Contacts of the helix formed by residues 681 - 700 (chain S) in PDB entry 1NVU
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 TYR 681 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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567S MET* 3.7 13.0 - - + -
569S LEU* 3.4 32.7 - - + +
570S PRO* 4.5 3.8 - - + +
575S TYR* 3.6 12.3 - + - -
577S PHE 4.2 6.6 + - - -
578S ALA* 5.3 0.5 - - - -
611S GLU* 5.7 0.2 - - - +
616S HIS* 3.6 36.6 - + + -
647S ARG* 2.6 29.9 + - - -
650S ILE* 3.9 31.0 - - + -
677S PHE* 2.9 38.5 + + + +
679S LYS 3.6 0.2 - - - -
680S GLU* 1.3 81.4 - - - +
682S ILE* 1.3 67.7 + - - +
683S GLN 3.5 0.7 - - - -
684S PRO* 3.6 1.4 - - - +
685S VAL* 3.1 31.8 + - + +
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Residues in contact with ILE 682 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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650S ILE* 4.0 27.8 - - + +
652S GLU* 4.0 27.6 - - + +
677S PHE* 3.1 42.1 + - + +
678S ARG* 3.8 17.5 - - + +
681S TYR* 1.3 75.4 - - - +
683S GLN* 1.3 61.3 + - + +
685S VAL* 3.7 0.3 - - - -
686S GLN* 2.8 64.7 + - + +
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Residues in contact with GLN 683 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63Q GLU 5.6 0.7 - - - +
64Q TYR* 3.6 35.2 - - + -
678S ARG* 2.8 30.6 + - - +
679S LYS* 4.0 22.0 + - - +
682S ILE* 1.3 76.5 - - - +
684S PRO* 1.3 64.2 - - + +
686S GLN* 4.0 3.8 - - - +
687S LEU* 2.9 35.6 + - - +
725S ALA* 5.0 12.9 - - - +
726S MET* 4.7 10.8 - - + +
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Residues in contact with PRO 684 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66Q ALA* 5.7 1.6 - - + -
67Q MET* 3.9 32.8 - - + -
70Q GLN* 5.4 1.1 - - - +
616S HIS* 4.0 20.0 - - + +
679S LYS 3.4 15.9 - - - +
680S GLU* 3.3 24.9 - - - +
681S TYR 3.6 8.7 - - - +
683S GLN* 1.3 96.5 - - + +
685S VAL* 1.3 55.6 + - - +
687S LEU* 3.4 0.7 + - - +
688S ARG* 2.9 43.6 + - - +
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Residues in contact with VAL 685 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
614S THR* 3.7 16.7 - - - +
616S HIS* 3.7 20.4 - - + +
647S ARG* 3.6 53.8 - - + +
650S ILE* 3.7 16.6 - - + -
681S TYR* 3.1 29.9 + - + +
682S ILE 3.8 2.0 - - - +
684S PRO* 1.3 75.6 - - - +
686S GLN* 1.3 58.9 + - - +
688S ARG* 3.3 3.1 + - - +
689S VAL* 2.9 27.4 + - + +
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Residues in contact with GLN 686 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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648S PHE* 2.8 68.9 + - + +
649S GLU* 5.0 0.6 - - - +
650S ILE* 4.4 9.0 + - + +
682S ILE* 2.8 45.1 + - + +
683S GLN* 4.1 3.6 + - - +
685S VAL* 1.3 70.1 - - - +
687S LEU* 1.3 67.0 + - - +
689S VAL* 3.3 2.9 + - - +
690S LEU* 3.0 28.7 + - - +
726S MET* 4.2 17.6 - - - +
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Residues in contact with LEU 687 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36Q ILE* 3.5 18.8 - - + +
64Q TYR* 3.5 42.6 - - + -
67Q MET* 3.8 20.9 - - - -
683S GLN 2.9 19.8 + - - +
684S PRO 3.9 2.9 - - - +
686S GLN* 1.3 76.5 - - - +
688S ARG* 1.3 59.3 + - - +
690S LEU* 3.2 6.7 + - + +
691S ASN* 2.8 28.7 + - - +
726S MET* 3.7 18.2 - - + -
729S TRP* 3.4 42.6 - - + +
