Contacts of the helix formed by residues 682 - 696 (chain A) in PDB entry 5OQN
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 ASP 682 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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675A VAL* 4.8 0.4 - - - -
676A ASP* 3.3 12.4 - - - +
677A GLY 5.6 0.7 + - - -
680A LYS 4.7 5.1 - - - +
681A VAL* 1.3 88.4 - - - +
683A SER* 1.3 65.1 + - - +
684A ILE* 3.2 15.0 + - + +
685A SER* 3.3 18.4 + - - +
686A LEU* 3.8 3.3 + - - +
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Residues in contact with SER 683 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
667A PHE* 6.2 1.1 - - - -
675A VAL* 4.5 14.4 - - - -
676A ASP* 2.6 34.3 + - - -
681A VAL 3.6 0.8 + - - -
682A ASP* 1.3 71.9 - - - +
684A ILE* 1.3 72.5 + - - +
686A LEU* 3.1 8.8 + - - +
687A HIS* 2.9 51.6 + - - -
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Residues in contact with ILE 684 (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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676A ASP* 5.5 0.7 - - - +
682A ASP* 3.1 10.0 - - + -
683A SER* 1.3 92.7 - - - +
685A SER* 1.3 63.0 + - - +
687A HIS* 3.4 13.9 + - + +
688A LYS* 3.0 34.2 + - + +
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Residues in contact with SER 685 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
681A VAL* 4.5 12.3 - - - +
682A ASP* 3.3 18.7 + - - +
683A SER 3.2 0.4 - - - -
684A ILE* 1.3 78.9 - - - +
686A LEU* 1.3 62.1 + - - +
688A LYS* 3.2 10.5 + - - +
689A ILE* 3.1 29.7 + - - +
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Residues in contact with LEU 686 (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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641A MET* 3.7 31.2 - - + +
645A GLY* 5.0 2.0 - - - -
663A ILE* 4.8 17.0 - - + -
667A PHE* 3.8 13.9 - - + -
675A VAL* 3.5 31.4 - - + -
681A VAL* 4.6 13.0 - - + -
682A ASP 4.3 9.2 - - - +
683A SER* 3.1 10.0 + - - +
685A SER* 1.3 74.1 - - - +
687A HIS* 1.3 72.7 + - + +
689A ILE* 3.0 23.6 + - + +
690A PHE* 2.9 34.2 + - + -
719A PHE* 6.1 0.4 - - + -
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Residues in contact with HIS 687 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
683A SER* 2.9 42.9 + - - +
684A ILE* 3.7 14.9 - - + +
686A LEU* 1.3 79.3 - - + +
688A LYS* 1.3 58.7 + - + +
690A PHE* 3.4 7.0 + + - +
691A TYR* 3.0 40.8 + - + -
719A PHE* 4.2 30.3 - + - -
721A ASP* 4.0 30.4 + - + +
724A LEU* 4.2 21.4 - - + +
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Residues in contact with LYS 688 (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 ILE* 3.0 26.4 + - + +
685A SER* 3.4 11.7 - - - +
686A LEU 3.1 0.2 - - - -
687A HIS* 1.3 79.0 - - + +
689A ILE* 1.3 62.3 + - + +
691A TYR* 3.4 23.9 - - + +
692A LYS* 3.1 21.5 + - - +
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Residues in contact with ILE 689 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
645A GLY* 3.4 36.1 - - - +
648A VAL* 3.5 34.8 - - + +
649A SER* 3.8 12.8 - - - +
660A LEU* 5.4 4.0 - - + -
663A ILE* 5.8 2.5 - - + -
685A SER* 3.1 17.4 + - - +
686A LEU* 3.0 22.5 + - + +
688A LYS* 1.3 76.4 - - + +
690A PHE* 1.3 65.1 + - - +
692A LYS* 3.3 6.9 + - + +
693A VAL* 3.1 24.1 + - + +
