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  
d2eiaa1  ( 148 )     pkAqnirQgakepYpeFVdrLlsqIkseghp-------qeiskfltdtl
d3ds2a-  ( 148 )     tsIldirQgpkepFrdYVdrFaktlraeqas-------qevknwmtetl
d3g21a-  ( 150 )    agpwadimQgpsesFvdFAnrLikAVegsdlp-------psarapvIidc
d4bhxa1  (   3 )              t--dseffhqrfrnl----iyvefvgprktliklrnlcld
d4e6sa-  (   1 )              grprpevAhqlfrcf----qyqedmgpraslgrlreLcnh
d4ph0a2  ( 132 )      pwstivQgpaesYveFVnrLqisLadnLpd-------gvpkepiidsl
d6saia1  (   1 )     psfntvrqgskepYpdFvarlqdvAqksiad-------ekarkvivelm
                                  aaaaaaaaaaaaa            aaaaaaaaaaa

                             60        70        80        90        100 
d2eiaa1  ( 190 )    Tiq------nAneeÇrnaMrhlrp----ed-tleeKmyaÇrdig      
d3ds2a-  ( 190 )    Lvq------nAnpdCktiLkalgp----gA-tleemmtaCqgvGg-----
d3g21a-  ( 193 )    Frq------kSqpdiqqlIrtAps----tlttpgeiikyVldrq      
d4bhxa1  (  37 )    wlqpetrtkeeiiellvleqyltiIp-------ekLkpwVrakkPencek
d4e6sa-  (  37 )    wlrpalhtkkqilellvLeqflsvlp-------phvlsrLhgaplrdgee
d4ph0a2  ( 173 )    Sya------nAnkeCqqiLqg---rglvaa-pvgqKlqaCahwa      
d6saia1  (  43 )    Aye------nAnpECqsAikplkgkvpagsdviseYvkaCdgigg-----
                    aaa         aaaaaaa             aaaaaaa           

                             110 
d2eiaa1                        
d3ds2a-  ( 224 )    -pghkarvl  
d3g21a-                        
d4bhxa1  (  80 )    Lvtllenykem
d4e6sa-  (  80 )    Vaqleg     
d4ph0a2                        
d6saia1  (  82 )    -amhkamlmaq

Domains
Outliers

Domain ID	Name	Family	Source	STRING-DB
d2eiaa1 # 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 d2eiaa1 # 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	EIAV capsid protein p26	Retrovirus capsid protein C-terminal domain	Equine infectious anemia virus [TaxId: 11665]	view
d3ds2a- # 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 d3ds2a- # 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	HIV capsid protein, dimerisation domain	Retrovirus capsid protein C-terminal domain	Human immunodeficiency virus 1 [TaxId: 11676]	view
d3g21a- # 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 d3g21a- # 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	automated matches	Retrovirus capsid protein C-terminal domain	Rous sarcoma virus [TaxId: 11888]	view
d4bhxa1 # 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 d4bhxa1 # 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	automated matches	automated matches	Human (Homo sapiens) [TaxId: 9606]	view
d4e6sa- # 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 d4e6sa- # 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	automated matches	automated matches	Mouse (Mus musculus) [TaxId: 10090]	view
d4ph0a2 # 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 d4ph0a2 # 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	automated matches	automated matches	Bovine leukemia virus [TaxId: 11901]	view
d6saia1 # 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 d6saia1 # 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	automated matches	automated matches	Human endogenous retrovirus k [TaxId: 45617]	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

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-	P	K	A	Q	N	I	R	Q	G	A	K	E	P	Y	P	E	F	V	D	R	L	L	S	Q	I	K	S	E	G	H	P	-	-	-	-	-	-	-	Q	E	I	S	K	F	L	T	D	T	L	T	I	Q	-	-	-	-	-	-	N	A	N	E	E	C	R	N	A	M	R	H	L	R	P	-	-	-	-	E	D	-	T	L	E	E	K	M	Y	A	C	R	D	I	G	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-
-	T	S	I	L	D	I	R	Q	G	P	K	E	P	F	R	D	Y	V	D	R	F	A	K	T	L	R	A	E	Q	A	S	-	-	-	-	-	-	-	Q	E	V	K	N	W	M	T	E	T	L	L	V	Q	-	-	-	-	-	-	N	A	N	P	D	C	K	T	I	L	K	A	L	G	P	-	-	-	-	G	A	-	T	L	E	E	M	M	T	A	C	Q	G	V	G	G	-	-	-	-	-	-	P	G	H	K	A	R	V	L	-	-
A	G	P	W	A	D	I	M	Q	G	P	S	E	S	F	V	D	F	A	N	R	L	I	K	A	V	E	G	S	D	L	P	-	-	-	-	-	-	-	P	S	A	R	A	P	V	I	I	D	C	F	R	Q	-	-	-	-	-	-	K	S	Q	P	D	I	Q	Q	L	I	R	T	A	P	S	-	-	-	-	T	L	T	T	P	G	E	I	I	K	Y	V	L	D	R	Q	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-
-	-	-	-	-	-	-	-	-	-	T	-	-	D	S	E	F	F	H	Q	R	F	R	N	L	-	-	-	-	I	Y	V	E	F	V	G	P	R	K	T	L	I	K	L	R	N	L	C	L	D	W	L	Q	P	E	T	R	T	K	E	E	I	I	E	L	L	V	L	E	Q	Y	L	T	I	I	P	-	-	-	-	-	-	-	E	K	L	K	P	W	V	R	A	K	K	P	E	N	C	E	K	L	V	T	L	L	E	N	Y	K	E	M
-	-	-	-	-	-	-	-	-	-	G	R	P	R	P	E	V	A	H	Q	L	F	R	C	F	-	-	-	-	Q	Y	Q	E	D	M	G	P	R	A	S	L	G	R	L	R	E	L	C	N	H	W	L	R	P	A	L	H	T	K	K	Q	I	L	E	L	L	V	L	E	Q	F	L	S	V	L	P	-	-	-	-	-	-	-	P	H	V	L	S	R	L	H	G	A	P	L	R	D	G	E	E	V	A	Q	L	E	G	-	-	-	-	-
-	-	P	W	S	T	I	V	Q	G	P	A	E	S	Y	V	E	F	V	N	R	L	Q	I	S	L	A	D	N	L	P	D	-	-	-	-	-	-	-	G	V	P	K	E	P	I	I	D	S	L	S	Y	A	-	-	-	-	-	-	N	A	N	K	E	C	Q	Q	I	L	Q	G	-	-	-	R	G	L	V	A	A	-	P	V	G	Q	K	L	Q	A	C	A	H	W	A	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-
-	P	S	F	N	T	V	R	Q	G	S	K	E	P	Y	P	D	F	V	A	R	L	Q	D	V	A	Q	K	S	I	A	D	-	-	-	-	-	-	-	E	K	A	R	K	V	I	V	E	L	M	A	Y	E	-	-	-	-	-	-	N	A	N	P	E	C	Q	S	A	I	K	P	L	K	G	K	V	P	A	G	S	D	V	I	S	E	Y	V	K	A	C	D	G	I	G	G	-	-	-	-	-	-	A	M	H	K	A	M	L	M	A	Q

