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  
d3s3na1  (   9 )    daeldqLlqghyikgYpqytyfledgkvkVsrpegvkiIPpqsdrqkiVl
d6vrga1  (   1 )                                             fldgidkAq
                                                                aaaaaa

                             60        70        80        90      
d3s3na1  (  60 )    qaHnlahtgreaTllkIanlywWpnmrkdVvkqlgrcqqclitnasn
d6vrga1  (  10 )    eeHekyhsnwraMasdf----nlp--pvvAkeivascdkcql     
                    aaaa     aaaaaaaa         aaaaaaaa

Domains
Outliers

Domain ID	Name	Family	Source	Domain	STRING-DB
d3s3na1 # 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 d3s3na1 # 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 spumaretrovirus [TaxId: 11963]		view
d6vrga1 # 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 d6vrga1 # 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	N-terminal Zn binding domain of HIV integrase	HIV/SIV integrase, N-terminal Zn binding domain	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										70										80										90
D	A	E	L	D	Q	L	L	Q	G	H	Y	I	K	G	Y	P	Q	Y	T	Y	F	L	E	D	G	K	V	K	V	S	R	P	E	G	V	K	I	I	P	P	Q	S	D	R	Q	K	I	V	L	Q	A	H	N	L	A	H	T	G	R	E	A	T	L	L	K	I	A	N	L	Y	W	W	P	N	M	R	K	D	V	V	K	Q	L	G	R	C	Q	Q	C	L	I	T	N	A	S	N
-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	F	L	D	G	I	D	K	A	Q	E	E	H	E	K	Y	H	S	N	W	R	A	M	A	S	D	F	-	-	-	-	N	L	P	-	-	P	V	V	A	K	E	I	V	A	S	C	D	K	C	Q	L	-	-	-	-	-

Member	Chain	UniProtKB	GO term

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

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

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