Contacts of the helix formed by residues 806 - 820 (chain A) in PDB entry 3BK0
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 SER 806 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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675A GLU* 5.1 10.1 - - - -
743A VAL* 4.9 1.3 - - - -
804A ARG 3.9 0.4 + - - -
805A PRO* 1.3 74.6 - - - +
807A PHE* 1.3 58.7 + - - +
808A SER* 3.5 9.9 + - - -
809A THR* 3.1 29.5 + - - -
810A ILE* 2.9 31.8 + - - +
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Residues in contact with PHE 807 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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668A ALA* 4.4 7.8 - - - +
671A MET* 3.5 53.2 - - + -
672A GLU* 3.8 22.6 - - - +
675A GLU* 4.0 20.2 + - + +
739A SER* 3.8 16.2 - - - -
742A ASP* 3.7 8.3 - - + -
743A VAL* 3.6 35.4 - - + -
746A PHE* 3.8 29.2 - + + -
805A PRO 4.1 0.2 + - - -
806A SER* 1.3 70.8 - - - +
808A SER* 1.3 61.1 + - - +
810A ILE* 3.7 14.2 - - + +
811A TYR* 2.9 29.8 + - - +
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Residues in contact with SER 808 (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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672A GLU* 2.5 34.2 + - - +
675A GLU* 4.8 4.4 + - - -
806A SER* 3.2 9.2 + - - -
807A PHE* 1.3 77.3 - - - +
809A THR* 1.3 62.6 + - - +
811A TYR* 3.4 2.5 + - - +
812A GLN* 3.0 40.6 + - - +
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Residues in contact with THR 809 (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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792A LEU* 5.1 6.5 - - + -
805A PRO* 4.1 15.0 - - + -
806A SER* 3.1 28.7 + - - -
808A SER* 1.3 76.8 - - - +
810A ILE* 1.3 58.4 + - - +
812A GLN* 3.2 8.9 + - - +
813A GLU* 2.8 32.7 + - + +
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Residues in contact with ILE 810 (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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668A ALA* 3.9 7.2 - - + -
743A VAL* 3.9 26.9 - - + -
746A PHE* 3.4 32.3 - - + -
792A LEU* 4.2 19.7 - - + +
796A CYS* 4.0 9.9 - - - -
805A PRO* 3.9 15.7 - - + -
806A SER 2.9 23.4 + - - +
807A PHE* 3.7 27.6 - - + +
809A THR* 1.3 76.5 - - - +
811A TYR* 1.3 63.6 + - - +
813A GLU* 3.3 0.7 + - - +
814A LEU* 2.9 34.0 + - + +
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Residues in contact with TYR 811 (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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665A GLY* 3.4 34.5 - - - -
668A ALA* 3.9 12.3 - - + -
669A ALA* 3.8 22.0 - - + -
672A GLU* 4.6 13.9 - - - +
807A PHE 2.9 18.0 + - - +
808A SER* 3.7 5.8 - - - +
810A ILE* 1.3 77.4 - - - +
812A GLN* 1.3 72.7 + - + +
814A LEU* 3.8 3.0 - - - +
815A GLN* 3.0 56.9 + - + +
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Residues in contact with GLN 812 (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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808A SER* 3.0 35.4 + - - +
809A THR* 3.8 7.4 + - - +
811A TYR* 1.3 87.1 - - + +
813A GLU* 1.3 58.2 + - - +
815A GLN* 3.5 11.0 + - - +
816A SER* 3.0 29.2 + - - -
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Residues in contact with GLU 813 (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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788A ALA* 4.2 11.3 - - - +
791A ARG* 5.2 2.8 + - - -
792A LEU* 4.1 28.5 - - + -
809A THR* 2.8 21.0 + - + +
810A ILE 3.8 2.7 - - - +
812A GLN* 1.3 78.2 - - - +
814A LEU* 1.3 56.8 + - - +
816A SER* 2.7 26.1 + - - -
817A ILE* 3.0 43.3 + - + +
820A ARG* 5.0 2.8 + - - -
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Residues in contact with LEU 814 (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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661A LEU* 3.9 30.1 - - + +
664A VAL* 3.8 33.9 - - + +
665A GLY* 4.1 9.2 - - - +
668A ALA* 4.1 5.2 - - + -
746A PHE* 4.1 7.6 - - + -
750A LEU* 4.0 16.2 - - + -
789A VAL* 4.6 9.4 - - + -
792A LEU* 4.0 18.2 - - + -
810A ILE* 2.9 36.9 + - + +
811A TYR* 3.8 3.4 - - - +
813A GLU* 1.3 75.6 - - - +
815A GLN* 1.3 56.9 + - - +
817A ILE* 3.4 6.8 + - + +
818A ARG* 2.9 29.9 + - - +
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Residues in contact with GLN 815 (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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665A GLY* 6.1 0.2 - - - -
811A TYR* 3.0 54.8 + - + +
812A GLN* 3.6 10.7 - - - +
814A LEU* 1.3 76.7 - - - +
816A SER* 1.3 60.8 + - - +
818A ARG* 3.3 13.8 + - - +
819A LYS* 3.1 56.6 + - - +
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Residues in contact with SER 816 (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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812A GLN 3.0 14.7 + - - -
813A GLU* 2.7 34.0 + - - -
815A GLN* 1.3 73.8 - - - +
817A ILE* 1.3 65.9 + - - +
819A LYS* 3.4 17.9 + - - +
820A ARG* 3.6 14.3 + - - +
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Residues in contact with ILE 817 (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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661A LEU* 3.9 17.3 - - + -
786A PRO* 4.6 3.8 - - + -
788A ALA* 3.6 33.9 - - + +
789A VAL* 3.8 28.0 - - + -
792A LEU* 5.3 0.2 - - + -
813A GLU* 3.0 42.8 + - + +
814A LEU* 3.7 11.4 - - + +
816A SER* 1.3 75.5 - - - +
818A ARG* 1.3 63.3 + - - +
820A ARG* 3.0 46.4 + - - +
821A HIS* 3.2 19.2 + - + +
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Residues in contact with ARG 818 (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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658A LYS* 3.4 58.1 - - + +
661A LEU* 3.6 21.0 - - + +
662A GLN* 4.3 19.5 - - - +
814A LEU 2.9 17.6 + - - +
815A GLN* 3.6 12.4 + - - +
817A ILE* 1.3 76.0 - - - +
819A LYS* 1.3 92.4 + - - +
821A HIS* 2.7 30.6 + - - +
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Residues in contact with LYS 819 (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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815A GLN* 3.1 52.6 + - + +
816A SER* 3.7 10.1 - - - +
817A ILE 3.2 0.6 - - - -
818A ARG* 1.3 103.8 - - - +
820A ARG* 1.3 55.2 + - - +
821A HIS 3.4 2.4 + - - -
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Residues in contact with ARG 820 (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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786A PRO* 5.4 3.2 - - - +
788A ALA* 3.9 24.5 - - - +
791A ARG* 5.1 4.4 - - - +
813A GLU* 5.0 3.2 + - - -
816A SER* 3.6 7.3 + - - +
817A ILE* 3.0 49.2 + - - +
819A LYS* 1.3 77.9 - - - +
821A HIS* 1.3 76.8 + - - +
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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