Contacts of the helix formed by residues 690 - 713 (chain A) in PDB entry 1WZ2
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 ARG 690 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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647A GLU* 2.8 17.1 + - - +
676A TYR* 2.8 21.0 + - - -
688A ASP* 3.8 25.8 - - - +
689A TRP* 1.3 81.7 - - - +
691A ARG* 1.3 66.4 + - - +
692A LYS* 4.7 16.4 - - + +
693A GLU* 2.7 64.4 + - + +
694A VAL* 3.1 14.4 + - - +
927C G 4.9 1.4 + - - -
928C C 4.2 33.7 + - - -
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Residues in contact with ARG 691 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
647A GLU* 2.6 18.5 + - - +
659A LEU* 6.6 0.7 - - - -
667A GLU* 5.1 11.3 + - - -
689A TRP* 4.4 6.1 - - - +
690A ARG* 1.3 67.6 - - - +
692A LYS* 1.3 78.3 - - + +
694A VAL* 2.6 31.6 - - + +
695A GLY* 3.0 6.4 + - - -
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Residues in contact with LYS 692 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
647A GLU* 6.1 1.1 - - - +
690A ARG* 4.7 18.8 - - + +
691A ARG* 1.3 86.7 - - + +
693A GLU* 1.3 67.5 + - - +
695A GLY* 2.9 14.4 + - - -
696A LYS* 3.0 15.5 + - - +
928C C 6.3 2.2 - - - -
929C G 5.4 6.0 + - - +
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Residues in contact with GLU 693 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
676A TYR* 3.3 26.2 + - + +
680A LEU* 3.2 30.8 - - - +
688A ASP 4.2 3.9 - - - +
690A ARG* 2.7 53.3 + - - +
691A ARG 3.3 0.2 - - - -
692A LYS* 1.3 79.3 - - - +
694A VAL* 1.3 57.1 - - - +
696A LYS* 3.6 6.3 + - - +
697A LEU* 3.0 26.7 + - - +
927C G 4.7 12.9 + - - +
928C C 5.6 3.1 - - - -
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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
----------------------------------------------------------
668A ASN* 4.0 25.5 + - + +
672A VAL* 4.1 9.4 - - + +
673A VAL* 5.4 0.4 - - - -
676A TYR* 3.7 40.4 - - + -
689A TRP* 4.0 21.3 - - + +
690A ARG 3.1 10.0 + - - +
691A ARG* 2.6 34.1 - - + +
692A LYS 3.0 0.2 + - - -
693A GLU* 1.3 77.6 - - - +
695A GLY* 1.3 66.4 + - - +
697A LEU* 3.4 2.1 + - - +
698A ARG* 3.0 21.1 + - - +
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Residues in contact with GLY 695 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
668A ASN* 5.2 4.9 - - - -
691A ARG 3.0 9.7 + - - -
692A LYS* 2.9 6.5 + - - -
694A VAL* 1.3 79.9 - - - +
696A LYS* 1.3 57.2 + - - +
698A ARG* 2.8 30.7 + - - +
699A LYS* 3.2 10.5 + - - +
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Residues in contact with LYS 696 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
692A LYS 3.0 15.0 + - - +
693A GLU* 3.8 6.5 - - - +
695A GLY* 1.3 71.7 - - - +
697A LEU* 1.3 65.3 + - - +
698A ARG 2.9 1.7 + - - -
699A LYS* 3.3 8.9 + - + +
700A GLN* 3.0 58.1 + - - +
927C G 5.2 3.8 + - - -
928C C 3.2 29.9 + - - +
942C U 4.9 12.3 - - - +
943C C 5.3 7.7 + - - -
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Residues in contact with LEU 697 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
672A VAL* 4.4 5.6 - - + +
675A LEU* 3.3 30.3 - - + -
676A TYR* 3.1 49.6 - - + +
679A SER* 4.4 5.8 - - - +
693A GLU 3.0 17.5 + - - +
694A VAL 3.8 4.3 - - - +
695A GLY 3.3 0.2 - - - -
696A LYS* 1.3 77.6 - - - +
698A ARG* 1.3 57.5 + - - +
700A GLN* 3.3 9.9 - - + +
701A ILE* 2.9 35.1 + - + +
757A PHE* 4.2 13.7 - - + -
758A TYR* 4.1 18.8 - - + +
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Residues in contact with ARG 698 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A LEU* 2.9 39.8 + - - +
