Contacts of the helix formed by residues 587 - 610 (chain O) in PDB entry 6CNF
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 ASN 587 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39O GLN* 3.7 10.8 - - - +
40O ARG* 2.8 58.8 - - - +
582O GLU 5.0 0.6 + - - +
583O TRP 2.7 24.5 + - - +
584O ASN* 2.8 6.9 + - - +
586O ALA* 1.3 72.1 - - - +
588O LEU* 1.3 55.2 + - - +
589O LEU 3.0 2.7 - - - -
590O PHE* 2.3 47.5 + - + +
591O LYS* 3.4 17.4 + - - +
314P GLU* 3.9 18.1 + - - +
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Residues in contact with LEU 588 (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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584O ASN* 2.5 46.7 + - + +
585O MET* 5.4 0.2 - - - -
587O ASN* 1.3 74.1 - - - +
589O LEU* 1.3 60.3 + - - +
591O LYS* 3.5 10.6 + - + +
592O LYS* 3.0 22.5 + - - +
633O ARG* 5.3 0.7 - - - +
637O VAL* 3.3 52.1 - - + +
640O ARG* 4.1 9.9 - - + -
641O LEU* 3.5 28.5 - - + +
644O LEU* 6.2 0.2 - - + -
308P GLU* 4.0 30.1 - - + +
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Residues in contact with LEU 589 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48O LEU 4.6 0.7 - - - +
51O GLU* 2.8 48.7 - - + +
52O LEU* 3.6 39.9 - - + +
55O ALA* 3.9 11.7 - - + -
584O ASN 3.5 2.2 + - - -
585O MET* 4.3 11.7 - - - +
586O ALA 4.1 4.0 - - - +
587O ASN 2.7 4.2 + - - -
588O LEU* 1.3 77.0 - - - +
590O PHE* 1.3 54.5 + - - -
592O LYS* 3.1 32.7 - - - +
593O GLU* 2.9 26.3 + - - +
637O VAL* 5.4 0.4 - - - -
641O LEU* 5.7 9.6 - - + -
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Residues in contact with PHE 590 (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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39O GLN* 3.0 40.2 - - + +
47O PHE* 3.1 45.3 - + - -
50O LYS* 6.3 1.6 - - + -
51O GLU* 2.8 45.8 + - + -
54O LYS* 5.1 13.2 - - + -
586O ALA 3.2 10.3 - - - -
587O ASN* 2.3 31.4 + - + +
589O LEU* 1.3 62.9 - - - +
591O LYS* 1.3 53.7 + - + +
592O LYS 2.9 3.8 - - - -
593O GLU* 2.4 13.5 + - + +
594O LYS* 2.3 42.7 + - + -
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Residues in contact with LYS 591 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34O ILE 5.6 4.9 - - - -
35O SER 5.2 1.6 + - - -
39O GLN* 5.8 5.7 + - - +
40O ARG* 3.4 28.9 - - - +
587O ASN* 3.4 22.8 + - - +
588O LEU* 3.5 10.5 + - + +
590O PHE* 1.3 80.1 - - + +
592O LYS* 1.3 60.6 + - - +
594O LYS* 4.0 13.0 - - + -
595O LEU* 3.1 23.9 + - - +
633O ARG* 3.2 25.2 + - - +
307P LYS* 3.9 42.7 + - + +
308P GLU* 5.2 2.9 - - + -
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Residues in contact with LYS 592 (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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55O ALA* 4.5 4.9 + - - +
588O LEU 3.0 14.0 + - - +
589O LEU* 3.1 36.3 - - + +
590O PHE 2.8 0.6 + - - -
591O LYS* 1.3 76.4 - - - +
593O GLU* 1.3 93.1 + - - +
595O LEU* 3.2 12.8 + - - +
596O LYS* 3.3 22.4 + - + +
633O ARG* 4.4 3.2 - - - +
634O GLU* 3.3 26.4 - - - +
637O VAL* 4.0 14.8 - - + -
638O PHE* 3.3 35.0 - - + -
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Residues in contact with GLU 593 (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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51O GLU* 3.6 15.3 - - + +
54O LYS* 5.2 9.7 - - + +
55O ALA* 3.5 30.2 - - + +
589O LEU 2.9 15.9 + - - +
590O PHE* 2.4 17.2 + - + +
592O LYS* 1.3 93.2 + - - +
594O LYS* 1.3 52.1 + - + +
596O LYS* 2.7 35.9 + - - +
597O GLN* 2.7 30.6 + - - +
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Residues in contact with LYS 594 (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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39O GLN* 4.0 22.7 - - - +
590O PHE* 2.3 42.2 + - + +
591O LYS* 4.0 11.4 - - + +
593O GLU* 1.3 69.3 - - + +
595O LEU* 1.3 57.4 + - - +
597O GLN* 3.2 25.3 + - - +
598O GLU* 3.8 13.7 + - - +
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Residues in contact with LEU 595 (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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591O LYS 3.1 16.3 + - - +
592O LYS 3.2 5.7 + - - +
593O GLU 3.1 1.0 - - - -
594O LYS* 1.3 75.4 - - - +
596O LYS* 1.3 66.9 + - - +
597O GLN 3.4 0.2 - - - -
598O GLU* 3.1 37.2 - - + +
599O ASN* 3.6 8.5 + - - +
603O LEU* 5.0 0.2 - - - +
630O VAL* 3.5 24.7 - - + +
633O ARG* 3.4 37.7 - - + +
634O GLU* 3.4 21.8 - - - +
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Residues in contact with LYS 596 (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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592O LYS* 3.3 23.0 + - + +
593O GLU* 2.7 43.0 + - - +
595O LEU* 1.3 71.1 - - - +
597O GLN* 1.3 56.3 + - - +
599O ASN 2.9 4.9 + - - -
600O SER* 2.5 36.5 + - - -
603O LEU* 3.2 33.9 - - + +
634O GLU* 5.3 6.7 - - - +
63Q LYS* 6.1 3.0 - - - +
66Q LYS* 6.2 1.8 - - - +
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Residues in contact with GLN 597 (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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593O GLU* 2.7 35.1 + - - +
594O LYS* 3.2 20.9 - - - +
595O LEU 3.4 0.2 - - - -
596O LYS* 1.3 76.6 - - - +
