Contacts of the helix formed by residues 690 - 714 (chain C) in PDB entry 6NYY
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 690 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
687B LYS* 3.6 6.5 - - - +
691B GLU* 3.3 13.0 - - - -
694B ALA* 3.4 24.3 + - - -
695B ARG* 3.9 4.5 - - - -
698B ASP* 2.9 15.9 + - - +
687C LYS* 5.2 0.8 - - - +
689C TYR* 1.3 83.1 - - - +
691C GLU* 1.3 60.0 + - - +
692C ALA* 3.5 6.1 + - - +
693C THR* 2.7 32.7 + - - -
694C ALA* 3.0 22.9 + - - +
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Residues in contact with GLU 691 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
691B GLU* 2.5 32.2 + - + +
687C LYS* 6.3 2.0 - - + -
689C TYR 5.5 0.9 - - - +
690C SER* 1.3 71.5 - - - +
692C ALA* 1.3 56.5 + - - +
693C THR 3.2 0.2 - - - -
694C ALA* 3.8 10.0 - - + +
695C ARG* 3.0 26.7 + - - +
686D GLU* 5.6 2.1 - - - +
690D SER* 4.7 3.5 - - - -
691D GLU* 4.3 30.7 + - + +
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Residues in contact with ALA 692 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
691B GLU* 3.6 4.3 + - + +
695B ARG* 3.7 44.6 - - + +
690C SER* 3.2 4.8 + - - +
691C GLU* 1.3 76.5 - - - +
693C THR* 1.3 60.2 + - - +
695C ARG* 3.9 22.0 + - - +
696C LEU* 3.5 17.5 + - - +
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Residues in contact with THR 693 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
698B ASP* 3.5 19.1 - - + +
699B ASP* 5.5 0.9 + - - -
702B ARG* 3.7 21.9 + - - +
670C VAL* 5.2 7.0 - - + -
675C PHE* 5.6 6.3 - - + -
689C TYR* 3.7 19.7 - - + -
690C SER* 2.7 28.1 + - - -
692C ALA* 1.3 77.4 - - - +
694C ALA* 1.3 59.5 + - - +
695C ARG 3.2 0.2 - - - -
696C LEU* 2.9 9.2 + - + +
697C ILE* 2.8 38.8 + - + +
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Residues in contact with ALA 694 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
687C LYS* 3.5 30.1 - - + +
689C TYR* 3.7 19.6 - - + +
690C SER 3.0 12.6 + - - +
691C GLU* 4.1 8.5 - - + +
693C THR* 1.3 73.2 - - - +
695C ARG* 1.3 64.8 + - - +
697C ILE* 3.8 6.2 - - - +
698C ASP* 3.2 21.7 + - - +
690D SER* 3.3 18.5 - - - -
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Residues in contact with ARG 695 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
695B ARG* 4.5 18.6 - - - +
691C GLU 3.0 19.3 + - - +
692C ALA* 4.0 18.8 + - - +
693C THR 3.2 0.2 - - - -
694C ALA* 1.3 77.4 - - - +
696C LEU* 1.3 63.2 + - - +
698C ASP* 4.2 1.1 - - - +
699C ASP* 2.9 46.3 + - - +
690D SER* 3.8 9.6 - - - -
692D ALA* 3.7 32.1 - - + +
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Residues in contact with LEU 696 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
702B ARG* 4.5 21.5 - - - +
669C LYS* 3.8 46.9 - - + +
670C VAL* 4.2 18.4 - - + -
692C ALA 3.5 11.4 + - - +
693C THR* 2.9 11.0 + - + +
695C ARG* 1.3 80.1 - - - +
697C ILE* 1.3 64.1 + - - +
699C ASP* 3.6 8.8 + - + +
700C GLU* 3.2 31.5 + - + +
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Residues in contact with ILE 697 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
658C TYR* 4.0 20.9 - - + -
661C ILE* 4.3 9.1 - - + +
662C VAL* 3.7 31.4 - - + -
670C VAL* 4.3 22.7 - - + -
675C PHE* 5.5 3.6 - - + -
689C TYR* 3.5 41.3 - - + +
693C THR* 2.8 23.5 + - + +
694C ALA* 4.0 5.4 - - - +
695C ARG 3.3 0.2 - - - -
696C LEU* 1.3 76.6 - - - +
698C ASP* 1.3 58.8 + - - +
700C GLU* 2.9 21.8 + - - +
701C VAL* 2.9 15.0 + - + +
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Residues in contact with ASP 698 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
658C TYR* 2.2 43.1 + - - +
