Contacts of the helix formed by residues 684 - 696 (chain A) in PDB entry 2OD1
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 684 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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672A GLU* 3.5 9.1 + - - -
682A TYR* 3.5 1.6 - - - +
683A CYS* 1.3 86.1 - - - +
685A SER* 1.3 61.7 + - - -
686A PHE* 3.3 16.8 - - - -
687A CYS* 3.5 3.6 + - - +
688A GLN* 2.7 34.6 + - - +
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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
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672A GLU* 4.0 5.1 + - - -
684A GLY* 1.3 69.4 - - - -
686A PHE* 1.3 67.6 - - - +
688A GLN* 3.1 17.3 + - - +
689A HIS* 3.1 42.7 + - - -
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Residues in contact with PHE 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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665A ASN* 5.2 1.8 - - - -
666A CYS* 4.9 3.8 - - - -
683A CYS* 4.0 11.7 - - - -
684A GLY* 4.0 15.0 - - - -
685A SER* 1.3 83.6 - - - +
687A CYS* 1.3 92.9 + - - +
689A HIS* 2.9 13.2 + - - +
690A LYS* 2.9 48.2 + - + +
901A ZN 4.6 0.2 - - - -
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Residues in contact with CYS 687 (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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663A CYS* 3.8 0.7 - - - -
665A ASN* 3.5 20.2 - - + +
666A CYS* 3.5 1.1 - - - -
682A TYR* 3.6 16.3 - - + -
684A GLY 3.5 11.4 + - - +
685A SER 3.3 0.6 - - - -
686A PHE* 1.3 109.2 - - + +
688A GLN* 1.3 62.0 + - - +
690A LYS* 3.8 5.6 - - - +
691A ASP* 3.1 30.2 + - - +
901A ZN 2.3 37.7 - - - -
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Residues in contact with GLN 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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672A GLU* 3.0 30.0 + - - +
673A THR 4.7 12.5 + - - -
674A CYS* 5.0 4.8 - - - +
675A SER* 5.6 3.4 + - - -
682A TYR* 3.1 39.2 - - + -
684A GLY 2.7 23.6 + - - +
685A SER* 3.1 14.9 + - - +
686A PHE 3.1 0.4 - - - -
687A CYS* 1.3 77.1 - - - +
689A HIS* 1.3 56.0 + - + +
691A ASP* 3.6 0.5 - - - +
692A TRP* 2.6 40.4 + - - +
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Residues in contact with HIS 689 (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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685A SER* 3.1 33.4 + - - -
686A PHE* 2.9 11.2 + - - +
688A GLN* 1.3 80.5 - - + +
690A LYS* 1.3 68.3 + - + +
692A TRP* 3.3 31.1 + + + +
693A GLU* 3.8 5.4 + - - +
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Residues in contact with LYS 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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665A ASN* 5.3 7.2 - - - +
686A PHE* 2.9 34.9 + - + +
687A CYS* 3.8 7.4 - - - +
688A GLN 3.4 0.2 - - - -
689A HIS* 1.3 81.6 - - - +
691A ASP* 1.3 65.8 + - - +
693A GLU* 4.1 2.8 + - - +
694A LYS* 3.3 24.7 - - - +
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Residues in contact with ASP 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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664A TRP* 3.8 23.6 - - - +
665A ASN* 3.3 25.0 - - - +
682A TYR* 3.1 41.1 - - + +
687A CYS 3.1 5.6 + - - +
690A LYS* 1.3 77.8 - - - +
692A TRP* 1.3 54.0 + - - +
693A GLU 3.2 2.7 - - - -
694A LYS* 3.0 15.9 + - + +
695A HIS* 2.6 36.7 + - - +
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Residues in contact with TRP 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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682A TYR* 5.3 0.2 - - - -
688A GLN 2.6 25.4 + - - +
689A HIS* 3.3 26.7 + + + +
691A ASP* 1.3 73.1 - - - +
693A GLU* 1.3 69.7 + - + +
695A HIS* 3.7 14.8 - + + -
696A HIS* 3.0 50.9 + + + +
699A CYS* 5.3 7.2 - - + -
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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
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689A HIS 3.8 5.9 + - - +
690A LYS 4.5 2.9 - - - +
691A ASP 3.2 0.6 - - - -
692A TRP* 1.3 84.4 + - + +
694A LYS* 1.3 71.9 + - + +
696A HIS* 2.6 59.3 + - + +
697A HIS* 4.8 0.7 - - - -
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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
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690A LYS 3.3 26.6 + - - +
691A ASP* 3.0 14.0 + - + +
693A GLU* 1.3 86.2 - - + +
695A HIS* 1.3 65.5 + - - +
697A HIS* 3.0 34.4 + - + +
698A ILE* 4.2 2.6 + - - +
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Residues in contact with HIS 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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664A TRP* 4.6 8.1 - + - -
674A CYS* 3.9 6.7 - - - -
677A CYS* 3.8 4.5 - - - -
680A ALA* 3.2 29.9 - - + +
682A TYR* 4.1 12.7 + + - +
691A ASP 2.6 22.1 + - - +
692A TRP* 3.0 19.3 + + + +
694A LYS* 1.3 69.1 - - - +
696A HIS* 1.3 51.3 + - - +
697A HIS 3.0 5.6 + - - -
698A ILE* 3.1 30.2 + - + +
699A CYS* 2.7 45.3 + - + +
902A ZN 2.0 36.8 - - - -
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Residues in contact with HIS 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 TRP* 3.0 40.3 + + + -
693A GLU* 2.6 54.9 + - + +
695A HIS* 1.3 74.4 - - - +
697A HIS* 1.3 90.3 + + - +
698A ILE 3.3 0.4 - - - -
699A CYS* 3.5 18.3 - - - +
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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
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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