Contacts of the helix formed by residues 657 - 676 (chain O) in PDB entry 5G04
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ILE 657 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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479O GLU 3.9 4.5 - - - +
480O GLN* 3.7 31.4 - - + +
481O GLY* 4.7 5.6 - - - -
655O GLY 3.0 3.4 - - - +
656O ALA* 1.3 76.9 - - - +
658O LEU* 1.3 60.0 + - - +
659O ASP 3.0 2.5 - - - +
660O LYS* 3.3 31.9 - - - +
661O GLY* 2.6 28.8 + - - -
700O TYR* 3.4 47.3 - - + +
701O PHE* 5.1 0.2 - - - -
703O LYS* 3.6 23.1 - - + -
704O VAL* 3.6 19.1 - - + -
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Residues in contact with LEU 658 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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517O ASP* 4.6 14.1 - - - +
521O ASN* 4.1 26.5 - - - +
656O ALA* 2.6 19.7 + - + +
657O ILE* 1.3 72.9 - - - +
659O ASP* 1.3 56.2 + - - +
662O ARG* 3.1 47.7 + - - +
701O PHE* 4.1 7.7 - - + -
704O VAL* 4.1 18.6 - - + -
706O CYS* 3.9 27.8 - - - -
709O ARG* 4.0 20.2 - - - +
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Residues in contact with ASP 659 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618O TYR* 4.1 18.5 - - - +
621O SER* 5.5 2.8 - - - -
622O GLU* 4.3 16.2 + - - +
625O LEU* 4.6 4.4 - - - +
651O ILE* 4.5 11.7 - - + +
655O GLY* 4.4 5.1 - - - -
656O ALA* 3.6 35.5 + - - +
657O ILE 3.8 0.4 - - - +
658O LEU* 1.3 78.2 - - - +
660O LYS* 1.3 53.6 - - - +
662O ARG* 2.9 33.8 + - - +
663O ALA* 2.7 36.4 + - - +
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Residues in contact with LYS 660 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367I LYS* 5.9 1.2 - - - +
371I SER* 4.6 1.3 - - - -
480O GLN* 4.2 11.1 + - - -
651O ILE* 3.8 9.2 - - - +
652O LEU* 3.2 57.5 + - + +
653O ALA 3.9 7.1 + - - -
655O GLY 3.8 18.4 + - - +
657O ILE* 3.2 31.2 + - - +
659O ASP* 1.3 78.4 - - - +
661O GLY* 1.3 57.1 + - - +
663O ALA* 3.9 7.1 - - - +
664O MET* 3.3 29.6 + - - +
700O TYR* 3.7 36.7 - - + +
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Residues in contact with GLY 661 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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657O ILE 2.6 20.2 + - - -
660O LYS* 1.3 68.7 - - - +
662O ARG* 1.3 65.5 + - - +
663O ALA 3.1 1.6 + - - -
664O MET 3.1 2.1 + - - -
665O PHE* 2.9 24.3 + - - +
697O ALA* 3.8 6.4 - - - +
700O TYR* 3.6 20.6 - - - +
701O PHE* 3.7 16.8 - - - -
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Residues in contact with ARG 662 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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589O GLU* 4.5 8.9 + - - -
622O GLU* 3.9 30.8 + - - +
625O LEU* 4.8 13.8 - - + +
658O LEU* 3.1 32.7 + - - +
659O ASP* 2.9 35.1 + - - +
661O GLY* 1.3 70.2 - - - +
663O ALA* 1.3 57.5 + - - +
665O PHE* 3.4 8.4 - - + +
666O LEU* 2.9 30.4 + - - +
701O PHE* 3.7 6.9 - - - -
709O ARG* 3.2 45.6 - - - +
755O LEU* 3.7 32.3 - - + +
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Residues in contact with ALA 663 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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625O LEU* 3.6 24.4 - - + +
644O LEU* 4.9 1.6 - - + +
648O ILE* 3.5 21.8 - - + -
651O ILE* 4.1 12.3 - - + -
652O LEU* 5.2 0.4 - - + -
659O ASP 2.7 18.9 + - - +
