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  
d3s3na3  ( 316 )    sPvvgqlVqervarpaslrprwhkpstVlkvlnprtVvIldhlG-nnrtv
d4fw1a2  ( 217 )    vlteGppVkIriet-----gewekgWnVlvw-grgyAAVknrdtdkviwv
d6t6ea1  ( 219 )    hi-qnFrvyYrdsrd----pvwkGpAkllwk-gegavviqdn--sdikvv
                          bbbb               bbbbbb    bbbbb      bbbb

                             60  
d3s3na3  ( 365 )    sidnLkptshq
d4fw1a2  ( 261 )    psrkVkpdi  
d6t6ea1  ( 261 )    prrkAkiird 
                    b333bbb

Domains
Outliers

Domain ID	Name	Family	Source	STRING-DB
d3s3na3 # 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 d3s3na3 # 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	DNA-binding domain of retroviral integrase	DNA-binding domain of retroviral integrase	Human spumaretrovirus [TaxID:11963]	view
d4fw1a2 # 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 d4fw1a2 # 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	Rous sarcoma virus [TaxId: 11888]	view
d6t6ea1 # 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 d6t6ea1 # 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	DNA-binding domain of retroviral integrase	DNA-binding domain of retroviral integrase	Human immunodeficiency virus type 1 [TaxId: 11676]	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
S	P	V	V	G	Q	L	V	Q	E	R	V	A	R	P	A	S	L	R	P	R	W	H	K	P	S	T	V	L	K	V	L	N	P	R	T	V	V	I	L	D	H	L	G	-	N	N	R	T	V	S	I	D	N	L	K	P	T	S	H	Q
V	L	T	E	G	P	P	V	K	I	R	I	E	T	-	-	-	-	-	G	E	W	E	K	G	W	N	V	L	V	W	-	G	R	G	Y	A	A	V	K	N	R	D	T	D	K	V	I	W	V	P	S	R	K	V	K	P	D	I	-	-
H	I	-	Q	N	F	R	V	Y	Y	R	D	S	R	D	-	-	-	-	P	V	W	K	G	P	A	K	L	L	W	K	-	G	E	G	A	V	V	I	Q	D	N	-	-	S	D	I	K	V	V	P	R	R	K	A	K	I	I	R	D	-

Member	Chain	UniProtKB	GO term

									10										20										30										40										50										60
S	P	V	V	G	Q	L	V	Q	E	R	V	A	R	P	A	S	L	R	P	R	W	H	K	P	S	T	V	L	K	V	L	N	P	R	T	V	V	I	L	D	H	L	G	-	N	N	R	T	V	S	I	D	N	L	K	P	T	S	H	Q
V	L	T	E	G	P	P	V	K	I	R	I	E	T	-	-	-	-	-	G	E	W	E	K	G	W	N	V	L	V	W	-	G	R	G	Y	A	A	V	K	N	R	D	T	D	K	V	I	W	V	P	S	R	K	V	K	P	D	I	-	-
H	I	-	Q	N	F	R	V	Y	Y	R	D	S	R	D	-	-	-	-	P	V	W	K	G	P	A	K	L	L	W	K	-	G	E	G	A	V	V	I	Q	D	N	-	-	S	D	I	K	V	V	P	R	R	K	A	K	I	I	R	D	-

									10										20										30										40										50										60
S	P	V	V	G	Q	L	V	Q	E	R	V	A	R	P	A	S	L	R	P	R	W	H	K	P	S	T	V	L	K	V	L	N	P	R	T	V	V	I	L	D	H	L	G	-	N	N	R	T	V	S	I	D	N	L	K	P	T	S	H	Q
V	L	T	E	G	P	P	V	K	I	R	I	E	T	-	-	-	-	-	G	E	W	E	K	G	W	N	V	L	V	W	-	G	R	G	Y	A	A	V	K	N	R	D	T	D	K	V	I	W	V	P	S	R	K	V	K	P	D	I	-	-
H	I	-	Q	N	F	R	V	Y	Y	R	D	S	R	D	-	-	-	-	P	V	W	K	G	P	A	K	L	L	W	K	-	G	E	G	A	V	V	I	Q	D	N	-	-	S	D	I	K	V	V	P	R	R	K	A	K	I	I	R	D	-

									10										20										30										40										50										60
S	P	V	V	G	Q	L	V	Q	E	R	V	A	R	P	A	S	L	R	P	R	W	H	K	P	S	T	V	L	K	V	L	N	P	R	T	V	V	I	L	D	H	L	G	-	N	N	R	T	V	S	I	D	N	L	K	P	T	S	H	Q
V	L	T	E	G	P	P	V	K	I	R	I	E	T	-	-	-	-	-	G	E	W	E	K	G	W	N	V	L	V	W	-	G	R	G	Y	A	A	V	K	N	R	D	T	D	K	V	I	W	V	P	S	R	K	V	K	P	D	I	-	-
H	I	-	Q	N	F	R	V	Y	Y	R	D	S	R	D	-	-	-	-	P	V	W	K	G	P	A	K	L	L	W	K	-	G	E	G	A	V	V	I	Q	D	N	-	-	S	D	I	K	V	V	P	R	R	K	A	K	I	I	R	D	-