Contacts of the helix formed by residues 681 - 705 (chain A) in PDB entry 6M0X
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 GLU 681 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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607A PHE 5.1 0.8 + - - -
608A ASP* 5.1 8.5 + - - +
659A LYS* 5.9 3.8 - - - +
680A ILE* 1.3 73.5 - - - +
682A ARG* 1.3 66.6 + - - +
683A ASN 3.0 2.0 - - - -
684A LEU* 2.9 35.3 + - - +
685A VAL* 3.1 16.8 + - - +
10B U 3.3 42.5 + - - +
11B U 3.5 10.7 + - - +
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Residues in contact with ARG 682 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A ALA 4.6 1.2 + - - -
41A GLU* 3.5 50.1 + - - +
44A LEU* 5.5 4.8 - - - +
479A ASN* 4.0 6.5 + - - -
480A PRO* 4.9 2.0 - - - +
481A VAL* 3.4 24.5 - - - +
607A PHE 5.7 1.7 + - - +
680A ILE* 3.2 14.2 - - + +
681A GLU* 1.3 77.4 - - - +
683A ASN* 1.3 63.5 + - - +
685A VAL* 4.6 0.4 - - - +
686A ASP* 3.0 40.2 + - - +
11B U 3.4 39.9 - - - +
12B A 3.5 44.2 + - - +
13B A 4.1 10.3 + - - -
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Residues in contact with ASN 683 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ILE* 3.4 37.2 - - + +
41A GLU* 3.5 8.8 - - - +
680A ILE* 3.2 42.4 + - - +
681A GLU 3.0 0.8 - - - -
682A ARG* 1.3 78.4 - - - +
684A LEU* 1.3 53.4 + - - +
687A THR* 2.3 39.1 + - - +
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Residues in contact with LEU 684 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511A ALA* 4.5 11.4 - - + -
680A ILE 4.0 1.3 + - - +
681A GLU* 2.9 34.2 + - - +
683A ASN* 1.3 78.1 - - - +
685A VAL* 1.3 66.8 + - + +
687A THR* 3.5 5.2 + - - -
688A ARG* 3.1 73.7 + - + +
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Residues in contact with VAL 685 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
681A GLU 3.1 14.3 + - - +
682A ARG 4.0 0.9 - - - +
684A LEU* 1.3 77.5 - - + +
686A ASP* 1.3 63.1 + - - +
688A ARG* 3.4 14.1 + - - +
689A TYR* 2.9 30.2 + - + +
10B U 3.3 42.0 - - + +
11B U 3.9 30.7 - - - +
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Residues in contact with ASP 686 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ILE* 4.4 13.7 - - + -
479A ASN* 3.1 29.3 + - - +
481A VAL* 4.4 8.6 - - + +
482A VAL* 3.3 20.7 - - + +
682A ARG* 3.0 47.7 + - - +
683A ASN* 5.3 0.2 - - - -
685A VAL* 1.3 80.0 - - - +
687A THR* 1.3 60.8 + - - +
689A TYR* 4.1 1.7 - - - +
690A ALA* 2.8 28.2 + - - +
11B U 3.8 11.1 + - - -
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Residues in contact with THR 687 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ILE 3.3 26.2 - - - +
11A GLY* 4.0 9.2 - - - -
12A ILE* 3.3 16.4 + - - +
511A ALA* 6.0 5.4 - - + -
683A ASN* 2.3 29.1 + - - +
684A LEU* 3.9 8.0 - - - -
685A VAL 3.4 0.2 - - - -
686A ASP* 1.3 74.7 - - - +
688A ARG* 1.3 65.4 + - - +
690A ALA* 4.0 3.4 - - - +
691A SER* 3.0 32.3 + - - +
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Residues in contact with ARG 688 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510A MET* 5.0 3.6 - - - +
511A ALA* 3.1 41.4 + - + +
512A ARG* 5.4 0.2 - - - +
513A GLU* 5.1 15.8 + - - +
684A LEU* 3.1 51.4 + - + +
685A VAL* 3.5 13.6 - - - +
687A THR* 1.3 76.5 - - - +
689A TYR* 1.3 62.8 + - - +
691A SER* 4.1 3.2 - - - -
692A ARG* 3.1 26.9 + - - +
9B A 6.2 2.4 - - - -
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Residues in contact with TYR 689 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477A ILE* 3.5 30.0 - - + +