660O LYS* 3.9 6.1 - - - +
662O ARG* 1.3 70.9 - - - +
664O MET* 1.3 60.2 + - - +
666O LEU* 2.9 8.5 + - - +
667O VAL* 2.9 32.6 + - - +
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Residues in contact with MET 664 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372I TRP* 3.4 39.5 - - + -
648O ILE* 4.3 1.1 - - - -
652O LEU* 3.8 29.8 - - + -
660O LYS 3.3 15.9 + - - +
661O GLY 3.1 4.1 + - - +
663O ALA* 1.3 78.4 - - - +
665O PHE* 1.3 56.6 + - - +
667O VAL* 3.4 19.4 + - - +
668O ALA* 3.0 26.9 + - - +
693O ASN* 4.1 31.1 - - - +
696O GLU* 3.5 34.3 - - + +
697O ALA* 4.2 11.4 - - + +
700O TYR* 4.9 2.5 - - + -
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Residues in contact with PHE 665 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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661O GLY 2.9 17.4 + - - +
662O ARG* 3.4 9.9 - - + +
664O MET* 1.3 77.2 - - - +
666O LEU* 1.3 52.9 + - + +
668O ALA* 3.2 5.4 + - - +
669O LYS* 2.8 61.1 + - + +
694O LEU* 3.4 18.6 - - + -
697O ALA* 3.6 12.8 - - + +
701O PHE* 4.5 12.6 - + + -
709O ARG* 5.8 6.1 - - + -
712O ASP* 3.6 24.0 - - - -
713O VAL* 3.3 35.2 - - + -
716O PHE* 4.3 8.1 - - + -
751O LEU* 4.3 9.6 - - + -
754O HIS* 5.8 5.8 - + - -
755O LEU* 4.5 11.9 - - + -
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Residues in contact with LEU 666 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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625O LEU* 3.5 40.4 - - + +
628O ALA* 4.0 2.2 - - + -
629O PHE* 3.7 38.6 - - + +
632O LEU* 3.9 13.9 - - + -
644O LEU* 3.8 20.8 - - + +
662O ARG 2.9 17.9 + - - +
663O ALA* 2.9 6.5 + - - +
665O PHE* 1.3 75.3 - - + +
667O VAL* 1.3 60.0 + - - +
669O LYS* 3.6 13.1 - - + +
670O CYS* 2.9 28.3 + - - +
755O LEU* 5.2 9.4 - - + -
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Residues in contact with VAL 667 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372I TRP* 3.6 21.1 - - + -
641O LEU* 4.3 11.2 - - + -
644O LEU* 3.8 22.4 - - + -
648O ILE* 3.9 23.3 - - + -
663O ALA 2.9 19.1 + - - +
664O MET* 3.5 15.7 - - - +
665O PHE 3.3 0.2 - - - -
666O LEU* 1.3 73.7 - - - +
668O ALA* 1.3 59.4 + - - +
670O CYS* 3.1 5.6 + - - +
671O GLN* 2.9 36.8 + - - +
693O ASN* 3.1 20.2 - - - +
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Residues in contact with ALA 668 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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664O MET 3.0 13.1 + - - +
665O PHE 3.3 8.5 - - - +
667O VAL* 1.3 74.3 - - - +
669O LYS* 1.3 64.0 + - - +
671O GLN* 3.0 16.9 + - - +
672O VAL* 3.0 20.5 + - - +
690O ALA* 3.5 21.3 - - + +
693O ASN* 3.8 10.9 + - + -
694O LEU* 3.4 26.7 - - + +
716O PHE* 4.4 3.1 - - + -
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Residues in contact with LYS 669 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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629O PHE* 3.6 19.0 - - - -
632O LEU* 4.5 21.7 - - + +
665O PHE* 2.8 56.0 + - + +
666O LEU* 3.6 15.3 - - + +
668O ALA* 1.3 71.5 - - - +
670O CYS* 1.3 60.9 + - - +
672O VAL* 3.9 1.7 + - - +
673O ALA* 3.2 24.3 + - - +
716O PHE* 3.8 26.7 - - + -
751O LEU* 3.1 29.1 - - + +
752O ILE* 4.1 7.9 - - - +
755O LEU 3.6 15.5 + - - +
