PASS2.8 - Home

solvent inaccessible: UPPER CASE X
solvent accesible: lower case x
alpha helix: red x

beta strand: blue x
3 - 10 helix: maroon x
hydrogen bond to main chain amide: bold x

hydrogen bond to mainchain carbonyl: underline x
disulphide bond: cedilla
positive phi: italic x

                             10        20        30        40        50  
d1r8ha-  ( 281 )    s-------------------------------saTPiVqFqg-esncLkc
d2bopa-  ( 326 )                                      sCfAlIsG-tanqVkc
d6vh6a1  ( 470 )    gqggsnpkfeniAeglrallarshverttdegtwvAGvfvygGsktSlyn
                                                       bbbbbbb  aaaaaa

                             60        70        80        90        100 
d1r8ha-  ( 299 )    FryrLndkhrhlFdlisstwhwasp-----------kaphkhaIVtVTYh
d2bopa-  ( 341 )    YrfrVkknhrhrYenctttwftvadn---------gaerqgqAqIlItFg
d6vh6a1  ( 520 )    lrrGtalAipqC--rltplsrlpfgmapgpgpqpgplresivcyFmvflq
                    aaaaaaaa                                  bbbbbb  

                             110       120       130       140 
d1r8ha-  ( 337 )    seeqrqqFlnvVkipp--------tIrhklgfms---mhll
d2bopa-  ( 382 )    spsqrqdFlkhVplpp--------gMnisgftas---ld-f
d6vh6a1  ( 568 )    thiFAevlkdAikdlvmtkpaptcnirvtvcsfddgv-dlp
                     aaaaaaaaaa               bbbbbb

Domains
Outliers

Domain ID	Name	Family	Source	STRING-DB
d1r8ha- # Domain Specific Files ATM file: Atomic coordinates by ASTRAL ATM2ALI file: Amino acid sequences by ATM2ALI SST file: Secondary structure by SSTRUC PSA file: solvent accessibility by PSA HBD file: Hydrogen bonds by HBOND PSE file: PyMol session file for conserved interactions PDBSUM1: Topological diagram d1r8ha- # Links to other databases and tools RCSB-PDB: Research Collaboratory for Structural Bioinformatics SCOP: Structural Classification of Proteins EBI: European Bioinformatics Institute HOMSTRAD: Homologous Structure Alignment Database DDBASE: Dial-Derived Domain Database CATH: Class Architecture Topology and Homologous sfily PALI: Phylogeny and ALIgnment of homologous protein structures MODBASE: A Database of Annotated Comparative Protein Structure Models 3Dee: A Database of Protein Domain Definition PQS: Protein Quaternary Structure Query Form at the EBI LPC/CSU: Ligand-Protein Contacts & Contacts of Structural LPFC: A Library of Protein Family Cores MMDB: Molecular Modelling DataBase,NCBI CE: Databases and Tools for 3-D Protein Structure Comparison and Alignment PDBSUM: Summaries and structural analyses of PDB data files Pfam: Protein families database of alignments and HMMs	Papillomavirus-1 E2 protein	Viral DNA-binding domain	Human papillomavirus type 6a [TaxId: 37122]	view
d2bopa- # Domain Specific Files ATM file: Atomic coordinates by ASTRAL ATM2ALI file: Amino acid sequences by ATM2ALI SST file: Secondary structure by SSTRUC PSA file: solvent accessibility by PSA HBD file: Hydrogen bonds by HBOND PSE file: PyMol session file for conserved interactions PDBSUM1: Topological diagram d2bopa- # Links to other databases and tools RCSB-PDB: Research Collaboratory for Structural Bioinformatics SCOP: Structural Classification of Proteins EBI: European Bioinformatics Institute HOMSTRAD: Homologous Structure Alignment Database DDBASE: Dial-Derived Domain Database CATH: Class Architecture Topology and Homologous sfily PALI: Phylogeny and ALIgnment of homologous protein structures MODBASE: A Database of Annotated Comparative Protein Structure Models 3Dee: A Database of Protein Domain Definition PQS: Protein Quaternary Structure Query Form at the EBI LPC/CSU: Ligand-Protein Contacts & Contacts of Structural LPFC: A Library of Protein Family Cores MMDB: Molecular Modelling DataBase,NCBI CE: Databases and Tools for 3-D Protein Structure Comparison and Alignment PDBSUM: Summaries and structural analyses of PDB data files Pfam: Protein families database of alignments and HMMs	Papillomavirus-1 E2 protein	Viral DNA-binding domain	Bovine papillomavirus type 1 [TaxId: 10559]	view
d6vh6a1 # Domain Specific Files ATM file: Atomic coordinates by ASTRAL ATM2ALI file: Amino acid sequences by ATM2ALI SST file: Secondary structure by SSTRUC PSA file: solvent accessibility by PSA HBD file: Hydrogen bonds by HBOND PSE file: PyMol session file for conserved interactions PDBSUM1: Topological diagram d6vh6a1 # Links to other databases and tools RCSB-PDB: Research Collaboratory for Structural Bioinformatics SCOP: Structural Classification of Proteins EBI: European Bioinformatics Institute HOMSTRAD: Homologous Structure Alignment Database DDBASE: Dial-Derived Domain Database CATH: Class Architecture Topology and Homologous sfily PALI: Phylogeny and ALIgnment of homologous protein structures MODBASE: A Database of Annotated Comparative Protein Structure Models 3Dee: A Database of Protein Domain Definition PQS: Protein Quaternary Structure Query Form at the EBI LPC/CSU: Ligand-Protein Contacts & Contacts of Structural LPFC: A Library of Protein Family Cores MMDB: Molecular Modelling DataBase,NCBI CE: Databases and Tools for 3-D Protein Structure Comparison and Alignment PDBSUM: Summaries and structural analyses of PDB data files Pfam: Protein families database of alignments and HMMs	Epstein barr virus nuclear antigen-1 (ebna1)	Viral DNA-binding domain	Epstein-barr virus (strain b95-8) [TaxId: 10377]	view

