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

PDA Analysis Report for 3clc (Protein-DNA Atom Contact Cutoff=4.8 Angstroms)
(Click Here for PDA analysis result for 3clc 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):    DDDDD      CCCCCCBBB       AAAAA   
HELIX  0 CONTACT TYPE (PROTEIN-DNA BASE)       :    MMMMM      MMMMMMMMM       MMMMM   
HELIX  0 DNA CHAIN ID (UPPER STRAND)           :    FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
HELIX  0 DNA SEQUENCE (UPPER STRAND)           : 5' ATGTTgactatAATCACACGgactataAGTCAcat
HELIX  0 BASE-PAIRING TYPE                     :    ...................~...............
HELIX  0 DNA SEQUENCE (LOWER STRAND)           : 3' tacAACTGatattagTGTGCCTGAtattcaGTGTA
HELIX  0 DNA CHAIN ID (LOWER STRAND)           :    EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE
HELIX  0 CONTACT TYPE (PROTEIN-DNA BASE)       :       MMMMM       MMMMMMMMM      MMMMM
HELIX  0 PROTEIN CHAIN ID (CONTACTING DNA BASE):       DDDDD       CCC**BBBB      AAAAA
HELIX  0 MDN: DA27:E D,C
HELIX  0 MDN: DA12:F C,D
HELIX  0 MDN: DG17:E B,C
HELIX  0 MDN: DC16:E B,C
HELIX  0 MDN: DA27:F A,B
PROTEIN
Number of protein chains = 4
Length of protein chains (in aa) = 76 ~ 77
Protein Chains in contact with DNA =

DNA
Number of double-stranded DNA = 1
Lengths of double-stranded DNAs (in bp) = 35 ~ 35
GC content of double-stranded DNAs = 0.535
Number of cracks4 in double-stranded DNAs = 2

PROTEIN-DNA Interactions
Average major/minor groove contact ratio = 1.000
Average base/backbone contact ratio = 0.535
Average number of DNA bases whose major groove is in contact with protein = 38
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 = 38
Average number of nucleotides whose backbone is in contact with protein = 33
Number of double-stranded DNA sides that are blocked by protein = 0.34

OTHER INFORMATION
Deposition date = 2008-03-18
Resolution = 2.80
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)