479A ASN* 4.7 12.6 - - + -
482A VAL* 3.6 32.1 - - + -
685A VAL* 2.9 21.0 + - + +
686A ASP* 4.1 1.8 - - - -
687A THR 3.2 0.2 - - - -
688A ARG* 1.3 77.3 - - - +
690A ALA* 1.3 60.9 + - - +
692A ARG* 3.6 4.8 - - + +
693A VAL* 3.1 41.2 + - + +
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Residues in contact with ALA 690 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ILE* 4.3 8.1 - - + -
11A GLY 5.3 1.8 - - - +
482A VAL* 3.8 7.1 - - + +
485A SER* 3.2 30.1 - - - +
486A VAL* 3.4 19.1 - - + +
686A ASP 2.8 21.0 + - - +
687A THR* 4.0 4.7 - - - +
689A TYR* 1.3 74.9 - - - +
691A SER* 1.3 63.3 + - - +
693A VAL 3.3 0.5 + - - -
694A VAL* 3.2 27.7 + - - +
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Residues in contact with SER 691 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ILE* 3.6 34.5 + - - +
508A ILE* 4.3 8.1 - - - +
509A GLU 4.0 12.7 + - - -
510A MET* 4.1 21.1 - - - -
511A ALA 6.0 0.2 - - - -
687A THR* 3.0 21.2 + - - +
688A ARG* 4.1 3.6 - - - -
690A ALA* 1.3 77.3 - - - +
692A ARG* 1.3 62.9 + - - +
694A VAL* 3.4 3.3 + - - +
695A LEU* 3.0 22.2 + - - +
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Residues in contact with ARG 692 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510A MET* 4.2 12.7 - - + +
512A ARG* 3.4 23.8 - - - +
688A ARG 3.1 18.7 + - - +
689A TYR* 3.6 7.0 - - + +
691A SER* 1.3 78.6 - - - +
693A VAL* 1.3 68.6 + - + +
695A LEU* 2.9 15.5 + - - +
696A ASN* 3.0 29.6 + - - +
2B U 3.1 25.9 + - - -
3B G 3.4 28.7 + - - -
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Residues in contact with VAL 693 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473A LEU* 4.3 20.9 - - + +
474A THR* 5.4 1.8 - - + -
477A ILE* 5.5 3.4 - - + -
482A VAL* 5.2 0.4 - - + -
486A VAL* 3.9 27.1 - - + -
689A TYR* 3.1 42.1 + - + +
690A ALA 3.8 3.6 - - - +
692A ARG* 1.3 78.7 - - + +
694A VAL* 1.3 62.8 + - - +
696A ASN* 3.6 4.9 + - - +
697A ALA* 2.9 24.1 + - - +
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Residues in contact with VAL 694 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A LEU* 4.8 4.7 - - + -
10A ILE* 3.7 26.5 - - + -
486A VAL* 3.9 16.8 - - + -
489A ALA* 3.8 17.0 - - + +
490A ILE* 3.5 30.0 - - + +
493A VAL* 5.8 0.2 - - + -
508A ILE* 4.0 10.1 - - + -
690A ALA 3.2 15.0 - - - +
691A SER 3.6 6.5 - - - +
692A ARG 3.2 0.4 - - - -
693A VAL* 1.3 77.6 - - - +
695A LEU* 1.3 63.6 + - - +
697A ALA* 3.8 2.5 - - - +
698A LEU* 3.0 36.8 + - + +
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Residues in contact with LEU 695 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508A ILE* 3.7 16.1 - - + +
510A MET* 4.1 18.8 - - + -
512A ARG* 4.8 0.2 - - - +
691A SER 3.0 12.8 + - - +
692A ARG* 2.9 10.5 + - - +
694A VAL* 1.3 74.9 - - - +
696A ASN* 1.3 73.2 + - - +
698A LEU* 2.8 14.5 + - - +
699A GLN* 3.0 32.1 + - - +
711A VAL* 3.5 29.8 - - + +
712A SER 5.1 0.2 - - - +
713A VAL* 3.5 32.8 - - + -
1B G 4.0 20.6 - - - +
2B U 4.5 1.6 - - - +
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Residues in contact with ASN 696 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
692A ARG* 3.0 40.2 + - - +
693A VAL* 4.0 5.3 - - - +
695A LEU* 1.3 74.3 - - - +
697A ALA* 1.3 63.8 + - - +
698A LEU 3.2 0.2 + - - -
699A GLN* 3.4 19.9 + - - +
700A GLU* 3.1 27.6 + - - +
2B U 3.1 31.3 + - - +
3B G 5.2 1.9 + - - -
