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

PDA Analysis Report for 1sx5 (Protein-DNA Atom Contact Cutoff=4.8 Angstroms)
(Click Here for PDA analysis result for 1sx5 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

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HELIX  0 PROTEIN CHAIN ID (CONTACTING DNA BASE):    ***A  
HELIX  0 CONTACT TYPE (PROTEIN-DNA BASE)       :    MAAm  
HELIX  0 DNA CHAIN ID (UPPER STRAND)           :    FFFFF 
HELIX  0 DNA SEQUENCE (UPPER STRAND)           : 5' ATCTt 
HELIX  0 BASE-PAIRING TYPE                     :    ..... 
HELIX  0 DNA SEQUENCE (LOWER STRAND)           : 3' TAGAaa
HELIX  0 DNA CHAIN ID (LOWER STRAND)           :    CCCCCC
HELIX  0 CONTACT TYPE (PROTEIN-DNA BASE)       :    AAAM  
HELIX  0 PROTEIN CHAIN ID (CONTACTING DNA BASE):    A**B  
HELIX  0 MDN: DA7:F B,A
HELIX  0 MDN: DA5:C B,A
HELIX  0 MDN: DT8:F A,B
HELIX  0 MDN: DG4:C B,A
HELIX  0 MDN: DC9:F A,B
HELIX  0 MDN: DC9:F B,A
HELIX  0 MDN: DT10:F A,B
HELIX  1 PROTEIN CHAIN ID (CONTACTING DNA BASE):      A**B
HELIX  1 CONTACT TYPE (PROTEIN-DNA BASE)       :      MAAA
HELIX  1 DNA CHAIN ID (UPPER STRAND)           :    EEEEEE
HELIX  1 DNA SEQUENCE (UPPER STRAND)           : 5' aaAGAT
HELIX  1 BASE-PAIRING TYPE                     :     .....
HELIX  1 DNA SEQUENCE (LOWER STRAND)           : 3'  tTCTA
HELIX  1 DNA CHAIN ID (LOWER STRAND)           :     DDDDD
HELIX  1 CONTACT TYPE (PROTEIN-DNA BASE)       :      mAMM
HELIX  1 PROTEIN CHAIN ID (CONTACTING DNA BASE):      B*A*
HELIX  1 MDN: DT10:D A,B
HELIX  1 MDN: DC9:D B,A
HELIX  1 MDN: DC9:D A,B
HELIX  1 MDN: DG4:E A,B
HELIX  1 MDN: DG4:E B,A
HELIX  1 MDN: DA5:E A,B
HELIX  1 MDN: DA7:D A,B
HELIX  1 MDN: DA7:D A,B
PROTEIN
Number of protein chains = 2
Length of protein chains (in aa) = 238 ~ 244
Protein Chains in contact with DNA =

DNA
Number of double-stranded DNA = 2
Lengths of double-stranded DNAs (in bp) = 6 ~ 6
GC content of double-stranded DNAs = 0.421
Number of cracks4 in double-stranded DNAs = 0

PROTEIN-DNA Interactions
Average major/minor groove contact ratio = 0.583
Average base/backbone contact ratio = 0.421
Average number of DNA bases whose major groove is in contact with protein = 7
Average number of DNA bases whose minor groove is in contact with protein = 6
Average number of DNA bases which are in contact with protein = 8
Average number of nucleotides whose backbone is in contact with protein = 11
Number of double-stranded DNA sides that are blocked by protein = 0.17

OTHER INFORMATION
Deposition date = 2004-03-30
Resolution = 1.50
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

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