Contacts of the helix formed by residues 775 - 789 (chain B) in PDB entry 2BKU
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 TYR 775 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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721B LEU* 3.5 30.7 - - + -
722B ASN* 2.9 45.4 + - - +
725B MET* 3.6 41.3 - - + -
771B ALA 3.7 17.7 - - - -
772B LEU* 2.8 22.8 + - + +
774B PRO* 1.3 91.7 - - + +
776B VAL* 1.3 66.4 + - - +
777B GLY 3.3 2.7 - - - -
778B THR* 3.1 22.4 + - - -
779B ILE* 3.1 16.8 + - + +
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Residues in contact with VAL 776 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
772B LEU* 4.0 9.6 - - + +
773B PHE* 3.3 18.4 + - - +
774B PRO 3.6 0.4 - - - -
775B TYR* 1.3 75.9 - - - +
777B GLY* 1.3 58.7 + - - +
779B ILE* 3.1 11.0 + - - +
780B PHE* 2.9 43.5 + - + +
809B ILE* 4.2 10.3 - - + -
813B PHE* 3.9 27.6 - - + -
818B ILE* 4.1 25.6 - - + -
821B PHE* 3.8 24.0 - - + -
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Residues in contact with GLY 777 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
774B PRO 5.2 1.2 + - - -
775B TYR 3.3 0.6 - - - -
776B VAL* 1.3 78.8 - - - +
778B THR* 1.3 55.7 + - - +
780B PHE* 3.4 1.7 + - - +
781B GLN* 2.8 32.2 + - - +
821B PHE* 3.6 28.3 - - - -
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Residues in contact with THR 778 (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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725B MET* 3.3 22.5 - - + +
729B VAL* 3.3 34.5 - - + +
732B GLN* 3.7 7.5 + - - +
758B TYR* 3.7 6.1 - - - +
774B PRO 5.0 1.6 + - - -
775B TYR* 3.1 20.7 + - - -
777B GLY* 1.3 75.0 - - - +
779B ILE* 1.3 62.3 + - - +
781B GLN* 3.4 16.3 + - - +
782B PHE* 3.2 16.1 + - - +
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Residues in contact with ILE 779 (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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725B MET* 4.4 3.8 - - + -
758B TYR* 3.9 37.5 - - + -
761B ILE* 5.7 1.3 - - + -
762B VAL* 4.5 8.3 - - + -
772B LEU* 3.9 28.0 - - + -
775B TYR* 3.5 15.9 - - + +
776B VAL* 3.1 7.0 + - - +
778B THR* 1.3 73.7 - - - +
780B PHE* 1.3 62.0 + - - +
782B PHE* 2.9 22.5 + - - +
783B ILE* 2.9 25.1 + - + +
805B LEU* 4.1 15.9 - - + -
809B ILE* 3.9 29.6 - - + -
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Residues in contact with PHE 780 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
776B VAL* 2.9 37.1 + - + +
777B GLY 3.9 3.6 - - - +
779B ILE* 1.3 77.4 - - - +
781B GLN* 1.3 59.3 + - - +
783B ILE* 3.3 12.5 + - + -
784B ALA* 3.0 17.7 + - - +
806B ILE* 4.4 18.4 - - + -
809B ILE* 4.5 13.5 - - + -
821B PHE* 4.0 37.9 - + + -
822B TYR* 3.6 39.7 - + - -
824B GLN* 5.0 0.7 - - - +
826B TRP* 3.3 35.5 - + + -
827B VAL* 4.1 24.9 - - + -
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Residues in contact with GLN 781 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
729B VAL* 5.9 4.8 - - - +
732B GLN* 4.1 11.3 - - - +
733B ASN* 4.8 12.1 + - - +
777B GLY 2.8 17.6 + - - +
778B THR* 3.4 17.9 + - - +
779B ILE 3.1 0.2 - - - -
780B PHE* 1.3 76.6 - - - +
782B PHE* 1.3 60.3 + - - +
784B ALA* 3.2 21.6 - - + +
785B GLN* 3.5 11.4 + - - +
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Residues in contact with PHE 782 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
732B GLN* 3.5 38.5 - - + +
