Contacts of the helix formed by residues 873 - 890 (chain B) in PDB entry 1GKU
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 ARG 873 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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800B GLU* 4.3 5.9 + - - -
871B GLY* 3.0 22.3 + - - +
872B LEU* 1.3 75.3 - - - +
874B TRP* 1.3 66.7 + - - +
875B GLU* 2.9 28.9 + - - +
876B HIS* 2.9 50.2 + - + +
877B PHE* 2.9 22.2 - - - -
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Residues in contact with TRP 874 (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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380B ASP* 4.5 14.8 - - - +
787B LEU* 5.1 10.3 - - + -
789B PHE* 4.6 15.9 - + - -
873B ARG* 1.3 73.7 - - - +
875B GLU* 1.3 109.6 + - + +
877B PHE* 3.1 12.7 + - - +
878B ALA* 2.9 47.4 + - + +
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Residues in contact with GLU 875 (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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789B PHE* 3.8 23.4 - - + -
793B GLN* 5.4 7.4 - - - +
797B ILE* 3.9 24.5 - - + +
873B ARG* 2.9 41.5 + - - +
874B TRP* 1.3 107.5 - - + +
876B HIS* 1.3 58.7 + - - +
878B ALA* 3.4 2.0 + - - +
879B LEU* 3.1 29.3 + - - +
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Residues in contact with HIS 876 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
797B ILE* 3.5 41.9 + - + +
800B GLU* 2.8 37.5 + - + -
801B LEU* 3.6 21.4 - - + +
871B GLY 3.7 0.8 + - - -
872B LEU* 3.5 23.5 - - + +
873B ARG* 2.9 59.8 + - + +
875B GLU* 1.3 81.1 + - + +
877B PHE* 1.3 57.6 + - + +
879B LEU 3.6 0.5 + - - -
880B TYR* 3.1 27.7 + - - +
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Residues in contact with PHE 877 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380B ASP* 4.9 3.4 - - - -
801B LEU* 5.9 1.1 - - + -
806B LEU* 5.9 1.1 - - + -
855B ARG* 3.2 22.0 - - + +
858B VAL* 4.2 13.2 - - + -
859B GLN* 3.4 47.1 - - + +
862B ILE* 3.9 28.7 - - + -
872B LEU* 3.9 36.3 - - + -
873B ARG* 2.9 31.9 - - - -
874B TRP* 3.1 10.2 + - - +
876B HIS* 1.3 75.5 - - + +
878B ALA* 1.3 60.8 + - - +
880B TYR* 3.8 8.4 - + + +
881B ASP 3.0 19.6 + - - -
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Residues in contact with ALA 878 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
787B LEU* 4.0 23.0 - - + +
789B PHE* 4.8 0.2 - - + -
855B ARG* 4.8 5.2 - - - +
874B TRP* 2.9 44.1 + - + +
875B GLU* 3.7 4.7 - - - +
877B PHE* 1.3 76.6 - - - +
879B LEU* 1.3 63.3 + - - +
881B ASP* 3.2 15.8 + - - +
882B LEU* 3.3 14.4 + - - +
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Residues in contact with LEU 879 (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 MET* 4.3 17.5 - - + -
783B ALA* 3.9 27.6 - - + -
787B LEU* 4.1 5.1 - - - +
789B PHE* 4.1 9.0 - - + -
794B THR* 3.8 13.0 - - + +
797B ILE* 3.4 33.7 - - + -
798B ALA* 3.8 20.6 - - + +
801B LEU* 4.2 4.5 - - + -
875B GLU 3.1 16.8 + - - +
876B HIS 4.0 1.6 - - - +
878B ALA* 1.3 77.1 - - - +
880B TYR* 1.3 57.2 + - - +
882B LEU* 3.1 16.0 - - + +
883B ILE* 3.1 38.7 + - + +
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Residues in contact with TYR 880 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
801B LEU* 4.3 11.6 - - + +
806B LEU* 3.5 38.0 + - + +
807B ILE* 4.0 18.8 - - + -
849B PRO* 3.6 24.8 - - + +
851B ARG* 3.6 7.4 + - - +
853B LEU* 2.8 29.7 + - - +
854B THR 3.8 11.9 - - - -
855B ARG* 4.2 14.1 - - + -
858B VAL* 3.9 19.6 - - + +
876B HIS 3.1 19.2 + - - +
877B PHE* 3.8 8.7 - + + +
879B LEU* 1.3 74.8 - - - +
881B ASP* 1.3 66.9 + - - +
882B LEU 3.0 1.8 - - - -
883B ILE* 3.9 4.2 - - + +
884B PHE* 3.0 27.2 + + + +
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Residues in contact with ASP 881 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
855B ARG* 2.7 50.3 + - - +
877B PHE 3.0 14.1 + - - +
878B ALA* 3.2 11.9 + - - +
880B TYR* 1.3 77.1 - - - +
882B LEU* 1.3 65.0 + - + +