598O GLU* 1.3 64.6 + - - +
600O SER* 3.5 20.1 + - - -
601O THR* 5.0 1.4 + - - +
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Residues in contact with GLU 598 (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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594O LYS 3.8 6.4 + - - +
595O LEU* 3.1 42.1 - - + +
596O LYS 3.0 0.8 + - - -
597O GLN* 1.3 80.1 - - - +
599O ASN* 1.3 66.0 + - - +
600O SER 3.3 0.4 + - - -
601O THR* 4.4 9.7 - - - +
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Residues in contact with ASN 599 (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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595O LEU* 3.6 4.3 + - - +
596O LYS 2.9 6.3 + - - +
598O GLU* 1.3 85.2 - - - +
600O SER* 1.3 54.7 + - - +
601O THR* 3.2 3.4 - - - -
602O LEU* 2.9 19.3 + - + +
603O LEU* 2.2 56.5 + - + -
626O GLN* 2.7 42.1 + - - +
630O VAL* 3.7 36.6 - - + +
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Residues in contact with SER 600 (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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596O LYS* 2.5 22.9 + - - -
597O GLN* 3.5 22.0 - - - +
598O GLU 3.3 2.4 - - - -
599O ASN* 1.3 69.5 - - - +
601O THR* 1.3 58.7 + - - +
603O LEU* 3.4 11.0 - - - +
604O LYS* 2.9 44.5 + - - +
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Residues in contact with THR 601 (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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597O GLN 5.0 1.1 + - - +
598O GLU 4.4 12.6 - - - +
599O ASN* 4.4 1.8 - - - +
600O SER* 1.3 80.3 + - - +
602O LEU* 1.3 71.5 + - + +
604O LYS* 3.2 19.5 + - - +
605O LYS* 3.2 11.1 + - - +
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Residues in contact with LEU 602 (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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599O ASN* 2.9 25.2 + - + +
601O THR* 1.3 77.9 - - + +
603O LEU* 1.3 57.2 + - + +
605O LYS* 2.9 15.7 + - + +
606O ALA* 2.4 62.6 + - + +
623O GLU* 4.0 27.4 - - + +
626O GLN* 3.2 31.9 - - + +
627O LEU* 4.9 7.0 - - + -
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Residues in contact with LEU 603 (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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596O LYS* 3.2 64.6 - - + +
599O ASN* 2.2 46.4 + - + +
600O SER* 3.4 10.1 - - - +
602O LEU* 1.3 67.3 - - + +
604O LYS* 1.3 61.2 + - - +
606O ALA* 4.7 3.8 - - + -
607O ASN* 2.6 48.0 + - - +
630O VAL* 5.7 9.2 - - + -
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Residues in contact with LYS 604 (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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600O SER* 2.9 29.8 + - - +
601O THR* 3.3 13.2 - - - +
602O LEU 3.1 0.2 - - - -
603O LEU* 1.3 78.5 - - + +
605O LYS* 1.3 62.2 + - - +
607O ASN* 4.3 1.7 - - - +
608O ARG* 3.4 47.1 + - - +
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Residues in contact with LYS 605 (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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601O THR 3.2 7.7 + - - +
602O LEU* 2.9 23.6 + - + +
604O LYS* 1.3 71.9 - - - +
606O ALA* 1.3 66.3 + - - +
607O ASN 3.1 2.2 - - - -
608O ARG* 3.0 20.9 + - - +
609O ASP* 3.0 16.5 + - + +
619O LEU* 4.2 31.2 - - - +
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Residues in contact with ALA 606 (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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602O LEU* 2.4 56.0 + - + +
603O LEU* 4.7 4.3 - - + +
605O LYS* 1.3 70.5 - - - +
607O ASN* 1.3 62.6 + - - +
608O ARG 3.5 0.2 + - - -
609O ASP* 3.6 17.2 + - - +
610O ASP* 4.4 4.3 + - - +
623O GLU* 5.3 5.6 - - - +
627O LEU* 5.4 6.3 - - + -
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Residues in contact with ASN 607 (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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603O LEU* 2.6 43.4 + - - +
604O LYS* 4.3 3.1 - - - +
605O LYS 3.1 1.0 - - - -
606O ALA* 1.3 82.4 - - - +
608O ARG* 1.3 63.3 + - + +
610O ASP 4.4 7.8 + - - +
63Q LYS* 2.8 33.8 + - - +
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Residues in contact with ARG 608 (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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604O LYS* 3.4 40.9 + - - +
605O LYS* 3.0 10.3 + - - +
607O ASN* 1.3 81.0 - - + +
609O ASP* 1.3 65.1 + - - +
610O ASP 3.6 6.1 - - - +
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Residues in contact with ASP 609 (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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605O LYS* 3.0 19.1 + - + +
606O ALA* 3.9 12.3 - - - +
607O ASN 3.4 1.6 - - - -
608O ARG* 1.3 80.1 - - - +
610O ASP* 1.3 76.3 + - - +
619O LEU* 3.2 31.1 - - - +
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Residues in contact with ASP 610 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
606O ALA 4.4 5.0 + - - +
607O ASN 4.4 7.4 + - - +
608O ARG* 3.9 8.5 - - - +
609O ASP* 1.3 99.1 - - - +
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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