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Residues in contact with ARG 688 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36Q ILE* 5.3 0.2 - - + -
37Q GLU* 3.0 37.7 + - - +
67Q MET* 3.1 26.4 - - + +
70Q GLN* 2.8 30.1 + - - +
71Q TYR* 4.4 3.0 - - - -
613S LEU 4.9 3.1 - - - +
614S THR* 4.0 21.5 - - - +
615S TYR 2.9 28.8 + - - +
616S HIS* 3.6 12.5 + - - +
618S TYR 3.3 11.6 + - - -
619S ALA* 3.3 15.8 - - - +
684S PRO* 2.9 22.3 + - - +
685S VAL 3.7 3.4 - - - +
686S GLN 3.2 0.2 - - - -
687S LEU* 1.3 75.8 - - - +
689S VAL* 1.3 64.2 + - - +
691S ASN* 3.2 9.3 + - + +
692S VAL* 3.0 27.5 + - - +
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Residues in contact with VAL 689 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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614S THR* 3.9 12.3 - - + -
644S ILE* 3.7 34.5 - - + +
647S ARG* 3.5 31.4 - - + -
648S PHE* 3.9 24.9 - - + +
685S VAL 2.9 16.7 + - - +
686S GLN 3.6 7.6 - - - +
688S ARG* 1.3 75.4 - - - +
690S LEU* 1.3 65.5 - - - +
692S VAL* 3.1 7.9 + - - +
693S CYS* 3.0 23.2 + - - -
717S PHE* 4.4 8.7 - - + -
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Residues in contact with LEU 690 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36Q ILE* 4.1 8.5 - - + -
648S PHE* 4.0 17.3 - - + -
686S GLN 3.0 15.2 + - - +
687S LEU* 3.2 9.2 + - + +
689S VAL* 1.3 76.9 - - - +
691S ASN* 1.3 62.3 + - - +
693S CYS* 3.2 5.1 + - - +
694S ARG* 3.0 23.6 + - - +
717S PHE* 4.3 12.8 - - + -
718S ILE* 4.2 23.8 - - + -
721S VAL* 4.7 9.0 - - + -
726S MET* 3.9 33.7 - - + +
729S TRP* 4.0 22.9 - - + -
730S VAL* 5.2 3.8 - - + +
733S ILE* 3.6 12.5 - - + +
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Residues in contact with ASN 691 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36Q ILE* 3.5 36.2 + - + +
37Q GLU* 3.4 34.3 + - - +
38Q ASP* 4.2 1.2 - - - +
621S PRO* 5.9 1.0 - - - +
624S VAL* 4.6 15.6 - - - +
687S LEU 2.8 13.6 + - - +
688S ARG* 3.4 12.9 - - - +
689S VAL 3.1 0.2 - - - -
690S LEU* 1.3 77.0 - - - +
692S VAL* 1.3 62.9 + - - +
694S ARG* 3.2 8.1 + - - +
695S HIS* 3.0 53.1 + - - -
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Residues in contact with VAL 692 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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613S LEU* 3.8 44.2 - - + +
614S THR* 4.2 8.1 - - + -
624S VAL* 4.6 16.2 - - + -
628S LEU* 3.9 20.7 - - + +
640S LEU* 5.5 2.0 - - + -
644S ILE* 4.2 21.5 - - + -
688S ARG 3.0 18.3 + - - +
689S VAL* 3.3 9.0 - - - +
691S ASN* 1.3 76.9 - - - +
693S CYS* 1.3 56.6 + - - +
695S HIS* 3.4 0.5 + - - -
696S TRP* 2.8 35.7 + - + +
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Residues in contact with CYS 693 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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644S ILE* 3.7 21.1 - - - -
689S VAL* 3.0 19.4 + - - -
690S LEU* 3.2 10.5 + - - +
692S VAL* 1.3 78.1 - - - +
694S ARG* 1.3 56.2 + - - +
696S TRP* 3.3 7.5 + - - +
697S VAL* 3.0 35.4 + - - +
714S MET* 3.7 31.6 - - - -
717S PHE* 4.0 21.1 - - - -
718S ILE* 4.3 11.2 - - + -
733S ILE* 4.5 3.8 - - + -
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Residues in contact with ARG 694 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33Q ASP* 3.5 34.4 + - - +
34Q PRO 3.8 15.4 + - - -
35Q THR* 4.8 5.3 + - - +
36Q ILE* 4.9 11.1 - - - +
38Q ASP* 3.5 30.9 + - - -
