Contacts of the helix formed by residues 808 - 817 (chain B) in PDB entry 5B2R
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 ASN 808 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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805B GLN 2.9 14.6 + - - +
806B LEU 3.5 1.0 - - - +
807B GLN* 1.3 77.6 - - - +
809B GLU* 1.3 66.1 + - - +
810B LYS* 3.3 10.6 + - - +
811B LEU* 3.0 33.3 + - + +
812B TYR* 3.0 25.7 + - - +
833B LEU* 5.4 1.0 - - - +
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Residues in contact with GLU 809 (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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780B ARG* 5.1 2.7 - - - +
807B GLN 3.5 4.3 + - - -
808B ASN* 1.3 76.0 - - - +
810B LYS* 1.3 61.3 + - + +
812B TYR* 3.2 7.2 + - - +
813B LEU* 2.9 35.2 + - + +
838B VAL* 3.3 30.0 - - - +
852B ILE* 4.6 8.3 - - + -
855B LYS* 2.3 49.0 + - - +
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Residues in contact with LYS 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 ASN* 3.3 8.9 + - - +
809B GLU* 1.3 81.4 - - + +
811B LEU* 1.3 58.1 + - - +
813B LEU* 3.4 6.6 + - - -
814B TYR* 2.9 23.9 + - - +
833B LEU* 2.9 37.3 + - + +
834B SER* 3.6 13.7 + - - +
836B TYR 2.7 29.4 + - - +
837B ASP* 4.9 0.2 - - - +
838B VAL* 3.5 31.2 - - + +
857B LEU* 3.4 21.4 - - + +
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Residues in contact with LEU 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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801B VAL* 4.2 12.1 - - + -
805B GLN* 3.9 39.9 - - + +
806B LEU* 4.7 2.5 - - + -
808B ASN* 3.0 23.7 + - + +
810B LYS* 1.3 73.5 - - - +
812B TYR* 1.3 65.9 + - - +
814B TYR* 3.4 2.8 + - + +
815B TYR* 3.2 45.9 + - + -
830B ILE* 4.2 15.5 - - + -
833B LEU* 3.9 22.6 - - + +
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Residues in contact with TYR 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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780B ARG* 3.5 63.9 - - + +
783B ARG* 4.6 7.6 - - - +
784B ILE* 3.6 22.9 - - + -
806B LEU* 3.4 19.4 + - + +
808B ASN 3.0 20.9 + - - +
809B GLU 3.5 3.1 - - - +
811B LEU* 1.3 77.4 - - - +
813B LEU* 1.3 61.0 + - - +
815B TYR* 3.4 2.9 + - - +
816B LEU* 3.0 56.4 + - + +
852B ILE* 3.7 33.3 - - + +
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Residues in contact with LEU 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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809B GLU* 2.9 23.5 + - + +
810B LYS* 3.7 3.1 - - - +
812B TYR* 1.3 73.2 - - - +
814B TYR* 1.3 66.4 + - - +
816B LEU* 3.2 7.1 + - + -
817B GLN* 3.0 40.3 + - + +
838B VAL* 3.8 28.0 - - + -
852B ILE* 4.1 24.2 - - + -
855B LYS* 3.7 23.6 - - + +
856B VAL* 3.7 22.7 - - - +
857B LEU* 3.7 17.0 - - + +
896B LYS* 4.3 9.0 - - - +
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Residues in contact with TYR 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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795B ILE* 3.7 21.2 - - + +
799B HIS* 3.8 16.6 + + - -
810B LYS 2.9 17.6 + - - +
811B LEU* 3.5 9.9 - - + +
812B TYR 3.3 0.4 - - - -
813B LEU* 1.3 78.8 - - - +
815B TYR* 1.3 79.1 - + - +
817B GLN* 3.5 4.6 + - - +
819B GLY* 2.7 52.6 + - - -
828B LEU* 3.7 31.8 + - + -
830B ILE* 3.5 45.1 + - + +
833B LEU* 4.1 17.0 - - + -
857B LEU* 3.7 12.1 - - + +
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Residues in contact with TYR 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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784B ILE* 3.6 36.3 - - + +
788B ILE* 3.9 15.1 - - - +
795B ILE* 4.2 29.8 - - + -
796B LEU* 4.6 6.1 - - + -
799B HIS* 2.5 42.5 + - + +
800B PRO 3.8 1.2 + - - -
801B VAL* 3.4 37.3 - - + +
806B LEU* 4.0 9.6 - - + -
811B LEU* 3.2 40.0 + - + +
812B TYR 4.1 1.1 - - - +
813B LEU 3.3 0.2 - - - -
814B TYR* 1.3 79.6 - + - +
816B LEU* 1.3 67.4 + - - +
817B GLN 3.1 2.0 - - - -
818B ASN* 3.1 12.7 + - - +
819B GLY 4.7 1.3 - - - +
830B ILE* 3.7 8.7 - - + +
891B LEU* 4.6 1.2 - - - +
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Residues in contact with LEU 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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783B ARG* 5.1 4.7 - - + -
784B ILE* 3.7 25.1 - - + +
812B TYR* 3.0 61.0 + - + +
813B LEU* 3.2 10.5 + - + +
815B TYR* 1.3 76.2 - - - +
817B GLN* 1.3 59.5 + - + +
818B ASN 3.4 0.4 - - - -
852B ILE* 3.8 20.6 - - + -
886B LEU* 3.7 5.9 - - - +
891B LEU* 3.2 63.1 - - + +
892B ILE* 5.3 1.4 - - + +
896B LYS* 5.5 2.2 - - - +
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Residues in contact with GLN 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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813B LEU* 3.0 24.0 + - + +
814B TYR* 4.1 2.7 - - - +
815B TYR 3.1 0.2 - - - -
816B LEU* 1.3 79.9 - - + +
818B ASN* 1.3 71.0 + - - +
819B GLY 3.0 2.0 + - - -
820B ARG* 2.7 36.2 + - - +
822B MET* 3.2 30.1 - - + +
828B LEU* 4.3 2.2 - - - +
856B VAL* 3.5 5.9 - - - +
857B LEU* 2.7 50.5 + - - +
882B TYR* 2.7 29.7 + - - +
886B LEU* 4.3 6.1 - - + -
892B ILE* 6.1 1.6 - - + -
896B LYS* 5.5 2.5 + - - +
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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