Contacts of the helix formed by residues 841 - 860 (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 SER 841 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
796B ASP* 2.6 30.8 + - - -
800B ARG* 3.7 7.4 + - - -
838B GLN* 4.5 1.3 - - - -
839B LEU 3.6 3.8 + - - -
840B PHE* 1.3 78.0 - - - +
842B GLN* 1.3 65.1 + - - +
843B ALA* 4.0 4.7 + - - +
844B THR* 3.3 10.9 + - - -
845B LYS* 3.1 20.0 + - - +
756D ASP* 3.2 22.4 - - - -
797D ALA* 5.1 1.4 - - - +
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Residues in contact with GLN 842 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
841B SER* 1.3 72.8 - - - +
843B ALA* 1.3 66.6 + - - +
845B LYS* 3.1 13.0 + - - +
846B ASP* 2.9 45.2 + - - +
668D ASN* 5.5 1.4 + - - -
704D SER 4.7 1.4 - - - +
707D GLY* 3.7 9.0 + - - -
708D ASP* 3.5 29.3 + - - +
711D SER* 3.3 28.5 + - - -
756D ASP* 3.2 43.1 + - + +
759D VAL* 3.7 7.9 - - + -
760D GLY* 3.5 14.4 - - - +
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Residues in contact with ALA 843 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
800B ARG* 3.3 32.9 - - - +
841B SER* 3.4 4.1 + - - +
842B GLN* 1.3 77.9 - - - +
844B THR* 1.3 56.6 + - - +
846B ASP* 3.4 5.4 + - - +
847B THR* 2.9 31.2 + - - -
756D ASP* 5.0 0.2 + - - -
759D VAL* 3.8 15.0 - - + +
801D ALA* 4.2 19.5 - - + -
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Residues in contact with THR 844 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
796B ASP* 2.6 40.1 + - - +
800B ARG* 3.2 36.0 + - + +
803B VAL* 4.4 0.3 - - - +
834B THR* 3.3 27.2 - - + +
840B PHE* 3.9 12.6 - - + -
841B SER* 3.3 8.7 + - - -
842B GLN 3.2 0.4 - - - -
843B ALA* 1.3 74.8 - - - +
845B LYS* 1.3 60.0 + - - +
847B THR* 3.2 4.2 + - - -
848B ALA* 2.9 27.6 + - - +
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Residues in contact with LYS 845 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
834B THR 3.7 18.4 - - - +
835B ARG* 2.9 47.9 + - - +
836B SER 4.2 2.7 - - - -
837B GLY 2.6 31.8 + - - +
838B GLN* 4.8 0.8 - - - +
840B PHE* 3.7 13.9 - - - +
841B SER 3.1 10.7 + - - +
842B GLN* 3.1 20.6 + - - +
844B THR* 1.3 78.5 - - - +
846B ASP* 1.3 58.2 + - - +
848B ALA* 3.4 4.0 + - - +
849B ARG 3.0 13.2 + - - -
664D ALA* 4.0 4.9 - - - +
668D ASN* 3.9 11.5 - - - +
708D ASP* 3.0 39.9 + - - +
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Residues in contact with ASP 846 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
835B ARG* 5.3 1.2 + - - -
842B GLN* 2.9 45.2 + - - +
843B ALA* 3.9 6.1 - - - +
845B LYS* 1.3 73.4 - - - +
847B THR* 1.3 65.3 + - - +
849B ARG* 3.4 11.3 + - - +
850B TRP* 3.2 19.6 + - - +
711D SER* 4.1 9.4 + - - -
759D VAL* 4.3 5.9 - - + +
763D ALA* 3.7 24.6 - - - +
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Residues in contact with THR 847 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
800B ARG* 3.3 28.2 - - + +
803B VAL* 3.9 2.9 - - + -
804B GLY* 3.6 33.4 - - - +
843B ALA 2.9 15.3 + - - -
844B THR 3.6 6.3 - - - -
846B ASP* 1.3 76.7 - - - +
848B ALA* 1.3 56.7 + - - +
850B TRP* 3.1 14.6 + - + +
851B ALA* 2.9 26.7 + - - +
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Residues in contact with ALA 848 (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* 3.8 16.0 - - + +
831B ILE* 3.5 9.9 - - - +
834B THR* 3.8 24.7 - - + -
835B ARG* 3.4 26.5 - - + -
844B THR 2.9 16.7 + - - +
845B LYS 3.6 1.6 - - - +
846B ASP 3.3 0.2 - - - -
847B THR* 1.3 72.9 - - - +
849B ARG* 1.3 61.3 + - - +
851B ALA* 3.8 0.2 - - - +
852B ARG* 2.9 28.6 + - - +
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Residues in contact with ARG 849 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
835B ARG* 3.5 38.5 - - - +
845B LYS 3.0 8.3 + - - +
846B ASP* 3.5 16.4 - - - +
848B ALA* 1.3 73.7 - - - +
850B TRP* 1.3 64.4 + - - +
852B ARG* 3.1 17.9 + - - +
853B GLU* 3.0 53.1 + - - +
631D LYS* 5.4 3.2 - - - +
668D ASN 4.1 3.8 + - - -
669D SER* 5.1 4.2 + - - +
671D GLU* 2.9 53.9 + - - +
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Residues in contact with TRP 850 (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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804B GLY* 4.9 2.7 - - - -
807B GLY* 3.8 17.4 - - - -
808B ASP* 3.6 22.6 + - - -
811B ALA* 4.3 18.8 - - + -
846B ASP 3.2 9.4 + - - +
847B THR* 3.1 23.0 + - + +
