Contacts of the helix formed by residues 691 - 709 (chain A) in PDB entry 1OY9
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 GLY 691 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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686A ASP* 5.1 2.4 - - - -
690A LEU* 1.3 77.5 - - - +
692A HIS* 1.3 66.2 + - - -
693A GLU* 3.1 7.2 + - - -
694A LYS* 3.3 17.7 + - - +
695A LEU* 3.1 25.1 + - - +
823A PRO* 5.9 2.2 - - - -
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Residues in contact with HIS 692 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A LYS* 4.2 16.8 - - - +
691A GLY* 1.3 71.0 - - - -
693A GLU* 1.3 62.7 + - + +
695A LEU* 3.7 10.5 + - - +
696A THR* 2.7 54.1 + - + -
721A LEU* 5.0 3.5 - - + +
723A ASP* 4.5 6.1 + - - -
811A TYR 5.9 0.9 - - - -
812A GLY* 4.9 1.5 - - - -
813A SER* 3.3 34.1 + - - -
816A LEU* 4.0 24.0 - - + +
823A PRO* 5.7 8.2 - - + +
825A MET* 3.9 19.5 - - + +
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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
----------------------------------------------------------
691A GLY* 4.9 3.1 - - - -
692A HIS* 1.3 85.3 - - + +
694A LYS* 1.3 73.2 + - + +
696A THR* 3.4 18.5 + - - -
697A GLN* 3.6 7.4 + - - +
811A TYR 5.0 7.1 - - - +
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Residues in contact with LYS 694 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
689A GLY 5.1 1.4 + - - -
690A LEU* 4.1 36.0 - - + +
691A GLY* 3.3 25.0 + - - +
693A GLU* 1.3 80.9 + - + +
695A LEU* 1.3 65.5 + - - +
697A GLN* 3.3 10.1 + - - +
698A ALA* 3.3 18.9 + - - +
855A VAL* 5.7 0.2 - - - +
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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
----------------------------------------------------------
684A LEU* 3.5 37.7 - - + +
686A ASP* 3.3 34.5 - - + +
690A LEU* 5.3 2.1 - - + +
691A GLY 3.1 17.0 + - - +
692A HIS* 3.8 9.2 - - - +
693A GLU 3.3 0.2 - - - -
694A LYS* 1.3 76.1 - - - +
696A THR* 1.3 63.8 + - - +
698A ALA* 3.2 14.7 + - + +
699A ARG 3.2 8.3 + - - -
823A PRO* 3.3 29.6 - - + +
824A SER* 4.4 2.0 - - - +
825A MET* 3.5 20.8 - - + +
855A VAL* 5.1 7.2 - - + -
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Residues in contact with THR 696 (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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692A HIS* 2.7 30.8 + - - -
693A GLU* 3.5 12.0 - - - -
694A LYS 3.2 0.4 - - - -
695A LEU* 1.3 77.0 - - - +
697A GLN* 1.3 56.5 + - - +
699A ARG* 3.4 15.7 + - - +
700A ASN* 2.8 43.4 + - - +
723A ASP* 4.5 15.8 + - - +
825A MET* 3.5 25.0 - - + +
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Residues in contact with GLN 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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693A GLU 3.6 7.2 + - - +
694A LYS* 3.3 11.6 + - - +
695A LEU 3.3 0.6 - - - -
696A THR* 1.3 76.0 - - - +
698A ALA* 1.3 60.2 + - - +
700A ASN* 3.3 18.6 + - - +
701A GLN* 3.1 35.7 + - - +
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Residues in contact with ALA 698 (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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684A LEU* 4.1 6.1 - - + -
694A LYS 3.3 9.1 + - - +
695A LEU 3.2 10.4 + - - +
697A GLN* 1.3 79.0 - - - +
699A ARG* 1.3 57.3 + - - +
701A GLN* 3.3 5.1 + - - +
702A LEU* 3.0 22.9 + - - +
851A LEU* 3.5 13.9 - - + +
852A PRO* 4.6 16.2 - - + -
855A VAL* 4.1 35.0 - - + -
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Residues in contact with ARG 699 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
684A LEU* 3.2 24.9 - - + +
695A LEU 3.2 4.8 + - - +
696A THR* 3.8 14.1 + - - +
697A GLN 3.3 0.2 - - - -
698A ALA* 1.3 75.6 - - - +
700A ASN* 1.3 95.5 + - - +
701A GLN 3.2 0.7 - - - -
702A LEU* 3.7 5.8 - - + -
703A LEU* 3.0 49.6 + - + +
718A PRO* 3.7 33.7 - - - +
721A LEU* 4.3 17.4 + - - +
825A MET* 3.5 38.8 - - + +
827A ILE* 4.3 12.0 - - + +
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Residues in contact with ASN 700 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