751B LEU* 3.2 44.6 - - + -
754B VAL* 3.7 13.9 - - + -
755B LEU* 3.7 34.1 - - + -
758B TYR* 3.7 20.6 - + + -
778B THR 3.2 3.3 + - - +
779B ILE 2.9 10.1 + - - +
781B GLN* 1.3 75.8 - - - +
783B ILE* 1.3 72.2 + - + +
785B GLN* 3.2 21.1 + - + +
786B VAL* 3.2 28.0 + - + +
792B LEU* 5.5 3.6 - - + -
802B ALA* 6.3 0.2 - - + -
805B LEU* 5.4 3.1 - - + -
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Residues in contact with ILE 783 (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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779B ILE* 2.9 31.9 + - + +
780B PHE* 3.7 21.5 - - + +
781B GLN 3.3 0.4 - - - -
782B PHE* 1.3 80.7 - - + +
784B ALA* 1.3 57.1 + - - +
786B VAL* 3.2 8.5 + - - +
787B ALA* 2.9 26.0 + - - +
802B ALA* 4.1 11.4 - - + +
805B LEU* 4.0 27.1 - - + -
806B ILE* 4.0 40.8 - - + +
809B ILE* 5.2 0.4 - - + -
826B TRP* 3.9 12.6 - - + -
830B TYR* 4.4 13.0 - - + -
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Residues in contact with ALA 784 (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 PHE 3.0 12.3 + - - +
781B GLN* 3.2 16.2 - - + +
783B ILE* 1.3 77.4 - - - +
785B GLN* 1.3 54.8 + - + +
787B ALA* 3.3 1.9 + - - +
788B GLU* 2.9 41.2 + - - +
826B TRP* 3.5 28.6 - - + -
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Residues in contact with GLN 785 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
732B GLN* 2.9 63.8 + - - +
733B ASN* 4.1 6.0 + - - -
747B GLN* 5.6 0.3 + - - -
751B LEU* 3.8 15.8 - - - +
781B GLN* 3.9 9.6 + - - +
782B PHE* 3.2 13.2 + - + +
784B ALA* 1.3 74.5 - - + +
786B VAL* 1.3 60.6 + - - +
788B GLU* 3.6 6.2 - - - +
789B ASP* 2.9 34.9 + - + +
792B LEU* 3.5 9.6 - - + +
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Residues in contact with VAL 786 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
755B LEU* 5.4 0.4 - - + -
782B PHE* 3.4 37.9 - - + +
783B ILE* 3.2 12.2 + - - +
785B GLN* 1.3 76.1 - - - +
787B ALA* 1.3 64.2 + - - +
788B GLU 3.1 1.4 + - - -
789B ASP 3.2 6.1 - - - +
792B LEU* 3.8 14.8 - - + -
793B TYR* 3.2 30.8 - - - +
798B THR* 4.0 23.6 - - + -
802B ALA* 3.9 17.7 - - + -
830B TYR* 3.5 22.9 - - - +
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Residues in contact with ALA 787 (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 ILE 2.9 13.0 + - - +
784B ALA 3.3 8.0 + - - +
786B VAL* 1.3 77.6 - - - +
788B GLU* 1.3 63.3 + - - +
793B TYR* 3.4 4.0 - - - -
826B TRP* 4.1 18.6 - - + +
830B TYR* 3.5 36.5 - - + -
833B ARG* 2.9 26.8 + - - +
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Residues in contact with GLU 788 (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 ALA* 2.9 29.2 + - - +
785B GLN* 3.6 9.0 - - - +
786B VAL 3.1 0.2 - - - -
787B ALA* 1.3 84.9 - - - +
789B ASP* 1.3 58.7 + - + +
790B PRO* 3.5 11.4 - - - +
793B TYR* 3.8 3.9 - - - -
826B TRP* 5.6 5.7 - - - +
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Residues in contact with ASP 789 (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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747B GLN* 5.1 3.6 - - - +
748B ILE* 4.9 4.6 - - - +
751B LEU* 5.3 2.6 - - - +
785B GLN* 2.9 20.5 + - + +
786B VAL 3.2 1.9 - - - +
788B GLU* 1.3 72.8 - - + +
790B PRO* 1.3 63.7 - - - +
791B GLN* 2.9 50.1 + - - +
792B LEU* 3.0 17.9 + - + +
793B TYR* 3.0 27.7 + - - -
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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