687C LYS* 5.0 0.9 + - - -
694C ALA* 3.2 11.7 + - - +
695C ARG 4.4 2.0 - - - +
697C ILE* 1.3 78.1 - - - +
699C ASP* 1.3 63.5 + - - +
700C GLU 3.4 0.2 + - - -
701C VAL* 4.2 3.6 - - - +
702C ARG* 3.4 30.9 + - - +
689D TYR* 3.4 7.2 - - - +
690D SER* 2.7 38.5 + - - +
693D THR* 3.3 21.0 + - - +
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Residues in contact with ASP 699 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
695C ARG* 2.9 40.4 + - - +
696C LEU* 3.9 9.9 - - + +
697C ILE 3.2 0.6 - - - -
698C ASP* 1.3 77.5 - - - +
700C GLU* 1.3 61.6 + - + +
702C ARG* 3.1 25.3 + - - +
703C ILE* 3.2 31.4 + - + +
692D ALA* 6.1 0.5 - - - +
693D THR* 5.5 0.7 + - - -
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Residues in contact with GLU 700 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
661C ILE* 3.7 8.6 - - + +
667C ASN* 3.3 37.7 + - - +
669C LYS* 3.2 40.7 + - + +
670C VAL* 4.7 1.6 - - + -
696C LEU* 3.2 17.9 - - + +
697C ILE* 2.9 9.2 + - - +
699C ASP* 1.3 80.1 - - - +
701C VAL* 1.3 60.4 + - - +
702C ARG 3.2 0.9 - - - -
703C ILE* 3.5 25.5 + - - +
704C LEU* 3.0 27.5 + - - +
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Residues in contact with VAL 701 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
654C THR 4.9 0.4 - - - +
657C ALA* 3.6 35.7 - - + +
658C TYR* 3.7 47.3 - - + +
661C ILE* 4.0 8.1 - - + -
697C ILE* 2.9 20.8 + - + +
698C ASP 4.2 4.5 - - - +
699C ASP 3.7 0.2 - - - -
700C GLU* 1.3 75.2 - - - +
702C ARG* 1.3 58.3 + - - +
704C LEU* 3.1 3.3 + - - +
705C ILE* 2.9 43.9 + - + +
673D ILE* 4.3 9.4 - - + -
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Residues in contact with ARG 702 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
698C ASP* 3.4 21.5 + - - +
699C ASP* 3.1 31.4 + - - +
700C GLU 3.2 0.4 - - - -
701C VAL* 1.3 80.9 - - - +
703C ILE* 1.3 57.4 + - + +
705C ILE* 4.7 2.8 - - - +
706C ASN* 2.6 48.6 + - - +
668D GLU 5.6 0.7 - - - +
669D LYS 3.5 19.9 + - - -
670D VAL* 2.9 26.3 + - - +
671D GLY* 4.7 2.2 - - - -
673D ILE* 4.4 15.4 - - + +
693D THR* 3.6 35.6 + - - +
696D LEU* 3.9 19.2 - - - +
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Residues in contact with ILE 703 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
669C LYS* 5.3 3.8 - - - +
699C ASP* 3.2 20.1 + - + +
700C GLU* 3.5 29.2 + - - +
701C VAL 3.2 0.2 - - - -
702C ARG* 1.3 77.0 - - + +
704C LEU* 1.3 60.4 + - - +
706C ASN* 3.5 3.4 + - - +
707C ASP* 2.9 51.3 + - - +
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Residues in contact with LEU 704 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618C LYS* 5.8 8.3 - - - -
622C LEU* 4.8 15.8 - - + +
625C MET* 4.2 9.4 - - + -
657C ALA* 3.7 32.3 - - + +
660C GLN* 3.3 27.6 - - - +
661C ILE* 4.2 11.9 - - + -
700C GLU 3.0 17.5 + - - +
701C VAL 3.1 4.5 + - - +
703C ILE* 1.3 78.3 - - - +
705C ILE* 1.3 58.2 + - - +
707C ASP* 3.4 9.1 + - + +
708C ALA* 3.0 24.9 + - - +
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Residues in contact with ILE 705 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
625C MET* 3.9 13.9 - - + -
629C LEU* 4.1 9.2 - - + -
653C VAL* 3.7 43.1 - - + +
654C THR* 4.4 3.6 - - - -
657C ALA* 3.9 5.2 - - + -
701C VAL* 2.9 30.0 + - + +
702C ARG* 4.7 2.9 - - - +
704C LEU* 1.3 76.8 - - - +
706C ASN* 1.3 54.5 + - - +
708C ALA* 3.0 3.5 + - - +
709C TYR* 2.5 36.1 + - + +
672D GLN* 4.0 27.6 - - + +
673D ILE* 3.7 27.6 - - + -
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Residues in contact with ASN 706 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