No outliers

Feature	Download
Superfamily
Distance Matrix
Conserved Interactions
Cusp Results
Alistat - Alignment Statistics
SMotif - Conserved Structural Motifs
MeanRMS
PCSSE Details
Absolutely Conserved Residues
Highly Conserved Residues

									10										20										30										40										50										60										70										80										90										100										110										120										130										140
S	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	S	A	T	P	I	V	Q	F	Q	G	-	E	S	N	C	L	K	C	F	R	Y	R	L	N	D	K	H	R	H	L	F	D	L	I	S	S	T	W	H	W	A	S	P	-	-	-	-	-	-	-	-	-	-	-	K	A	P	H	K	H	A	I	V	T	V	T	Y	H	S	E	E	Q	R	Q	Q	F	L	N	V	V	K	I	P	P	-	-	-	-	-	-	-	-	T	I	R	H	K	L	G	F	M	S	-	-	-	M	H	L	L
-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	S	C	F	A	L	I	S	G	-	T	A	N	Q	V	K	C	Y	R	F	R	V	K	K	N	H	R	H	R	Y	E	N	C	T	T	T	W	F	T	V	A	D	N	-	-	-	-	-	-	-	-	-	G	A	E	R	Q	G	Q	A	Q	I	L	I	T	F	G	S	P	S	Q	R	Q	D	F	L	K	H	V	P	L	P	P	-	-	-	-	-	-	-	-	G	M	N	I	S	G	F	T	A	S	-	-	-	L	D	-	F
G	Q	G	G	S	N	P	K	F	E	N	I	A	E	G	L	R	A	L	L	A	R	S	H	V	E	R	T	T	D	E	G	T	W	V	A	G	V	F	V	Y	G	G	S	K	T	S	L	Y	N	L	R	R	G	T	A	L	A	I	P	Q	C	-	-	R	L	T	P	L	S	R	L	P	F	G	M	A	P	G	P	G	P	Q	P	G	P	L	R	E	S	I	V	C	Y	F	M	V	F	L	Q	T	H	I	F	A	E	V	L	K	D	A	I	K	D	L	V	M	T	K	P	A	P	T	C	N	I	R	V	T	V	C	S	F	D	D	G	V	-	D	L	P

Member	Chain	UniProtKB	GO term
d1r8ha_	A	Q84294	GO:0003677
d1r8ha_	A	Q84294	GO:0003700
d1r8ha_	A	Q84294	GO:0006275
d1r8ha_	A	Q84294	GO:0006355
d1r8ha_	A	Q84294	GO:0042025
d2bopa_	A	P03122	GO:0003677
d2bopa_	A	P03122	GO:0003700
d2bopa_	A	P03122	GO:0006275
d2bopa_	A	P03122	GO:0006355
d2bopa_	A	P03122	GO:0042025