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Residues in contact with PHE 690 (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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660A LEU* 3.7 30.7 - - + -
663A ILE* 4.9 12.8 - - + -
664A VAL* 4.6 15.3 - - + -
667A PHE* 5.4 2.0 - + - -
686A LEU* 2.9 29.7 + - + -
687A HIS* 3.4 11.6 + + - +
689A ILE* 1.3 78.6 - - - +
691A TYR* 1.3 63.5 + - - +
693A VAL* 4.0 2.7 - - - +
694A LEU* 2.9 27.5 + - - +
706A ALA* 4.8 12.4 - - + +
710A LEU* 3.7 42.0 - - + -
713A LEU* 4.3 13.2 - - + -
719A PHE* 3.6 30.5 - + - -
724A LEU* 5.0 5.2 - - + -
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Residues in contact with TYR 691 (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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687A HIS* 3.0 31.6 + - + +
688A LYS* 3.4 27.8 - - + +
689A ILE 3.2 0.2 - - - -
690A PHE* 1.3 75.3 - - - +
692A LYS* 1.3 57.6 + - - +
694A LEU* 3.7 5.1 - - - +
695A LYS* 2.8 34.5 + - - +
723A ASP* 2.9 31.2 + - - +
724A LEU* 3.5 31.4 - - + -
727A THR* 3.1 26.4 + - + -
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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
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648A VAL 6.0 1.3 - - - +
649A SER* 6.0 6.7 - - - +
688A LYS 3.1 10.2 + - - +
689A ILE* 3.3 10.0 + - + +
691A TYR* 1.3 78.7 - - - +
693A VAL* 1.3 66.5 + - + +
695A LYS* 3.8 17.8 - - + +
696A ASN* 2.9 50.9 + - - +
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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
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648A VAL* 3.7 33.7 - - + +
656A LYS* 4.9 8.5 - - + -
660A LEU* 3.8 13.0 - - + -
689A ILE* 3.1 17.1 + - + +
690A PHE* 4.0 3.4 - - - +
692A LYS* 1.3 79.3 - - + +
694A LEU* 1.3 65.1 + - - +
696A ASN* 3.3 19.8 + - - +
699A LEU 5.3 0.3 - - - +
702A CYS* 3.3 39.6 - - + +
703A GLN* 3.8 6.8 + - - +
706A ALA* 3.6 13.2 - - + -
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Residues in contact with LEU 694 (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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690A PHE 2.9 18.6 + - - +
691A TYR* 3.7 4.7 - - - +
693A VAL* 1.3 78.8 - - - +
695A LYS* 1.3 63.5 + - - +
703A GLN* 3.7 33.2 - - + +
706A ALA* 4.3 9.1 - - + +
707A ALA* 5.0 10.8 - - + +
710A LEU* 4.0 14.4 - - + -
724A LEU* 5.6 3.6 - - + -
727A THR* 4.4 17.5 - - + +
728A LEU* 3.8 28.0 - - + -
731A SER* 3.6 31.9 - - - +
737A ASN* 4.9 4.4 + - - +
743A LEU* 5.2 3.4 - - + -
747A PHE* 5.3 0.2 - - + -
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Residues in contact with LYS 695 (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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691A TYR 2.8 21.9 + - - +
692A LYS* 3.9 19.8 - - + +
694A LEU* 1.3 73.8 - - - +
696A ASN* 1.3 69.9 + - - +
697A ASN* 3.0 7.8 + - - +
703A GLN* 4.1 1.2 + - - -
736A ILE* 5.9 1.0 - - - +
737A ASN* 5.1 2.9 - - - +
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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
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656A LYS* 5.0 7.7 - - - +
692A LYS* 2.9 39.4 + - - +
693A VAL* 3.3 9.8 + - - +
695A LYS* 1.3 74.9 - - - +
697A ASN* 1.3 53.0 + - - +
698A GLY* 2.6 35.8 + - - -
699A LEU* 4.2 27.0 - - + +
703A GLN* 2.3 34.5 + - - +
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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