Web Server of Protein-DNA Complex Structure Analyzer1,2
Last updated on: Feb 20, 2013

PDA Analysis Report for 1gtw (Protein-DNA Atom Contact Cutoff=4.8 Angstroms)
(Click Here for PDA analysis result for 1gtw in text)
PDA analysis







Legends Blue: major groove atoms in contact with protein
Red: minor groove atoms in contact with protein
Yellow: protein residues in contact with DNA bases

Mouse operation Rotation: left click + drag
Translation: shift + left double click + drag
Scale: shift + left click + drag
Menu: right click
Quick Links PDB

PDBSum

CATH

SCOP

MMDB

BIPA

NDB

NPIDB

PDBSWS

OCA

ProNuc

JenaLib


PDAgram
HELIX  0 PROTEIN CHAIN ID (CONTACTING DNA BASE):        AAAA*BBBB    
HELIX  0 CONTACT TYPE (PROTEIN-DNA BASE)       :        MMMMMMMMM    
HELIX  0 DNA CHAIN ID (UPPER STRAND)           :    DDDDDDDDDDDDDDDD 
HELIX  0 DNA SEQUENCE (UPPER STRAND)           : 5' taggATTGCGCCAcat 
HELIX  0 BASE-PAIRING TYPE                     :     ............... 
HELIX  0 DNA SEQUENCE (LOWER STRAND)           : 3'  tcctAACGCGGTGtaa
HELIX  0 DNA CHAIN ID (LOWER STRAND)           :     CCCCCCCCCCCCCCCC
HELIX  0 CONTACT TYPE (PROTEIN-DNA BASE)       :         MMMMMMMMM   
HELIX  0 PROTEIN CHAIN ID (CONTACTING DNA BASE):         AAAA*BBBB   
HELIX  0 MDN: DC10:C A,F
HELIX  0 MDN: DG9:C A,F
HELIX  0 MDN: DC109:D A,B
HELIX  0 MDN: DC8:C A,B
HELIX  0 MDN: DC8:C A,E,F
HELIX  1 PROTEIN CHAIN ID (CONTACTING DNA BASE):        EEEE*FFFF    
HELIX  1 CONTACT TYPE (PROTEIN-DNA BASE)       :        MMMMMMMMM    
HELIX  1 DNA CHAIN ID (UPPER STRAND)           :    HHHHHHHHHHHHHHHH 
HELIX  1 DNA SEQUENCE (UPPER STRAND)           : 5' taggATTGCGCCAcat 
HELIX  1 BASE-PAIRING TYPE                     :     ............... 
HELIX  1 DNA SEQUENCE (LOWER STRAND)           : 3'  tcctAACGCGGTGtaa
HELIX  1 DNA CHAIN ID (LOWER STRAND)           :     GGGGGGGGGGGGGGGG
HELIX  1 CONTACT TYPE (PROTEIN-DNA BASE)       :         MMMMMMMMM   
HELIX  1 PROTEIN CHAIN ID (CONTACTING DNA BASE):         EEEE*FFFF   
HELIX  1 MDN: DC10:G B,E
HELIX  1 MDN: DG9:G B,E
HELIX  1 MDN: DC109:H E,F
HELIX  1 MDN: DC8:G E,F
HELIX  1 MDN: DC8:G E,A,B
PROTEIN
Number of protein chains = 4
Length of protein chains (in aa) = 66 ~ 68
Protein Chains in contact with DNA =

DNA
Number of double-stranded DNA = 2
Lengths of double-stranded DNAs (in bp) = 17 ~ 17
GC content of double-stranded DNAs = 0.514
Number of cracks4 in double-stranded DNAs = 0

PROTEIN-DNA Interactions
Average major/minor groove contact ratio = 1.000
Average base/backbone contact ratio = 0.514
Average number of DNA bases whose major groove is in contact with protein = 18
Average number of DNA bases whose minor groove is in contact with protein = 0
Average number of DNA bases which are in contact with protein = 18
Average number of nucleotides whose backbone is in contact with protein = 17
Number of double-stranded DNA sides that are blocked by protein = 0.47

OTHER INFORMATION
Deposition date = 2002-01-22
Resolution = 1.85
Number of protein-DNA binding units = 2
1Kim R. and Guo, J-T. "PDA: an automatic and comprehensive analysis program for protein-DNA complex structures", BMC Genomics,10(Supple 1):S13, 2009
2This work is supported by the NSF CAREER award DBI-0844749
33DNA v1.5 reference: Xiang-Jun Lu & Wilma K. Olson (2003). Nucleic Acids. Res., 31(17), 5108-5121
4Severe deformation of a double-stranded DNA with a break in its backbone

Department of Bioinformatics and Genomics, 9201 University City Blvd, Charlotte, NC 28223
Contact: ude.ccnu@6mikr, ude.ccnu@4ougj (please reverse the email addresses)