Contacts of the helix formed by residues 795 - 813 (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 GLU 795 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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752B GLU* 4.6 10.9 - - - +
790B PRO 4.3 0.2 + - - -
791B GLN 4.1 13.2 - - - +
792B LEU 3.1 12.4 + - - +
793B TYR 3.5 5.0 - - - +
794B SER* 1.3 79.9 + - - +
796B ASP* 1.3 68.6 + - - +
797B ALA* 3.3 11.0 + - - +
798B THR* 3.1 15.3 + - - +
799B SER 3.1 19.2 + - - -
795D GLU* 5.2 6.4 - - - +
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Residues in contact with ASP 796 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
794B SER 3.4 5.6 + - - +
795B GLU* 1.3 75.1 + - - +
797B ALA* 1.3 61.9 + - - +
799B SER* 3.4 1.4 + - - -
800B ARG* 3.1 29.1 + - - +
839B LEU 4.6 8.5 - - - +
840B PHE* 3.2 19.1 - - + -
841B SER* 2.6 41.3 + - - -
844B THR* 2.6 25.9 + - - -
797D ALA* 3.5 15.8 - - + +
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Residues in contact with ALA 797 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
795B GLU* 3.3 10.3 + - - +
796B ASP* 1.3 79.1 - - - +
798B THR* 1.3 63.7 + - - +
800B ARG* 4.7 1.3 - - - +
801B ALA* 3.1 11.8 + - - +
796D ASP* 3.5 28.0 - - + +
797D ALA* 4.2 19.6 - - + +
800D ARG* 3.1 31.0 + - - +
841D SER* 5.2 0.7 - - - +
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Residues in contact with THR 798 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
752B GLU* 3.6 26.7 + - + +
755B LEU* 3.6 26.2 - - + +
786B VAL* 4.0 14.8 - - + -
792B LEU* 3.4 42.3 + - + +
795B GLU* 3.1 11.5 + - - +
797B ALA* 1.3 78.1 - - - +
799B SER* 1.3 57.7 + - - +
801B ALA* 3.4 3.0 + - - +
802B ALA* 3.0 26.3 + - - +
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Residues in contact with SER 799 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
793B TYR* 2.5 33.8 + - - +
795B GLU 3.1 7.6 + - - -
796B ASP 3.9 2.5 - - - -
798B THR* 1.3 75.8 - - - +
800B ARG* 1.3 57.1 + - - +
802B ALA* 3.2 1.2 + - - +
803B VAL* 2.8 39.6 + - - +
830B TYR* 3.1 23.2 + - - -
834B THR* 4.6 5.6 + - - -
840B PHE* 3.6 22.6 - - - -
844B THR* 4.5 4.0 - - - -
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Residues in contact with ARG 800 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
796B ASP* 3.1 31.9 + - - +
797B ALA* 4.7 0.2 - - - +
799B SER* 1.3 76.3 - - - +
801B ALA* 1.3 58.1 + - - +
803B VAL* 3.6 9.7 - - - +
804B GLY* 3.0 23.0 + - - -
841B SER* 3.7 4.8 + - - -
843B ALA* 3.3 45.2 - - - +
844B THR* 3.2 26.9 + - + +
847B THR* 3.3 16.5 - - + +
797D ALA* 3.1 31.7 + - - +
800D ARG* 3.4 52.4 - - - +
801D ALA* 3.6 6.5 - - - +
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Residues in contact with ALA 801 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
755B LEU* 3.7 24.7 - - + -
759B VAL* 4.3 10.0 - - + +
797B ALA 3.1 14.1 + - - +
798B THR 3.6 8.1 - - - +
799B SER 3.1 0.2 - - - -
800B ARG* 1.3 75.6 - - - +
802B ALA* 1.3 59.1 + - - +
804B GLY* 3.1 2.8 + - - -
805B LEU* 2.9 34.7 + - - +
800D ARG* 3.8 2.8 - - - +
843D ALA* 4.3 16.4 - - + -
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Residues in contact with ALA 802 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
755B LEU* 4.5 4.2 - - + +
782B PHE* 6.3 0.4 - - + -
783B ILE* 4.1 11.7 - - + +
786B VAL* 3.9 20.2 - - + -
798B THR 3.0 17.5 + - - +
799B SER 3.5 0.2 - - - +
801B ALA* 1.3 75.6 - - - +
803B VAL* 1.3 61.3 + - - +
805B LEU* 3.2 25.5 + - - +
806B ILE* 3.2 17.4 + - - +
830B TYR* 3.5 24.0 - - + +
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Residues in contact with VAL 803 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
799B SER 2.8 23.3 + - - +
800B ARG* 3.6 13.0 - - - +
802B ALA* 1.3 73.7 - - - +
804B GLY* 1.3 63.7 + - - +
806B ILE* 3.4 13.1 - - + +
807B GLY 3.3 6.8 + - - -
830B TYR* 4.3 8.7 - - + -
831B ILE* 4.3 20.6 - - + -
834B THR* 4.4 12.1 - - + +
844B THR 4.4 0.7 - - - +
847B THR* 3.9 13.2 - - + -
848B ALA* 3.8 24.9 - - + +
851B ALA* 3.3 40.9 - - + +
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Residues in contact with GLY 804 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
800B ARG 3.0 17.5 + - - -
801B ALA 3.1 4.5 + - - -
803B VAL* 1.3 76.0 - - - +
805B LEU* 1.3 59.0 + - - +
807B GLY* 3.4 1.1 + - - -
808B ASP* 2.8 40.6 + - - +
847B THR* 3.6 15.9 - - - -
850B TRP* 4.7 3.0 + - - -
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Residues in contact with LEU 805 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