5A ASN* 3.9 8.1 + - - +
6A PHE* 4.3 19.2 - - - -
667A GLU 5.4 1.3 + - - -
668A ASN* 3.3 40.2 + - - +
669A GLY* 5.3 0.2 - - - -
672A VAL* 3.7 22.2 - - + +
694A VAL 3.0 13.1 + - - +
695A GLY* 2.8 18.1 + - - +
697A LEU* 1.3 74.3 - - - +
699A LYS* 1.3 65.7 + - - +
701A ILE* 2.7 20.9 + - + +
702A GLU* 3.0 27.3 + - - +
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Residues in contact with LYS 699 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
695A GLY 3.2 9.0 + - - +
696A LYS* 3.7 9.6 - - - +
698A ARG* 1.3 77.2 - - - +
700A GLN* 1.3 71.5 + - - +
702A GLU* 2.8 32.0 + - - +
703A ARG* 2.9 16.0 + - - +
941C A 2.3 60.1 + - - -
942C U 3.5 23.5 - - - +
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Residues in contact with GLN 700 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
696A LYS* 3.0 56.1 + - - +
697A LEU* 3.3 15.3 - - + +
698A ARG 3.2 0.2 - - - -
699A LYS* 1.3 85.0 - - - +
701A ILE* 1.3 61.0 + - - +
703A ARG* 3.4 8.3 + - - +
704A PHE* 3.0 22.5 + - - +
757A PHE* 4.0 24.0 - - + -
758A TYR* 4.5 15.9 - - + -
761A MET* 4.5 16.0 - - + +
765A ARG* 6.2 1.1 - - - +
942C U 5.2 5.3 + - - -
943C C 4.7 14.6 + - - +
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Residues in contact with ILE 701 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A PHE* 4.6 10.3 - - + -
671A ASP* 5.8 0.2 - - + -
672A VAL* 4.4 23.8 - - + +
675A LEU* 4.0 29.6 - - + -
697A LEU* 2.9 30.5 + - + +
698A ARG* 2.7 20.5 + - + +
700A GLN* 1.3 72.3 - - - +
702A GLU* 1.3 49.6 + - + +
704A PHE* 3.0 9.2 - - + +
705A TYR* 2.7 31.2 + - - +
757A PHE* 4.0 16.4 - - + -
794A MET* 4.6 5.6 - - + -
798A THR* 4.9 4.9 - - + -
801A ILE* 3.6 28.0 - - + -
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Residues in contact with GLU 702 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A LEU* 3.6 48.4 - - + +
6A PHE* 4.6 9.9 - - + -
698A ARG* 3.0 42.3 + - + +
699A LYS* 2.8 20.9 + - - +
701A ILE* 1.3 73.7 - - - +
703A ARG* 1.3 55.5 + - - +
705A TYR* 2.6 29.3 + - - +
706A GLU* 2.7 31.5 + - + +
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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
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699A LYS* 2.9 12.6 + - - +
700A GLN* 3.6 11.0 - - - +
702A GLU* 1.3 75.0 - - - +
704A PHE* 1.3 65.9 + - - +
706A GLU* 3.9 17.9 + - - +
707A LEU* 3.0 46.1 + - + +
761A MET* 3.3 26.8 - - + +
942C U 2.7 56.3 + - - -
943C C 4.1 9.5 + - - -
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Residues in contact with PHE 704 (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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700A GLN 3.0 13.4 + - - +
701A ILE* 3.0 13.5 - - + +
703A ARG* 1.3 79.5 - - - +
705A TYR* 1.3 74.2 + - - +
707A LEU* 3.5 4.3 - - - +
708A ILE* 3.1 40.0 + - + +
757A PHE* 4.0 14.4 - + + -
761A MET* 4.7 2.4 - - - +
790A TRP* 3.5 54.3 - + + -
791A VAL* 4.5 11.2 - - + -
794A MET* 4.1 35.0 - - + -
798A THR* 4.8 1.1 - - - -
801A ILE* 4.4 21.1 - - + -
802A CYS* 4.9 4.0 - - - -
805A LEU* 4.5 9.9 - - + -
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Residues in contact with TYR 705 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A LEU 5.2 5.8 - - - -
6A PHE* 3.7 33.0 - + + -
9A ILE* 3.8 6.9 - - + +
701A ILE 2.7 12.4 + - - +
702A GLU* 2.6 19.3 + - - +
704A PHE* 1.3 75.5 - - + +
706A GLU* 1.3 73.3 + - + +
708A ILE* 3.0 10.6 + - - +
709A SER* 3.2 21.3 + - - -
801A ILE* 3.8 26.7 - - + -
