Contacts of the helix formed by residues 682 - 704 (chain G) in PDB entry 4P6X
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 SER 682 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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586G ASN 4.5 2.4 + - - -
587G LEU* 3.8 14.7 - - - -
588G HIS* 2.9 32.0 + - - +
591G ASP* 2.7 12.7 + - - -
680G LEU* 4.5 1.1 - - - -
681G LYS* 1.3 76.6 + - - +
683G GLN* 1.3 63.4 + - - +
684G ALA 3.2 3.3 + - - -
685G LEU* 3.2 11.3 + - - -
686G PHE* 3.0 23.0 + - - +
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Residues in contact with GLN 683 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
695A LYS* 4.2 11.0 - - - +
675G ILE* 3.8 18.3 - - - +
679G GLY* 3.6 7.8 - - - -
680G LEU* 2.8 44.5 + - - +
681G LYS 3.4 3.6 + - - -
682G SER* 1.3 75.4 - - - +
684G ALA* 1.3 57.8 + - - +
686G PHE* 3.4 17.9 - - - +
687G ASP* 2.9 64.1 + - - +
770G LYS* 5.0 3.3 - - - +
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Residues in contact with ALA 684 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
687A ASP 5.1 1.1 - - - +
688A ALA* 4.2 31.4 - - + +
691A MET* 4.2 15.8 - - + +
682G SER 3.2 0.8 - - - -
683G GLN* 1.3 76.7 - - - +
685G LEU* 1.3 66.4 + - - +
687G ASP* 3.2 10.3 + - - +
688G ALA* 3.0 22.2 + - - +
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Residues in contact with LEU 685 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525C LEU* 3.7 25.6 - - + -
583G GLY 3.9 7.2 - - - +
586G ASN* 3.1 40.4 - - + +
587G LEU* 3.8 9.0 - - + -
682G SER* 3.2 14.1 + - - +
684G ALA* 1.3 78.4 - - - +
686G PHE* 1.3 62.0 + - - +
688G ALA* 3.2 8.6 + - + +
689G ILE* 3.1 44.7 + - + +
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Residues in contact with PHE 686 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587G LEU* 3.5 13.5 - - + +
595G LEU* 3.8 27.4 - - + -
672G LEU* 3.5 45.5 - - + -
675G ILE* 3.6 17.3 - - + -
680G LEU* 3.4 24.0 - - + -
682G SER 3.0 13.4 + - - +
683G GLN* 3.4 20.9 - - - +
685G LEU* 1.3 76.0 - - - +
687G ASP* 1.3 80.9 + - - +
689G ILE* 3.0 8.2 + - + +
690G ARG* 2.9 34.0 + - - +
772G LEU* 3.9 15.7 - - + -
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Residues in contact with ASP 687 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
691A MET* 3.8 22.5 - - + +
695A LYS* 3.2 36.9 + - + +
683G GLN* 2.9 44.1 + - - +
684G ALA* 3.2 7.4 + - - +
686G PHE* 1.3 84.6 - - - +
688G ALA* 1.3 57.3 + - - +
690G ARG* 3.9 6.1 - - - +
691G MET* 3.0 32.9 + - + +
772G LEU* 5.9 0.2 - - - +
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Residues in contact with ALA 688 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
691A MET* 3.9 19.9 - - + +
523C ALA 4.6 15.3 - - - +
528C LEU* 5.1 1.1 - - + -
684G ALA 3.0 12.7 + - - +
685G LEU* 3.4 12.6 - - + +
686G PHE 3.1 0.2 - - - -
687G ASP* 1.3 74.2 - - - +
689G ILE* 1.3 61.3 + - + +
691G MET* 3.3 5.3 + - - +
692G THR* 2.9 33.6 + - - +
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Residues in contact with ILE 689 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525C LEU* 5.7 0.4 - - + -
528C LEU* 4.1 13.9 - - + -
581G ILE* 5.2 4.9 - - + -
582G PRO 4.5 4.5 - - - +
583G GLY* 3.3 41.1 - - - +
584G PHE* 3.8 6.7 - - + +
587G LEU* 4.4 12.3 - - + -
672G LEU* 3.7 22.4 - - + -
685G LEU* 3.1 27.0 + - + +
686G PHE* 3.0 7.0 + - - +
688G ALA* 1.3 75.0 - - + +
690G ARG* 1.3 63.8 + - - +
692G THR* 3.1 2.3 + - - -
693G TYR* 3.1 46.5 + - + -