849B ARG* 1.3 78.6 - - - +
851B ALA* 1.3 58.8 + - + +
853B GLU* 3.4 7.1 + - + +
854B GLN* 3.0 73.7 + - + +
857B ARG* 5.7 3.1 - - - -
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Residues in contact with ALA 851 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
803B VAL* 3.3 42.0 - - + +
806B ILE* 4.2 9.7 - - + +
807B GLY* 4.1 16.8 - - - +
831B ILE* 4.1 5.6 - - + +
847B THR 2.9 13.2 + - - +
848B ALA 3.8 2.0 - - - +
850B TRP* 1.3 73.9 - - + +
852B ARG* 1.3 60.7 + - - +
854B GLN* 3.9 1.6 - - - +
855B GLN* 3.0 31.4 + - - +
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Residues in contact with ARG 852 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
828B ILE* 3.5 26.8 - - - +
831B ILE* 3.7 21.7 - - + +
832B LYS* 5.3 13.0 - - - +
835B ARG* 4.8 5.6 - - - -
848B ALA 2.9 19.4 + - - +
849B ARG* 3.4 25.8 - - - +
851B ALA* 1.3 77.6 - - - +
853B GLU* 1.3 57.9 + - + +
855B GLN* 2.9 37.2 + - - +
856B LYS* 3.1 51.3 + - + +
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Residues in contact with GLU 853 (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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849B ARG* 3.0 55.2 + - - +
850B TRP* 3.9 7.4 - - + +
852B ARG* 1.3 74.9 - - + +
854B GLN* 1.3 70.1 + - - +
856B LYS* 3.2 17.4 + - - +
857B ARG* 3.2 33.2 + - - +
671D GLU* 4.7 2.9 - - - +
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Residues in contact with GLN 854 (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 5.3 0.2 - - - +
807B GLY* 3.9 10.8 - - - +
810B ALA* 3.9 18.0 - - + +
811B ALA* 3.9 21.5 + - - +
850B TRP* 3.0 68.1 + - + +
851B ALA 3.9 4.3 - - - +
853B GLU* 1.3 77.0 - - - +
855B GLN* 1.3 62.0 + - - +
857B ARG* 3.5 40.9 + - - +
858B GLN* 3.4 24.6 + - - +
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Residues in contact with GLN 855 (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* 5.2 0.2 - - + -
822B TYR* 3.5 46.6 - - + +
827B VAL* 4.9 2.2 - - + -
828B ILE* 3.3 20.5 + - - +
831B ILE* 3.8 20.9 - - + +
851B ALA 3.0 19.8 + - - +
852B ARG* 2.9 37.9 + - - +
853B GLU 3.2 0.2 - - - -
854B GLN* 1.3 74.9 - - - +
856B LYS* 1.3 80.7 + - - +
858B GLN* 3.5 9.8 + - - +
859B LEU* 3.5 17.0 + - - +
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Residues in contact with LYS 856 (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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828B ILE* 5.7 1.8 - - - +
852B ARG* 3.1 47.3 + - + +
853B GLU* 3.2 11.4 + - - +
855B GLN* 1.3 96.3 - - - +
857B ARG* 1.3 64.0 + - + +
859B LEU* 3.5 26.8 + - - +
860B SER* 3.2 21.2 + - - -
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Residues in contact with ARG 857 (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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850B TRP* 5.7 2.4 - - - -
853B GLU* 3.2 27.5 + - - +
854B GLN* 3.7 38.4 + - - +
855B GLN 3.3 0.2 - - - -
856B LYS* 1.3 74.5 - - + +
858B GLN* 1.3 66.8 + - + +
860B SER* 3.1 22.4 + - - +
861B LEU* 3.2 23.2 - - + +
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Residues in contact with GLN 858 (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 ALA* 3.4 23.0 + - + +
813B PHE 3.3 24.2 + - - +
814B PRO* 4.6 1.4 - - - +
816B GLY* 4.3 2.4 - - - -
818B ILE* 3.9 5.4 - - - +
819B LYS* 3.2 55.8 + - + +
822B TYR* 3.5 38.3 - - + -
854B GLN 3.4 14.2 + - - +
855B GLN 3.7 8.1 - - - +
856B LYS 3.3 0.6 - - - -
857B ARG* 1.3 78.8 - - - +
859B LEU* 1.3 61.4 + - - +
861B LEU* 3.3 22.1 + - - +
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Residues in contact with LEU 859 (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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819B LYS* 4.2 16.8 - - + +
822B TYR* 3.7 13.2 - - + +
823B GLY* 3.6 33.4 - - - +
828B ILE* 4.7 9.4 - - + -
855B GLN* 3.5 12.8 + - - +
856B LYS* 3.5 36.0 + - - +
857B ARG 3.3 0.2 - - - -
858B GLN* 1.3 75.0 - - - +
860B SER* 1.3 56.8 + - - +
861B LEU 3.2 9.5 + - - +
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Residues in contact with SER 860 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
856B LYS 3.2 12.6 + - - -
857B ARG* 3.1 18.7 + - - +
859B LEU* 1.3 75.8 - - - +
861B LEU* 1.3 62.3 + - - +
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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