696A THR* 2.8 29.1 + - - +
697A GLN* 3.6 25.9 + - - +
699A ARG* 1.3 98.1 + - - +
701A GLN* 1.3 56.8 + - - +
703A LEU* 4.5 6.8 - - - +
704A ALA* 3.0 27.4 + - - +
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Residues in contact with GLN 701 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
697A GLN* 3.1 23.1 + - - +
698A ALA* 3.6 6.3 - - - +
700A ASN* 1.3 77.6 - - - +
702A LEU* 1.3 58.5 + - - +
704A ALA* 3.8 4.9 - - - +
705A GLU* 3.1 38.2 + - + +
850A LYS 4.1 5.9 - - - +
851A LEU* 3.5 24.7 - - + +
852A PRO* 3.9 19.3 - - - +
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Residues in contact with LEU 702 (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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682A PHE* 3.5 29.6 - - + -
684A LEU* 5.3 7.0 - - + -
698A ALA 3.0 16.8 + - - +
699A ARG* 3.4 6.5 + - - +
701A GLN* 1.3 76.0 - - - +
703A LEU* 1.3 86.3 + - + +
704A ALA 3.2 0.2 - - - -
705A GLU* 3.5 3.9 + - - +
706A ALA* 3.3 23.0 + - + +
716A VAL* 6.0 1.3 - - + -
827A ILE* 4.1 21.3 - - + -
844A MET* 4.3 21.8 - - + -
847A LEU* 4.7 6.6 - - + +
848A ALA* 4.3 11.2 - - + +
851A LEU* 4.0 24.4 - - + +
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Residues in contact with LEU 703 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
699A ARG* 3.0 46.2 + - + +
700A ASN* 4.5 6.3 - - - +
702A LEU* 1.3 84.0 - - + +
704A ALA* 1.3 60.4 + - - +
706A ALA* 4.2 2.4 - - - +
707A ALA* 3.6 21.8 + - - +
716A VAL* 4.3 16.2 - - + +
717A ARG* 4.1 22.2 - - - +
718A PRO* 4.0 25.1 - - + -
827A ILE* 3.6 33.0 - - + -
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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
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700A ASN 3.0 22.2 + - - +
701A GLN* 4.0 6.7 - - + +
702A LEU 3.2 0.8 - - - -
703A LEU* 1.3 75.7 - - - +
705A GLU* 1.3 57.1 + - - +
706A ALA 3.3 0.7 - - - -
707A ALA* 3.4 3.8 + - - +
708A LYS* 2.8 36.8 + - - +
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Residues in contact with GLU 705 (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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701A GLN* 3.1 33.2 + - + +
702A LEU* 3.5 4.5 + - - +
704A ALA* 1.3 76.1 - - + +
706A ALA* 1.3 63.2 + - - +
708A LYS* 3.4 30.1 - - - +
709A HIS* 3.0 43.5 + - - -
847A LEU* 3.9 25.1 - - + +
851A LEU* 6.0 1.6 - - + -
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Residues in contact with ALA 706 (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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702A LEU* 3.3 13.3 + - + +
703A LEU 4.3 0.4 - - - +
704A ALA 3.3 0.4 - - - -
705A GLU* 1.3 80.3 - - - +
707A ALA* 1.3 57.6 + - - +
709A HIS 3.3 2.8 - - - -
710A PRO* 3.1 34.0 - - - +
714A THR* 4.3 9.0 + - + +
716A VAL* 3.6 28.9 - - + -
844A MET* 4.6 9.4 - - + -
847A LEU* 3.9 16.5 - - + +
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Residues in contact with ALA 707 (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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703A LEU 3.6 15.6 + - - +
704A ALA* 3.4 5.2 + - - +
706A ALA* 1.3 76.4 - - - +
708A LYS* 1.3 64.2 + - - +
709A HIS 3.3 0.2 - - - -
710A PRO* 3.6 15.4 - - - +
716A VAL* 4.8 5.3 - - + +
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Residues in contact with LYS 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 ALA 2.8 19.1 + - - +
705A GLU* 3.4 34.1 - - - +
707A ALA* 1.3 79.3 - - - +
709A HIS* 1.3 62.3 + - + +
710A PRO* 3.8 2.3 - - - +
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Residues in contact with HIS 709 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
705A GLU* 3.0 35.3 + - - +
706A ALA* 3.3 7.1 - - - +
708A LYS* 1.3 86.4 - - + +
710A PRO* 1.3 63.6 - - - +
846A GLN* 5.1 7.7 + - - -
847A LEU* 4.0 27.7 - - + +
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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) + - + + + + + -
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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