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Residues in contact with CYS 670 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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628O ALA* 5.2 2.5 - - - -
632O LEU* 4.2 27.1 - - - +
637O PRO* 3.8 22.7 - - - +
640O ALA* 4.2 6.7 - - - -
641O LEU* 3.6 25.4 - - + -
644O LEU* 4.8 7.9 - - + -
666O LEU* 2.9 15.9 + - - +
667O VAL* 3.3 10.3 - - - +
668O ALA 3.0 0.2 + - - -
669O LYS* 1.3 75.2 - - - +
671O GLN* 1.3 56.3 + - - +
673O ALA* 3.1 5.3 + - - +
674O SER* 2.6 38.5 + - - -
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Residues in contact with GLN 671 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372I TRP* 4.0 4.6 - - - -
374I GLN* 3.6 19.5 + - - +
375I LYS* 6.2 0.4 - - - +
641O LEU* 3.6 23.6 - - + +
645O HIS* 5.3 3.2 - - - -
667O VAL* 2.9 27.3 + - - +
668O ALA 3.0 3.6 + - - +
670O CYS* 1.3 71.8 - - - +
672O VAL* 1.3 53.1 + - - +
674O SER* 3.3 6.3 + - - -
675O ALA* 2.8 36.1 + - - +
678O TYR* 5.9 0.2 - - - -
686O ALA* 3.9 9.0 - - - +
687O LEU* 5.1 0.2 - - - -
689O ALA* 4.4 3.5 - - - +
690O ALA* 3.7 30.0 + - + +
693O ASN* 3.3 23.8 + - - -
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Residues in contact with VAL 672 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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668O ALA 3.0 13.7 + - - +
669O LYS 4.1 0.2 - - - +
671O GLN* 1.3 73.3 - - - +
673O ALA* 1.3 61.1 + - - +
675O ALA* 2.9 16.5 + - - +
676O ALA* 3.0 12.1 + - - +
683O LYS* 5.3 2.9 + - - +
687O LEU* 3.8 26.0 - - + -
690O ALA* 4.0 11.4 - - + -
716O PHE* 3.6 26.7 - - + -
720O LEU* 3.5 39.3 - - + -
723O THR* 6.0 2.2 - - + -
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Residues in contact with ALA 673 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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632O LEU* 5.1 12.1 - - + -
637O PRO* 4.0 21.0 - - + +
669O LYS 3.2 17.4 + - - +
670O CYS* 3.1 5.6 + - - +
672O VAL* 1.3 78.1 - - - +
674O SER* 1.3 60.5 + - - +
676O ALA* 3.4 20.1 - - - +
677O SER* 4.4 1.0 + - - -
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Residues in contact with SER 674 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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637O PRO* 3.7 19.2 - - - +
638O GLU* 3.7 28.5 - - - +
641O LEU* 3.5 14.7 - - - +
670O CYS 2.6 26.0 + - - -
671O GLN 3.3 6.2 + - - -
673O ALA* 1.3 72.2 - - - +
675O ALA* 1.3 62.2 + - - +
676O ALA 3.2 1.3 - - - -
677O SER* 3.3 16.2 + - - +
678O TYR* 3.3 20.1 - - - -
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Residues in contact with ALA 675 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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671O GLN 2.8 20.8 + - - +
672O VAL 2.9 7.8 + - - +
674O SER* 1.3 72.5 - - - +
676O ALA* 1.3 58.2 + - - +
677O SER 3.1 2.2 - - - -
678O TYR* 2.9 43.5 + - + +
683O LYS* 3.2 16.8 - - + +
686O ALA* 5.4 7.4 - - + -
687O LEU* 3.6 24.5 - - + -
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Residues in contact with ALA 676 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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672O VAL 3.0 9.1 + - - +
673O ALA* 3.4 16.6 - - - +
674O SER 3.2 0.4 - - - -
675O ALA* 1.3 77.5 - - - +
677O SER* 1.3 59.0 + - - +
678O TYR 3.5 4.5 + - - +
679O ASP* 4.1 5.7 + - - +
683O LYS* 4.1 14.7 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il