 25 0 0 0.000 0 1.00
53 53 A 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 25 0 0 0.000 0 1.00
54 54 A 88 0 0 0 0 0 0 0 12 0 0 0 0 0 0 0 0 0 0 0 25 0 0 0.367 12 0.58
55 55 A 0 0 4 0 0 0 0 0 0 0 0 92 0 0 4 0 0 0 0 0 25 0 0 0.334 11 0.68
56 56 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 96 0 4 25 0 0 0.168 5 0.94
## INSERTION LIST
AliNo IPOS JPOS Len Sequence
22 26 483 1 gLg
23 37 228 1 dLg
24 38 80 1 gLg
//