755B LEU* 4.1 20.9 - - + -
758B TYR* 4.1 11.2 - - + -
759B VAL* 3.7 34.3 - - + +
762B VAL* 4.0 25.1 - - + -
779B ILE* 4.1 19.7 - - + -
782B PHE* 5.4 2.0 - - + -
783B ILE* 4.0 18.6 - - + -
801B ALA 2.9 16.4 + - - +
802B ALA* 3.2 8.9 + - - +
804B GLY* 1.3 72.5 - - - +
806B ILE* 1.3 67.0 + - - +
808B ASP* 4.5 4.7 - - - +
809B ILE* 2.8 35.4 + - + +
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Residues in contact with ILE 806 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
780B PHE* 4.4 11.7 - - + -
783B ILE* 4.0 31.6 - - + +
802B ALA 3.2 7.5 + - - +
803B VAL* 3.4 21.5 - - + +
804B GLY 3.3 0.2 - - - -
805B LEU* 1.3 75.7 - - - +
807B GLY* 1.3 63.4 + - - +
809B ILE* 5.0 0.2 - - - -
810B ALA* 3.3 1.7 + - - +
822B TYR* 2.8 49.9 + - + -
826B TRP* 5.6 0.9 - - + -
827B VAL* 4.4 17.7 - - + -
830B TYR* 4.0 20.6 - - + -
831B ILE* 4.4 14.8 - - + -
851B ALA* 4.2 13.9 - - + +
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Residues in contact with GLY 807 (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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803B VAL 3.3 7.7 + - - -
804B GLY 3.7 2.0 - - - -
805B LEU 3.2 0.2 - - - -
806B ILE* 1.3 78.6 - - - +
808B ASP* 1.3 63.7 + - - +
810B ALA* 3.1 6.6 + - - +
811B ALA* 3.0 20.6 + - - +
850B TRP* 3.8 20.2 - - - -
851B ALA* 4.1 15.5 - - - -
854B GLN* 3.9 11.3 - - - +
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Residues in contact with ASP 808 (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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762B VAL* 3.9 22.0 - - + +
766B HIS* 6.1 1.5 - - + -
804B GLY* 2.8 27.2 + - - +
805B LEU* 4.1 3.2 - - - +
807B GLY* 1.3 67.6 - - - +
809B ILE* 1.3 66.5 + - - +
811B ALA* 3.2 17.3 + - - +
812B MET* 3.3 16.6 + - - +
850B TRP* 3.6 17.5 + - - +
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Residues in contact with ILE 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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762B VAL* 3.9 21.3 - - + -
772B LEU* 4.7 5.2 - - + -
776B VAL* 4.2 14.8 - - + -
779B ILE* 3.9 42.2 - - + -
780B PHE* 4.5 13.0 - - + -
783B ILE* 5.2 0.7 - - + -
805B LEU* 2.8 28.6 + - + +
808B ASP* 1.3 70.7 - - - +
810B ALA* 1.3 64.2 + - - +
812B MET* 3.0 18.9 + - - +
813B PHE* 3.3 24.1 - - + -
818B ILE* 3.6 22.0 - - + -
822B TYR* 3.7 6.7 - - - +
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Residues in contact with ALA 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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806B ILE 3.3 5.3 + - - +
807B GLY 3.1 11.3 + - - +
809B ILE* 1.3 75.1 - - - +
811B ALA* 1.3 61.1 + - - +
812B MET 3.1 1.2 + - - -
813B PHE 3.2 12.8 + - - -
814B PRO* 4.0 1.9 - - - +
818B ILE* 4.4 1.8 - - - -
822B TYR* 2.9 35.2 + - + +
854B GLN* 3.9 21.5 - - + +
858B GLN* 3.4 29.9 + - + +
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Residues in contact with ALA 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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766B HIS* 5.8 8.7 - - + +
807B GLY 3.0 12.2 + - - +
808B ASP* 3.2 12.7 + - - +
810B ALA* 1.3 75.8 - - - +
812B MET* 1.3 60.0 + - + +
813B PHE 3.4 0.2 - - - -
814B PRO* 4.1 12.8 - - - +
850B TRP* 4.3 16.4 - - + -
854B GLN* 3.9 15.0 + - - +
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Residues in contact with MET 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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762B VAL* 4.1 28.0 - - - +
765B LEU 3.1 26.2 - - - +
766B HIS* 4.2 25.6 - - + +
769B PRO* 3.6 42.8 - - + +
772B LEU* 3.7 32.1 - - + -
808B ASP 3.3 10.0 + - - +
809B ILE* 3.0 11.7 + - - +
811B ALA* 1.3 74.9 - - + +
813B PHE* 1.3 64.6 + - + +
814B PRO* 3.1 14.4 - - - +
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Residues in contact with PHE 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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769B PRO* 3.4 41.1 - - + -
770B GLU* 5.4 0.2 - - - -
772B LEU* 4.3 13.5 - - + -
773B PHE* 3.7 38.8 - + + -
776B VAL* 3.9 16.2 - - + -
809B ILE* 3.3 16.4 - - + -
810B ALA 3.2 6.6 + - - -
812B MET* 1.3 90.4 - - + +
814B PRO* 1.3 57.9 - - - +
815B ASP* 3.1 17.4 + - - +
816B GLY* 3.6 6.9 + - - -
817B SER* 4.4 8.9 + - - -
818B ILE* 3.6 32.3 - - + -
858B GLN* 3.3 17.3 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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