Contacts of the helix formed by residues 809 - 818 (chain B) in PDB entry 3KZ1
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 ILE 809 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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735B ARG* 4.8 2.0 - - - +
739B ILE* 3.7 30.7 - - + -
742B LEU* 4.5 5.8 - - + -
743B PHE* 4.0 19.5 - - + -
799B LEU* 5.7 2.5 - - + -
806B ILE* 4.4 9.2 - - + -
807B LYS 4.3 4.0 - - - +
808B GLU* 1.3 72.4 - - - +
810B SER* 1.3 68.6 + - - +
811B ASP* 3.3 2.9 - - - -
812B LEU* 3.1 18.4 + - + +
813B MET* 3.1 41.3 + - + +
892B ILE* 4.5 16.8 - - + -
902B GLU* 3.0 17.7 + - - +
906B LEU* 4.3 15.7 - - + -
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Residues in contact with SER 810 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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808B GLU* 4.8 0.6 - - - +
809B ILE* 1.3 78.8 - - - +
811B ASP* 1.3 64.0 + - - +
813B MET* 3.2 8.0 + - - +
814B LEU* 3.0 28.4 + - - +
902B GLU* 3.0 45.9 + - - -
905B LYS* 3.5 34.1 - - - +
906B LEU* 3.6 10.6 + - - +
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Residues in contact with ASP 811 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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799B LEU* 6.5 0.7 - - + -
808B GLU* 5.4 5.5 - - - +
809B ILE* 3.3 1.6 - - - +
810B SER* 1.3 76.5 - - - +
812B LEU* 1.3 58.0 + - - +
814B LEU* 3.3 8.0 + - - +
815B ALA* 2.9 28.3 + - - +
905B LYS* 2.6 33.1 + - - -
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Residues in contact with LEU 812 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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743B PHE* 4.0 18.2 - - + -
792B TRP* 3.0 39.3 + - + +
795B ALA* 3.5 30.3 - - + +
796B MET* 3.7 31.0 - - + +
799B LEU* 4.2 24.3 - - + +
809B ILE* 3.1 17.3 + - + +
811B ASP* 1.3 78.5 - - - +
813B MET* 1.3 70.9 + - + +
815B ALA* 3.2 15.6 - - + +
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Residues in contact with MET 813 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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742B LEU* 3.9 16.8 - - + -
792B TRP* 3.6 28.3 - - + -
796B MET* 5.0 1.3 - - + -
809B ILE* 3.1 41.5 + - + +
810B SER* 3.2 7.1 + - - +
812B LEU* 1.3 80.5 - - + +
814B LEU* 1.3 53.1 - - - +
815B ALA 2.9 4.0 - - - -
816B ARG* 2.7 27.5 + - - +
817B PHE* 2.9 25.5 + - + -
889B LEU* 3.7 30.3 - - + -
892B ILE* 5.4 0.4 - - - -
906B LEU* 4.0 12.3 - - + -
909B ALA* 3.9 18.2 - - + -
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Residues in contact with LEU 814 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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810B SER 3.0 17.0 + - - +
811B ASP* 3.8 7.4 - - - +
813B MET* 1.3 75.3 - - - +
815B ALA* 1.3 59.6 + - - +
816B ARG 3.0 1.1 + - - -
817B PHE 3.9 0.9 - - - -
818B ASP* 3.2 57.7 + - + +
821B ALA* 4.4 0.7 - - - +
905B LYS* 3.7 44.0 - - + +
908B ARG* 4.6 8.7 - - + -
909B ALA* 4.1 25.6 - - + +
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Residues in contact with ALA 815 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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792B TRP* 4.7 5.0 - - + +
795B ALA* 5.8 2.2 - - + -
811B ASP 2.9 12.9 + - - +
812B LEU* 3.2 25.1 - - + +
813B MET 2.9 0.6 + - - -
814B LEU* 1.3 75.7 - - - +
816B ARG* 1.3 60.9 + - - +
821B ALA* 3.2 16.0 - - - +
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Residues in contact with ARG 816 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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788B ILE* 3.5 40.2 + - - +
789B HIS* 6.3 1.8 - - + +
791B SER* 3.9 8.9 + - - -
792B TRP* 3.5 51.6 - - + +
813B MET 2.7 8.7 + - - +
815B ALA* 1.3 83.5 + - - +
817B PHE* 1.3 70.7 + - + +
818B ASP 3.6 1.6 - - - -
821B ALA* 2.9 57.2 + - - +
822B ARG* 4.0 0.7 - - - -
824B GLU* 2.7 28.5 + - - -
825B LEU* 3.9 24.9 - - - +
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Residues in contact with PHE 817 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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742B LEU* 6.3 0.2 - - + -
792B TRP* 3.8 29.8 - + - -
813B MET* 2.9 33.3 + - + +
814B LEU* 5.7 0.4 - - - -
816B ARG* 1.3 88.2 - - + +
818B ASP* 1.3 56.5 + - - +
822B ARG* 3.6 13.1 - - - +
825B LEU* 3.8 21.8 - - + -
882B LEU* 5.5 0.7 - - + -
885B TYR* 3.4 47.1 - + + -
889B LEU* 4.4 11.9 - - + -
909B ALA* 4.1 11.2 - - - +
912B GLN* 3.2 23.8 - - + +
913B CYS* 3.4 30.3 - - - -
916B ILE* 4.2 10.6 - - + +
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Residues in contact with ASP 818 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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814B LEU* 3.2 48.8 + - + +
816B ARG 3.6 1.2 + - - -
817B PHE* 1.3 80.4 - - - +
819B GLY* 1.3 70.8 + - - +
820B PRO* 3.2 5.9 - - - +
821B ALA* 3.3 13.5 + - - +
822B ARG* 3.9 2.2 - - - -
908B ARG* 3.6 20.6 + - - -
912B GLN* 2.6 33.5 + - - +
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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