702C ARG* 2.6 39.3 + - - +
703C ILE* 4.0 4.0 - - - +
704C LEU 3.4 0.4 - - - -
705C ILE* 1.3 80.2 - - - +
707C ASP* 1.3 59.5 + - - +
709C TYR* 3.8 15.5 - - + +
710C LYS* 3.0 44.1 + - + +
668D GLU 5.6 2.6 + - - -
671D GLY* 5.0 11.7 - - - -
672D GLN* 5.1 6.9 + - - +
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Residues in contact with ASP 707 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
622C LEU* 5.1 5.0 - - + +
703C ILE* 2.9 39.7 + - - +
704C LEU* 3.7 10.0 - - + +
706C ASN* 1.3 78.8 - - - +
708C ALA* 1.3 60.2 + - - +
710C LYS* 4.4 8.9 + - - +
711C ARG* 3.5 21.8 + - - +
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Residues in contact with ALA 708 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
622C LEU* 3.8 21.2 - - + +
625C MET* 4.0 23.8 - - + -
626C CYS* 3.3 20.6 - - - +
629C LEU* 4.1 7.9 - - + +
704C LEU 3.0 13.3 + - - +
705C ILE* 3.0 9.0 + - - +
707C ASP* 1.3 76.3 - - - +
709C TYR* 1.3 61.1 + - - +
712C THR* 3.1 24.4 + - - -
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Residues in contact with TYR 709 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
629C LEU* 3.8 15.9 - - + -
632C ARG* 5.3 5.1 + - + +
633C VAL* 3.6 25.6 - - + +
636C GLU* 4.0 28.8 + - - +
642C ILE* 5.9 1.4 - - - +
705C ILE* 2.5 20.7 + - + +
706C ASN* 3.8 16.4 - - - +
707C ASP 3.2 0.2 - - - -
708C ALA* 1.3 72.9 - - - +
710C LYS* 1.3 69.7 + - + +
712C THR* 3.2 5.5 + - - -
713C VAL* 3.0 42.9 + - + +
672D GLN* 3.1 44.0 + - - +
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Residues in contact with LYS 710 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
706C ASN* 3.0 29.3 + - + +
707C ASP* 4.5 8.9 + - - +
709C TYR* 1.3 83.7 - - + +
711C ARG* 1.3 56.9 + - - +
713C VAL* 3.9 6.8 - - - +
714C ALA* 3.1 29.5 + - - +
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Residues in contact with ARG 711 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
585C LEU* 3.9 19.3 - - + +
586C GLU 6.0 0.6 - - - +
619C GLU* 5.2 2.2 + - - +
622C LEU* 3.4 28.2 - - - +
623C ASP* 2.8 34.8 + - - -
626C CYS* 3.6 16.6 - - + -
707C ASP 3.5 17.2 + - - +
708C ALA 3.9 5.2 - - - +
709C TYR 3.2 0.8 - - - -
710C LYS* 1.3 78.7 - - - +
712C THR* 1.3 57.0 + - - +
714C ALA* 3.4 5.7 - - - +
715C LEU* 3.1 26.8 + - + +
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Residues in contact with THR 712 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581C ALA* 4.8 3.4 - - + -
626C CYS* 2.8 37.0 + - - +
629C LEU* 4.6 3.1 - - - +
630C GLY* 3.7 24.2 - - - +
633C VAL* 3.8 15.9 - - + +
708C ALA 3.1 13.8 + - - -
709C TYR* 3.2 9.2 + - - -
711C ARG* 1.3 76.5 - - - +
713C VAL* 1.3 58.9 + - - +
715C LEU* 2.9 9.1 + - + +
716C LEU* 2.9 38.2 + - + +
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Residues in contact with VAL 713 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
633C VAL* 3.7 22.0 - - + -
636C GLU* 4.9 10.5 - - - +
637C ILE* 4.5 6.1 - - + +
709C TYR* 3.0 49.7 + - + +
710C LYS* 4.1 6.5 - - - +
712C THR* 1.3 74.4 - - - +
714C ALA* 1.3 57.2 + - - +
715C LEU 3.3 2.3 + - - -
716C LEU 4.2 0.3 - - - -
717C THR* 3.2 29.9 + - + +
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Residues in contact with ALA 714 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
710C LYS 3.1 19.7 + - - +
711C ARG* 3.4 7.0 - - - +
712C THR 3.2 0.2 - - - -
713C VAL* 1.3 74.5 - - - +
715C LEU* 1.3 54.6 + - - +
717C THR* 4.1 8.3 - - + -
718C GLU* 2.9 22.3 - - - +
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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