690S LEU 3.0 12.8 + - - +
691S ASN* 3.2 16.7 + - - +
693S CYS* 1.3 76.6 - - - +
695S HIS* 1.3 63.8 + - + +
697S VAL* 3.4 2.6 + - - +
698S GLU* 2.9 55.2 + - - +
729S TRP* 6.0 1.1 - - - -
732S SER* 4.6 5.7 + - - -
733S ILE* 4.1 22.8 - - + +
736S ILE* 4.0 24.5 - - + +
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Residues in contact with HIS 695 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37Q GLU 3.9 4.1 + - - -
38Q ASP* 2.5 38.1 + - + -
39Q SER 5.7 0.4 - - - -
621S PRO* 6.2 2.7 - - + -
624S VAL* 4.2 8.0 - - + +
628S LEU* 3.7 17.7 - - + -
691S ASN* 3.0 48.2 + - - +
692S VAL 3.9 0.4 - - - +
694S ARG* 1.3 83.2 + - + +
696S TRP* 1.3 61.0 + - - +
698S GLU* 4.4 6.1 - - - -
699S HIS* 2.9 35.8 + + - +
700S HIS* 3.6 8.3 - - - -
1047S PO4 2.6 35.0 + - - +
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Residues in contact with TRP 696 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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628S LEU* 3.5 18.3 - - + +
631S TYR* 3.4 20.0 + + - -
632S ARG* 5.0 0.4 - - - -
637S PRO 3.5 21.3 - - - -
640S LEU* 3.3 28.0 - - + -
641S LEU* 3.8 16.6 - - + -
644S ILE* 4.0 22.9 - - + -
692S VAL* 2.8 24.4 + - + +
693S CYS* 3.4 5.2 - - - +
695S HIS* 1.3 76.9 - - - +
697S VAL* 1.3 57.7 + - - +
700S HIS* 3.0 45.6 + - + +
703S ASP* 2.8 24.1 + - - -
704S PHE* 3.4 25.3 - + + -
710S LEU* 4.3 12.8 - - + -
714S MET* 3.7 20.9 - - + -
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Residues in contact with VAL 697 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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693S CYS 3.0 20.1 + - - +
694S ARG* 4.0 3.8 - - - +
696S TRP* 1.3 77.1 - - - +
698S GLU* 1.3 62.8 + - - +
701S PHE* 3.2 34.5 - - + +
704S PHE* 3.9 27.4 - - + -
711S LEU* 5.5 0.7 - - + -
714S MET* 4.3 9.2 - - + -
733S ILE* 5.1 3.6 - - + -
736S ILE* 3.9 17.5 - - + -
737S ILE* 3.7 44.0 - - + -
740S LYS* 3.8 5.8 - - + -
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Residues in contact with GLU 698 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33Q ASP* 4.3 4.9 - - - +
694S ARG* 2.9 42.5 + - - +
695S HIS* 4.1 4.1 + - - +
697S VAL* 1.3 78.8 - - - +
699S HIS* 1.3 90.5 + - + +
736S ILE* 3.0 40.6 - - + +
739S ARG* 4.9 4.6 + - - +
740S LYS* 3.1 31.9 + - - +
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Residues in contact with HIS 699 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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695S HIS* 2.9 18.9 + + - +
698S GLU* 1.3 111.4 + - + +
700S HIS* 1.3 75.6 + - + +
701S PHE 3.7 1.6 - - - -
702S TYR* 5.5 0.5 - - - -
740S LYS* 5.8 0.4 - - - -
800S GLN* 5.5 2.6 - - - +
801S PRO* 6.1 0.9 - - - +
1047S PO4 2.5 33.8 + - - +
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Residues in contact with HIS 700 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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628S LEU* 3.6 37.4 + - + +
629S THR* 3.6 27.0 - - + -
632S ARG* 3.7 17.3 + - - +
695S HIS 3.6 13.2 - - - -
696S TRP* 3.0 23.1 + - + +
699S HIS* 1.3 86.2 + - + +
701S PHE* 1.3 57.0 + - - +
702S TYR* 3.0 26.9 + - + -
703S ASP* 3.3 17.3 + - - +
704S PHE* 4.2 0.2 - - - -
801S PRO* 5.7 8.3 - - + +
1047S PO4 2.6 28.1 + - - -
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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