Contacts of the helix formed by residues 693 - 699 (chain J) in PDB entry 6K71
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 693 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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654J LEU* 3.6 40.3 - - + +
657J GLU* 3.7 35.9 - - + +
692J ASP* 1.3 73.4 - - - +
694J GLY* 1.3 58.6 + - - +
695J GLN 3.2 2.5 - - - -
696J GLN* 3.1 32.5 + - + +
697J LEU 3.0 22.9 + - - -
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Residues in contact with GLY 694 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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654J LEU* 3.4 21.3 - - - +
684J TRP* 6.5 0.7 - - - -
689J ASP 3.4 20.1 + - - -
692J ASP* 3.2 3.0 - - - +
693J LYS* 1.3 77.4 - - - +
695J GLN* 1.3 57.5 + - - +
697J LEU* 4.3 1.1 - - - -
698J ARG* 2.9 45.2 + - - +
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Residues in contact with GLN 695 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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687J GLN 4.9 4.8 + - - -
688J ARG* 3.4 36.9 + - - +
689J ASP 4.7 0.2 + - - -
692J ASP 3.6 15.5 + - - +
693J LYS 3.2 0.6 - - - -
694J GLY* 1.3 72.7 - - - +
696J GLN* 1.3 63.8 + - - +
698J ARG* 4.4 13.9 - - - +
699J LYS* 3.3 51.3 + - + +
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Residues in contact with GLN 696 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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657J GLU* 3.3 39.3 + - - +
692J ASP 4.7 0.2 + - - -
693J LYS* 3.1 42.1 + - + +
695J GLN* 1.3 77.7 - - - +
697J LEU* 1.3 74.6 + - - +
699J LYS* 3.0 29.0 + - - +
700J ASN* 3.2 7.6 + - - +
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Residues in contact with LEU 697 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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650J GLU* 3.7 29.8 - - + -
653J PHE* 3.9 25.1 - - + -
654J LEU* 3.8 21.5 - - + -
657J GLU* 3.6 24.5 - - - +
660J GLY 5.1 3.1 - - - +
663J MET* 4.1 17.0 - - + -
693J LYS 3.0 13.8 + - - +
694J GLY* 4.4 0.9 - - - +
696J GLN* 1.3 82.5 - - - +
698J ARG* 1.3 64.7 + - + +
700J ASN* 3.3 37.6 - - + +
703J LEU* 3.3 9.3 - - + +
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Residues in contact with ARG 698 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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684J TRP* 3.4 59.0 + - + +
685J PHE* 3.3 59.7 + - + +
687J GLN* 3.8 15.9 + - - +
688J ARG 4.2 4.2 + - - -
689J ASP 2.5 37.3 + - - -
694J GLY* 2.9 26.8 + - - +
695J GLN* 4.5 12.5 - - - +
697J LEU* 1.3 77.7 - - + +
699J LYS* 1.3 52.0 + - + +
700J ASN 3.2 2.0 + - - -
703J LEU* 4.1 8.9 - - - +
704J GLN* 2.4 34.9 + - - +
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Residues in contact with LYS 699 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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685J PHE* 5.8 5.4 - - + -
695J GLN* 3.3 42.3 + - - +
696J GLN* 3.0 9.6 + - - +
698J ARG* 1.3 78.7 - - + +
700J ASN* 1.3 63.4 + - - +
701J GLN* 3.7 1.6 + - - -
704J GLN* 3.5 13.5 - - - +
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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