Contacts of the helix formed by residues 863 - 867 (chain A) in PDB entry 1HKC
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 THR 863 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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678A VAL 3.6 0.2 + - - -
679A GLY* 3.8 9.0 - - - -
680A THR* 4.3 4.2 + - - +
784A THR* 3.9 14.8 + - - +
862A GLY* 1.3 71.6 - - - -
864A LEU* 1.3 57.4 + - - +
866A LYS* 4.4 7.9 - - + -
867A LEU* 2.9 46.1 + - + +
920A PO4 2.5 34.0 + - - +
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Residues in contact with LEU 864 (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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678A VAL* 3.4 25.0 + - + +
679A GLY* 4.0 6.7 - - - +
745A ILE 3.5 24.9 - - - +
747A GLY* 4.1 9.4 - - - +
750A LEU* 3.9 26.0 - - + -
784A THR* 3.6 25.3 - - + +
787A LEU* 4.8 4.5 - - + -
862A GLY 3.2 0.6 - - - -
863A THR* 1.3 77.2 + - - +
865A TYR* 1.3 61.4 + - - +
868A HIS* 2.9 58.9 + - + +
871A PHE* 4.0 17.7 - - + +
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Residues in contact with TYR 865 (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 LEU* 5.0 2.2 - - + -
678A VAL* 3.4 20.7 + - + +
860A VAL* 3.3 34.2 - - + +
861A ASP 4.5 4.9 - - - +
862A GLY 3.4 5.8 + - - +
864A LEU* 1.3 80.5 - - - +
866A LYS* 1.3 65.8 + - - +
868A HIS* 4.1 8.8 - - - +
871A PHE* 4.1 14.8 - + - -
872A SER* 3.3 38.7 + - - -
875A MET* 3.5 33.0 - - + -
876A HIS* 2.9 25.6 + - - -
890A PHE* 3.6 12.5 + - - +
892A LEU* 4.1 20.9 + - + -
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Residues in contact with LYS 866 (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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861A ASP* 5.1 4.9 - - - +
862A GLY 3.0 18.8 + - - +
863A THR* 4.3 6.1 - - + +
865A TYR* 1.3 86.3 - - - +
867A LEU* 1.3 76.1 + - + +
868A HIS 4.3 2.6 - - - +
892A LEU* 3.9 30.5 - - + -
894A GLU* 3.0 28.2 + - - +
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Residues in contact with LEU 867 (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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784A THR* 5.0 1.8 - - + -
785A LYS* 3.6 44.9 - - + +
788A SER* 3.4 20.5 - - - +
863A THR* 2.9 34.2 + - + +
866A LYS* 1.3 94.0 - - + +
868A HIS* 1.3 63.9 + - - +
869A PRO* 3.5 3.5 - - - +
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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