804A GLU* 3.4 23.3 - - + +
805A LEU* 3.3 40.6 - - + +
808A LYS* 3.9 15.1 - - - -
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Residues in contact with GLU 706 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A LEU* 5.9 1.2 + - - +
702A GLU* 2.7 27.2 + - + +
703A ARG* 3.9 20.4 + - - +
705A TYR* 1.3 77.6 - - + +
707A LEU* 1.3 55.9 + - + +
709A SER* 2.6 39.7 + - - -
710A GLN* 2.9 19.0 + - + +
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Residues in contact with LEU 707 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
703A ARG* 3.0 49.3 + - + +
704A PHE* 3.5 5.8 - - - +
706A GLU* 1.3 78.8 - - + +
708A ILE* 1.3 66.4 + - - +
710A GLN* 2.9 27.1 + - - +
711A PHE* 3.1 53.8 + - + -
761A MET* 4.7 9.0 - - + -
764A LEU* 4.3 13.0 - - + -
768A LEU* 4.6 15.3 - - + -
790A TRP* 5.2 6.1 - - + -
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Residues in contact with ILE 708 (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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704A PHE* 3.4 37.2 - - + +
705A TYR 3.0 7.4 + - - +
707A LEU* 1.3 77.4 - - - +
709A SER* 1.3 55.1 + - - +
711A PHE* 3.2 9.8 + - + +
712A ALA* 2.7 35.5 + - + +
787A ALA* 3.9 21.0 - - + +
790A TRP* 4.0 13.0 - - + -
791A VAL* 3.3 25.4 - - + -
805A LEU* 3.7 20.2 - - + +
808A LYS* 5.9 0.2 - - + -
809A LEU* 3.5 29.8 - - + -
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Residues in contact with SER 709 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
705A TYR* 3.2 16.8 + - - -
706A GLU* 2.6 20.4 + - - -
708A ILE* 1.3 74.9 - - - +
710A GLN* 1.3 62.8 + - - +
712A ALA* 2.9 19.2 - - - +
713A GLU* 3.7 10.8 + - - +
805A LEU* 3.4 7.4 - - - +
808A LYS* 3.3 40.1 + - - +
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Residues in contact with GLN 710 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
706A GLU* 2.9 18.5 + - + +
707A LEU* 2.9 24.8 + - - +
709A SER* 1.3 71.6 - - - +
711A PHE* 1.3 64.7 + - + +
712A ALA 2.4 18.2 + - - -
713A GLU* 2.5 32.5 + - - +
714A TYR* 3.6 10.8 + - + +
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Residues in contact with PHE 711 (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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707A LEU* 3.1 45.9 + - + -
708A ILE* 3.7 7.4 - - + +
710A GLN* 1.3 85.1 - - + +
712A ALA* 1.3 61.2 + - - +
713A GLU 3.1 1.1 + - - -
714A TYR* 3.2 29.4 - + - -
764A LEU* 4.1 21.5 - - + -
768A LEU* 4.6 6.3 - - + -
783A LEU* 3.2 63.5 - - + +
784A ARG* 3.1 25.3 - - - +
786A LEU* 4.8 3.4 - - + -
787A ALA* 4.0 15.0 - - + -
790A TRP* 5.7 2.9 - + - -
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Residues in contact with ALA 712 (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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708A ILE 2.7 13.4 + - - +
709A SER* 2.9 22.4 - - - +
710A GLN 2.4 12.1 + - - -
711A PHE* 1.3 68.0 - - - +
713A GLU* 1.3 65.6 + - - +
784A ARG* 3.5 22.7 + - - +
808A LYS* 4.0 32.1 - - + +
809A LEU* 4.3 10.3 - - + -
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Residues in contact with GLU 713 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
709A SER 4.0 8.6 - - - +
710A GLN* 2.5 26.4 + - - +
712A ALA* 1.3 74.0 - - - +
714A TYR* 1.3 78.0 + - + +
715A GLU* 3.4 6.6 + - - +
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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
------------------------------------------------------------
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