Contacts of the helix formed by residues 683 - 704 (chain O) in PDB entry 5KHR
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 LYS 683 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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682O LYS* 3.8 24.0 - - - +
684O ALA* 3.8 29.2 - - - +
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Residues in contact with ALA 684 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
683O LYS* 3.8 28.9 - - - +
685O GLU* 3.8 25.4 - - - +
687O LEU* 4.7 15.3 - - - +
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Residues in contact with GLU 685 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
684O ALA* 3.8 28.5 - - - +
686O ALA* 3.8 26.0 - - - +
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Residues in contact with ALA 686 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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685O GLU* 3.8 25.6 - - - +
687O LEU* 3.8 28.5 - - - +
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Residues in contact with LEU 687 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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684O ALA* 4.7 14.8 - - - +
686O ALA* 3.8 29.6 - - - +
688O GLU* 3.8 25.8 - - - +
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Residues in contact with GLU 688 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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687O LEU* 3.8 29.8 - - - +
689O ALA* 3.8 24.2 - - - +
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Residues in contact with ALA 689 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
688O GLU* 3.8 25.6 - - - +
690O ALA* 3.8 28.9 - - - +
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Residues in contact with ALA 690 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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689O ALA* 3.8 26.2 - - - +
691O ILE* 3.8 28.7 - - - +
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Residues in contact with ILE 691 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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690O ALA* 3.8 28.5 - - - +
692O GLU* 3.8 25.4 - - - +
694O LEU* 4.7 15.5 - - - +
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Residues in contact with GLU 692 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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691O ILE* 3.8 28.7 - - - +
693O ASN* 3.8 24.2 - - - +
695O ASN* 4.6 15.7 - - - +
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Residues in contact with ASN 693 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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692O GLU* 3.8 25.1 - - - +
694O LEU* 3.8 29.4 - - - +
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Residues in contact with LEU 694 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
691O ILE* 4.7 15.5 - - - +
693O ASN* 3.8 29.4 - - - +
695O ASN* 3.8 25.4 - - - +
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Residues in contact with ASN 695 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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692O GLU* 4.6 16.6 - - - +
694O LEU* 3.8 28.5 - - - +
696O GLU* 3.8 26.0 - - - +
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Residues in contact with GLU 696 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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695O ASN* 3.8 25.8 - - - +
697O ALA* 3.8 29.4 - - - +
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Residues in contact with ALA 697 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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661O GLY* 4.7 20.2 - - - +
696O GLU* 3.8 28.5 - - - +
698O LYS* 3.8 25.1 - - - +
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Residues in contact with LYS 698 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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697O ALA* 3.8 25.1 - - - +
699O ASN* 3.8 28.3 - - - +
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Residues in contact with ASN 699 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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698O LYS* 3.8 26.9 - - - +
700O TYR* 3.8 28.9 - - - +
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Residues in contact with TYR 700 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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699O ASN* 3.8 28.7 - - - +
701O PHE* 3.8 26.5 - - - +
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Residues in contact with PHE 701 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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700O TYR* 3.8 28.5 - - - +
702O ALA* 3.8 24.9 - - - +
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Residues in contact with ALA 702 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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701O PHE* 3.8 28.5 - - - +
703O LYS* 3.8 25.4 - - - +
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Residues in contact with LYS 703 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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702O ALA* 3.8 26.9 - - - +
704O VAL* 3.8 28.5 - - - +
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Residues in contact with VAL 704 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
703O LYS* 3.8 28.5 - - - +
705O ASP* 3.9 24.9 - - - +
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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