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Residues in contact with ARG 690 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
712A TRP* 5.1 5.1 - - - -
669G LEU* 3.7 13.5 + - + +
672G LEU* 3.1 43.7 + - + +
673G SER* 5.4 3.0 - - - +
686G PHE* 2.9 24.6 + - + +
687G ASP* 3.9 9.4 - - - +
689G ILE* 1.3 76.5 - - - +
691G MET* 1.3 64.4 + - - +
693G TYR 3.2 2.1 + - - +
694G ILE* 3.0 45.8 + - + +
772G LEU* 3.7 39.2 + - - +
773G LEU 4.5 6.5 + - - -
774G PHE* 3.6 33.1 - - - -
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Residues in contact with MET 691 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
691A MET* 5.2 10.1 - - + -
694A ILE* 4.8 12.1 - - + -
695A LYS* 6.0 4.3 - - + -
712A TRP* 4.8 11.7 - - + -
715A PHE* 4.3 30.5 - - + -
687G ASP* 3.0 21.2 + - + +
688G ALA* 3.5 6.7 - - - +
689G ILE 3.3 0.2 - - - -
690G ARG* 1.3 76.4 - - - +
692G THR* 1.3 64.6 + - - +
694G ILE* 3.1 20.4 + - + +
695G LYS* 2.9 46.3 + - + +
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Residues in contact with THR 692 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528C LEU* 3.3 24.6 - - + +
532G LEU* 3.3 31.4 - - + -
688G ALA 2.9 18.8 + - - -
689G ILE 3.4 9.0 - - - -
691G MET* 1.3 77.4 - - - +
693G TYR* 1.3 57.6 + - + +
695G LYS* 3.4 18.7 + - - +
696G GLU* 2.8 25.2 + - - +
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Residues in contact with TYR 693 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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528C LEU* 3.5 21.4 - - + +
532G LEU* 3.9 19.8 + - + +
536G LEU* 4.0 25.9 - - + +
581G ILE* 3.3 27.2 - - + +
582G PRO* 3.3 22.7 - - - +
665G CYS* 4.5 5.8 - - - +
668G VAL* 3.5 26.9 - - + -
669G LEU* 3.7 23.7 - - + +
672G LEU* 4.6 0.4 - - + -
689G ILE* 3.1 39.9 + - + +
690G ARG* 3.2 0.8 + - - -
692G THR* 1.3 74.8 - - - +
694G ILE* 1.3 60.6 + - - +
695G LYS 3.3 0.4 - - - -
696G GLU* 3.6 12.6 - - + +
697G LEU* 2.9 28.4 + - - +
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Residues in contact with ILE 694 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
712A TRP* 3.9 25.4 - - + -
669G LEU* 3.8 16.2 - - + -
690G ARG* 3.0 43.5 + - + +
691G MET* 3.1 18.8 + - + +
693G TYR* 1.3 77.2 - - - +
695G LYS* 1.3 63.7 + - + +
697G LEU* 3.4 5.0 + - - +
698G GLY* 3.1 16.3 + - - -
715G PHE* 3.8 30.6 - - + -
774G PHE* 3.4 29.6 - - + -
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Residues in contact with LYS 695 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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773A LEU 5.2 2.2 + - - -
774A PHE* 3.1 30.8 + - - +
775A HIS* 4.3 14.6 - - + +
776A GLN 5.7 1.0 - - - +
691G MET* 2.9 35.6 + - + +
692G THR* 3.6 20.3 + - - +
694G ILE* 1.3 76.6 - - + +
696G GLU* 1.3 59.5 + - - +
698G GLY* 3.0 4.4 + - - -
699G LYS* 2.8 36.3 + - + +
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Residues in contact with GLU 696 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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531G THR* 2.7 25.3 + - - -
532G LEU* 3.3 27.3 + - + +
533G VAL* 2.8 21.0 + - + +
665G CYS* 3.6 17.9 - - - -
692G THR* 2.8 17.9 + - - +
693G TYR* 3.7 16.2 - - + +
694G ILE 3.3 0.2 - - - -
695G LYS* 1.3 77.8 - - - +
697G LEU* 1.3 61.4 + - - +
699G LYS* 2.9 32.8 + - - +
700G ALA* 3.0 22.5 + - - +
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Residues in contact with LEU 697 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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662G GLU* 3.7 30.1 - - + +