Member	Chain	UniProtKB	GO term
d2eiaa1	A	P69732	GO:0016032
d2eiaa1	A	P69732	GO:0016032

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-	P	K	A	Q	N	I	R	Q	G	A	K	E	P	Y	P	E	F	V	D	R	L	L	S	Q	I	K	S	E	G	H	P	-	-	-	-	-	-	-	Q	E	I	S	K	F	L	T	D	T	L	T	I	Q	-	-	-	-	-	-	N	A	N	E	E	C	R	N	A	M	R	H	L	R	P	-	-	-	-	E	D	-	T	L	E	E	K	M	Y	A	C	R	D	I	G	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-
-	T	S	I	L	D	I	R	Q	G	P	K	E	P	F	R	D	Y	V	D	R	F	A	K	T	L	R	A	E	Q	A	S	-	-	-	-	-	-	-	Q	E	V	K	N	W	M	T	E	T	L	L	V	Q	-	-	-	-	-	-	N	A	N	P	D	C	K	T	I	L	K	A	L	G	P	-	-	-	-	G	A	-	T	L	E	E	M	M	T	A	C	Q	G	V	G	G	-	-	-	-	-	-	P	G	H	K	A	R	V	L	-	-
A	G	P	W	A	D	I	M	Q	G	P	S	E	S	F	V	D	F	A	N	R	L	I	K	A	V	E	G	S	D	L	P	-	-	-	-	-	-	-	P	S	A	R	A	P	V	I	I	D	C	F	R	Q	-	-	-	-	-	-	K	S	Q	P	D	I	Q	Q	L	I	R	T	A	P	S	-	-	-	-	T	L	T	T	P	G	E	I	I	K	Y	V	L	D	R	Q	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-
-	-	-	-	-	-	-	-	-	-	T	-	-	D	S	E	F	F	H	Q	R	F	R	N	L	-	-	-	-	I	Y	V	E	F	V	G	P	R	K	T	L	I	K	L	R	N	L	C	L	D	W	L	Q	P	E	T	R	T	K	E	E	I	I	E	L	L	V	L	E	Q	Y	L	T	I	I	P	-	-	-	-	-	-	-	E	K	L	K	P	W	V	R	A	K	K	P	E	N	C	E	K	L	V	T	L	L	E	N	Y	K	E	M
-	-	-	-	-	-	-	-	-	-	G	R	P	R	P	E	V	A	H	Q	L	F	R	C	F	-	-	-	-	Q	Y	Q	E	D	M	G	P	R	A	S	L	G	R	L	R	E	L	C	N	H	W	L	R	P	A	L	H	T	K	K	Q	I	L	E	L	L	V	L	E	Q	F	L	S	V	L	P	-	-	-	-	-	-	-	P	H	V	L	S	R	L	H	G	A	P	L	R	D	G	E	E	V	A	Q	L	E	G	-	-	-	-	-
-	-	P	W	S	T	I	V	Q	G	P	A	E	S	Y	V	E	F	V	N	R	L	Q	I	S	L	A	D	N	L	P	D	-	-	-	-	-	-	-	G	V	P	K	E	P	I	I	D	S	L	S	Y	A	-	-	-	-	-	-	N	A	N	K	E	C	Q	Q	I	L	Q	G	-	-	-	R	G	L	V	A	A	-	P	V	G	Q	K	L	Q	A	C	A	H	W	A	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-
-	P	S	F	N	T	V	R	Q	G	S	K	E	P	Y	P	D	F	V	A	R	L	Q	D	V	A	Q	K	S	I	A	D	-	-	-	-	-	-	-	E	K	A	R	K	V	I	V	E	L	M	A	Y	E	-	-	-	-	-	-	N	A	N	P	E	C	Q	S	A	I	K	P	L	K	G	K	V	P	A	G	S	D	V	I	S	E	Y	V	K	A	C	D	G	I	G	G	-	-	-	-	-	-	A	M	H	K	A	M	L	M	A	Q

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

									10										20										30										40										50										60										70										80										90										100										110
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