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Residues in contact with ALA 697 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468A ILE* 4.8 9.0 - - + +
473A LEU* 3.7 37.7 - - + -
490A ILE* 5.3 2.7 - - + -
693A VAL 2.9 19.9 + - - +
694A VAL* 3.8 4.7 - - - +
696A ASN* 1.3 76.0 - - - +
698A LEU* 1.3 63.2 + - + +
700A GLU* 4.4 6.7 - - - +
701A HIS* 3.1 25.5 + - - +
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Residues in contact with LEU 698 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A LEU* 4.8 4.3 - - + -
468A ILE* 4.4 15.9 - - + -
490A ILE* 5.1 4.3 - - + -
493A VAL* 4.4 23.8 - - + -
506A ILE* 4.4 22.9 - - + -
508A ILE* 3.7 25.1 - - + -
694A VAL* 3.0 30.7 + - + +
695A LEU 2.8 8.6 + - - +
697A ALA* 1.3 75.4 - - + +
699A GLN* 1.3 65.7 + - - +
701A HIS* 3.2 4.2 + - + +
702A PHE* 3.0 49.5 + - + -
711A VAL* 4.3 11.0 - - + -
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Residues in contact with GLN 699 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
695A LEU* 3.0 36.5 + - + +
696A ASN* 3.8 26.1 - - - +
698A LEU* 1.3 73.7 - - - +
700A GLU* 1.3 62.9 + - - +
702A PHE* 3.0 15.3 + - - +
703A ARG* 3.2 22.1 + - + +
711A VAL* 4.2 24.2 - - + +
1B G 2.9 30.4 + - - +
2B U 4.2 5.5 - - - -
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Residues in contact with GLU 700 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
696A ASN* 3.1 15.1 + - - +
697A ALA* 4.4 6.0 - - - +
699A GLN* 1.3 79.5 - - - +
701A HIS* 1.3 61.8 + - - +
703A ARG* 4.2 20.1 + - - +
704A ALA* 3.3 28.5 + - + +
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Residues in contact with HIS 701 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467A TYR* 3.8 37.2 + + - -
468A ILE* 3.8 31.5 - - + +
497A ILE* 6.3 1.6 - - + -
697A ALA 3.1 21.4 + - - +
698A LEU* 3.6 5.8 - - - +
699A GLN 3.1 0.4 - - - -
700A GLU* 1.3 80.7 - - - +
702A PHE* 1.3 77.9 + + + +
704A ALA* 5.1 0.7 - - - -
705A HIS* 3.3 60.5 + + + +
707A ILE* 5.2 4.5 - - + -
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Residues in contact with PHE 702 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468A ILE* 6.0 1.3 - - + -
497A ILE* 4.8 11.7 - - + -
502A ASP* 4.7 5.2 - - - -
506A ILE* 3.9 18.2 - - + -
698A LEU* 3.0 34.8 + - + +
699A GLN* 3.0 7.1 + - - +
701A HIS* 1.3 91.4 - + - +
703A ARG* 1.3 60.3 + - + +
706A LYS* 3.2 5.9 + - - -
707A ILE* 3.1 50.4 + - + +
708A ASP* 3.8 5.6 + - - +
709A THR* 3.3 53.8 - - + +
711A VAL* 3.5 16.6 - - + -
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Residues in contact with ARG 703 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
699A GLN* 3.2 18.9 + - + +
700A GLU* 4.2 17.6 + - - +
701A HIS 3.3 0.2 - - - -
702A PHE* 1.3 80.0 - - + +
704A ALA* 1.3 66.1 + - - +
705A HIS 2.9 4.7 - - - -
706A LYS* 2.9 17.5 + - - +
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Residues in contact with ALA 704 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
700A GLU* 3.3 19.6 + - + +
701A HIS* 5.1 0.2 - - - -
703A ARG* 1.3 80.9 - - - +
705A HIS* 1.3 71.8 + - + +
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Residues in contact with HIS 705 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467A TYR 5.8 4.0 - - - -
701A HIS* 3.3 54.9 + + + +
703A ARG 2.9 0.4 - - - -
704A ALA* 1.3 91.2 + - + +
706A LYS* 1.3 70.3 + - - +
707A ILE* 3.4 22.0 + - + +
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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