665G CYS* 3.7 15.4 - - + -
666G MET* 3.9 17.5 - - + -
669G LEU* 3.9 20.4 - - + -
693G TYR 2.9 17.7 + - - +
694G ILE* 3.6 5.4 - - - +
696G GLU* 1.3 76.0 - - - +
698G GLY* 1.3 62.0 + - - +
700G ALA* 3.2 2.1 + - - +
701G ILE* 3.1 33.5 + - + +
715G PHE* 4.6 6.1 - - + -
718G LEU* 4.0 23.1 - - + -
719G THR* 4.4 16.2 - - + -
722G LEU* 4.3 8.3 - - + -
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Residues in contact with GLY 698 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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694G ILE 3.1 10.0 + - - -
695G LYS* 3.0 8.7 + - - -
697G LEU* 1.3 77.2 - - - +
699G LYS* 1.3 61.1 + - - +
701G ILE* 3.1 7.8 + - - +
702G VAL* 3.1 30.4 + - - +
715G PHE* 4.5 14.8 - - - -
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Residues in contact with LYS 699 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531G THR* 3.3 21.4 + - - -
533G VAL* 5.4 1.0 - - - +
695G LYS* 2.8 21.5 + - + +
696G GLU* 2.9 36.1 + - - +
698G GLY* 1.3 75.7 - - - +
700G ALA* 1.3 57.1 + - - +
702G VAL* 3.5 5.9 + - - +
703G LYS* 3.0 29.3 + - - +
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Residues in contact with ALA 700 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533G VAL* 5.3 4.7 - - + -
659G SER* 5.0 0.3 + - - -
661G GLU* 4.1 30.6 - - + +
662G GLU* 4.1 18.2 - - + +
665G CYS* 4.3 4.7 - - - -
696G GLU 3.0 12.2 + - - +
697G LEU 3.5 9.0 - - - +
698G GLY 3.2 0.2 - - - -
699G LYS* 1.3 77.1 - - - +
701G ILE* 1.3 61.9 + - - +
703G LYS* 3.4 10.4 + - - +
704G ARG* 3.2 25.8 + - - +
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Residues in contact with ILE 701 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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662G GLU* 3.6 19.7 - - - +
697G LEU* 3.1 17.6 + - + +
698G GLY* 3.1 7.8 + - - +
700G ALA* 1.3 75.8 - - - +
702G VAL* 1.3 65.2 + - + +
703G LYS 3.1 0.2 - - - -
704G ARG* 3.3 18.6 + - - +
705G GLU* 4.1 4.4 + - - +
706G GLY 4.4 0.2 + - - -
711G ASN* 3.6 35.0 - - + +
714G ARG* 4.1 16.8 - - + -
715G PHE* 3.5 43.5 - - + +
718G LEU* 3.6 20.0 - - + -
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Residues in contact with VAL 702 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
698G GLY* 3.1 17.1 + - - +
699G LYS* 4.0 5.8 - - - +
701G ILE* 1.3 77.3 - - + +
703G LYS* 1.3 61.3 + - - +
706G GLY* 3.2 20.2 - - - +
708G SER* 5.5 1.8 - - - +
711G ASN* 3.7 32.5 - - + +
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Residues in contact with LYS 703 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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527G GLN* 5.8 7.6 + - - +
533G VAL* 5.6 8.4 - - + +
661G GLU* 4.1 31.8 + - + +
699G LYS 3.0 19.3 + - - +
700G ALA* 3.7 9.9 - - - +
701G ILE 3.1 0.2 - - - -
702G VAL* 1.3 78.2 - - - +
704G ARG* 1.3 68.1 + - - +
705G GLU 4.9 0.3 - - - -
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Residues in contact with ARG 704 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
656G LEU 4.5 0.8 + - - -
657G GLN* 3.2 28.5 + - - +
659G SER* 3.5 32.9 - - - +
661G GLU* 5.1 3.4 - - - +
662G GLU* 3.9 15.0 + - - +
700G ALA 3.2 19.0 + - - +
701G ILE 3.3 8.3 + - - +
703G LYS* 1.3 84.2 - - - +
705G GLU* 1.3 93.3 + - - +
714G ARG* 3.4 29.5 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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