									10										20										30										40										50										60										70										80										90										100										110										120										130										140
S	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	S	A	T	P	I	V	Q	F	Q	G	-	E	S	N	C	L	K	C	F	R	Y	R	L	N	D	K	H	R	H	L	F	D	L	I	S	S	T	W	H	W	A	S	P	-	-	-	-	-	-	-	-	-	-	-	K	A	P	H	K	H	A	I	V	T	V	T	Y	H	S	E	E	Q	R	Q	Q	F	L	N	V	V	K	I	P	P	-	-	-	-	-	-	-	-	T	I	R	H	K	L	G	F	M	S	-	-	-	M	H	L	L
-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	S	C	F	A	L	I	S	G	-	T	A	N	Q	V	K	C	Y	R	F	R	V	K	K	N	H	R	H	R	Y	E	N	C	T	T	T	W	F	T	V	A	D	N	-	-	-	-	-	-	-	-	-	G	A	E	R	Q	G	Q	A	Q	I	L	I	T	F	G	S	P	S	Q	R	Q	D	F	L	K	H	V	P	L	P	P	-	-	-	-	-	-	-	-	G	M	N	I	S	G	F	T	A	S	-	-	-	L	D	-	F
G	Q	G	G	S	N	P	K	F	E	N	I	A	E	G	L	R	A	L	L	A	R	S	H	V	E	R	T	T	D	E	G	T	W	V	A	G	V	F	V	Y	G	G	S	K	T	S	L	Y	N	L	R	R	G	T	A	L	A	I	P	Q	C	-	-	R	L	T	P	L	S	R	L	P	F	G	M	A	P	G	P	G	P	Q	P	G	P	L	R	E	S	I	V	C	Y	F	M	V	F	L	Q	T	H	I	F	A	E	V	L	K	D	A	I	K	D	L	V	M	T	K	P	A	P	T	C	N	I	R	V	T	V	C	S	F	D	D	G	V	-	D	L	P

									10										20										30										40										50										60										70										80										90										100										110										120										130										140
S	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	S	A	T	P	I	V	Q	F	Q	G	-	E	S	N	C	L	K	C	F	R	Y	R	L	N	D	K	H	R	H	L	F	D	L	I	S	S	T	W	H	W	A	S	P	-	-	-	-	-	-	-	-	-	-	-	K	A	P	H	K	H	A	I	V	T	V	T	Y	H	S	E	E	Q	R	Q	Q	F	L	N	V	V	K	I	P	P	-	-	-	-	-	-	-	-	T	I	R	H	K	L	G	F	M	S	-	-	-	M	H	L	L
-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	S	C	F	A	L	I	S	G	-	T	A	N	Q	V	K	C	Y	R	F	R	V	K	K	N	H	R	H	R	Y	E	N	C	T	T	T	W	F	T	V	A	D	N	-	-	-	-	-	-	-	-	-	G	A	E	R	Q	G	Q	A	Q	I	L	I	T	F	G	S	P	S	Q	R	Q	D	F	L	K	H	V	P	L	P	P	-	-	-	-	-	-	-	-	G	M	N	I	S	G	F	T	A	S	-	-	-	L	D	-	F
G	Q	G	G	S	N	P	K	F	E	N	I	A	E	G	L	R	A	L	L	A	R	S	H	V	E	R	T	T	D	E	G	T	W	V	A	G	V	F	V	Y	G	G	S	K	T	S	L	Y	N	L	R	R	G	T	A	L	A	I	P	Q	C	-	-	R	L	T	P	L	S	R	L	P	F	G	M	A	P	G	P	G	P	Q	P	G	P	L	R	E	S	I	V	C	Y	F	M	V	F	L	Q	T	H	I	F	A	E	V	L	K	D	A	I	K	D	L	V	M	T	K	P	A	P	T	C	N	I	R	V	T	V	C	S	F	D	D	G	V	-	D	L	P

									10										20										30										40										50										60										70										80										90										100										110										120										130										140
S	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	S	A	T	P	I	V	Q	F	Q	G	-	E	S	N	C	L	K	C	F	R	Y	R	L	N	D	K	H	R	H	L	F	D	L	I	S	S	T	W	H	W	A	S	P	-	-	-	-	-	-	-	-	-	-	-	K	A	P	H	K	H	A	I	V	T	V	T	Y	H	S	E	E	Q	R	Q	Q	F	L	N	V	V	K	I	P	P	-	-	-	-	-	-	-	-	T	I	R	H	K	L	G	F	M	S	-	-	-	M	H	L	L
-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	S	C	F	A	L	I	S	G	-	T	A	N	Q	V	K	C	Y	R	F	R	V	K	K	N	H	R	H	R	Y	E	N	C	T	T	T	W	F	T	V	A	D	N	-	-	-	-	-	-	-	-	-	G	A	E	R	Q	G	Q	A	Q	I	L	I	T	F	G	S	P	S	Q	R	Q	D	F	L	K	H	V	P	L	P	P	-	-	-	-	-	-	-	-	G	M	N	I	S	G	F	T	A	S	-	-	-	L	D	-	F
G	Q	G	G	S	N	P	K	F	E	N	I	A	E	G	L	R	A	L	L	A	R	S	H	V	E	R	T	T	D	E	G	T	W	V	A	G	V	F	V	Y	G	G	S	K	T	S	L	Y	N	L	R	R	G	T	A	L	A	I	P	Q	C	-	-	R	L	T	P	L	S	R	L	P	F	G	M	A	P	G	P	G	P	Q	P	G	P	L	R	E	S	I	V	C	Y	F	M	V	F	L	Q	T	H	I	F	A	E	V	L	K	D	A	I	K	D	L	V	M	T	K	P	A	P	T	C	N	I	R	V	T	V	C	S	F	D	D	G	V	-	D	L	P