884B PHE* 3.7 6.1 - - - +
885B ARG* 2.9 60.0 + - - +
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Residues in contact with LEU 882 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
774B TYR* 3.6 23.8 + - + +
782B ASP* 4.5 4.3 - - + -
783B ALA* 4.0 22.9 - - - +
786B ILE* 4.3 24.2 - - + -
787B LEU* 3.8 31.4 - - + -
878B ALA 3.3 7.2 + - - +
879B LEU* 3.1 17.9 - - + +
880B TYR 3.0 0.2 - - - -
881B ASP* 1.3 79.8 - - + +
883B ILE* 1.3 67.3 + - - +
885B ARG* 3.0 12.7 + - - +
886B ARG* 2.9 23.9 + - - +
927B TYR* 5.0 7.0 - - + -
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Residues in contact with ILE 883 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
774B TYR* 3.6 21.9 - - + -
779B MET* 4.0 17.5 - - + -
801B LEU* 4.6 2.9 - - + -
807B ILE* 4.2 26.2 - - + -
847B ILE* 3.3 49.3 - - + +
848B ARG* 4.0 12.6 - - - -
849B PRO* 4.4 1.6 - - + -
879B LEU* 3.1 28.9 - - + +
880B TYR* 3.9 6.5 - - + +
882B LEU* 1.3 75.6 - - + +
884B PHE* 1.3 57.4 + - - +
886B ARG* 4.0 1.2 - - - +
887B PHE* 3.1 29.0 + - - +
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Residues in contact with PHE 884 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
828B TYR* 3.7 26.7 - + - -
849B PRO* 3.6 26.4 - - + +
851B ARG 4.5 0.2 - - - -
852B PRO* 4.2 1.1 - - + -
853B LEU 3.6 33.0 - - - -
854B THR* 3.6 35.4 - - + -
855B ARG 5.3 0.9 - - - +
880B TYR* 3.0 26.5 + - + +
881B ASP* 3.7 6.7 - - - +
883B ILE* 1.3 75.3 - - - +
885B ARG* 1.3 70.7 + - + +
887B PHE* 4.0 0.7 - - - +
888B MET* 3.0 61.8 + - + +
926B LEU* 4.9 5.8 - - + -
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Residues in contact with ARG 885 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
881B ASP* 2.9 48.7 + - - +
882B LEU* 3.0 11.3 + - - +
884B PHE* 1.3 82.7 - - + +
886B ARG* 1.3 65.6 + - - +
888B MET* 4.1 2.6 - - - +
889B ALA* 2.9 28.2 + - - +
925B GLU 3.7 7.3 + - - -
926B LEU* 2.7 62.8 + - + +
927B TYR* 4.0 11.3 - - + +
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Residues in contact with ARG 886 (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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771B LEU* 3.4 35.4 - - - +
772B PRO* 2.8 45.4 + - - +
773B PRO* 4.0 7.2 + - - -
774B TYR* 3.2 57.4 - - + +
778B THR* 3.7 29.6 - - - +
782B ASP* 4.0 9.7 + - - -
882B LEU 2.9 7.4 + - - +
885B ARG* 1.3 76.4 - - - +
887B PHE* 1.3 62.3 + - - +
889B ALA* 3.7 3.3 - - - +
890B SER* 3.1 23.0 + - - -
927B TYR* 3.7 30.4 + - + -
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Residues in contact with PHE 887 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
773B PRO* 4.2 11.0 - - + -
817B VAL* 3.7 26.5 - - + -
821B GLY 3.1 31.0 - - - -
824B ILE* 4.6 4.3 - - + -
825B ALA* 4.0 17.3 - - + -
846B CYS* 4.0 8.1 - - - -
847B ILE 4.6 2.9 - - - +
848B ARG* 3.3 34.1 - - + -
849B PRO* 3.4 24.2 - - + -
883B ILE 3.1 18.0 + - - +
884B PHE 4.0 0.2 - - - +
886B ARG* 1.3 77.6 - - - +
888B MET* 1.3 80.1 + - + +
890B SER* 2.9 21.1 + - - -
891B GLN* 3.3 20.9 - - + +
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Residues in contact with MET 888 (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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824B ILE* 4.3 18.4 - - + +
825B ALA* 3.9 22.9 - - - +
828B TYR* 3.6 39.3 - - + -
829B LEU* 3.6 9.4 - - + +
849B PRO* 4.9 1.3 - - + -
852B PRO* 4.4 2.2 - - + -
884B PHE* 3.0 55.2 + - + +
885B ARG 4.1 0.9 - - - +
887B PHE* 1.3 87.1 - - + +
889B ALA* 1.3 58.3 + - - +
891B GLN* 2.8 22.3 + - - +
892B CYS* 3.1 9.9 + - - +
926B LEU* 3.9 22.0 - - + -
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Residues in contact with ALA 889 (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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770B PRO* 3.0 33.0 - - + +
771B LEU 5.6 0.7 - - - +
885B ARG 2.9 19.8 + - - +
886B ARG* 3.7 4.9 - - - +
888B MET* 1.3 78.9 - - - +
890B SER* 1.3 60.5 + - - +
891B GLN 3.2 0.7 + - - -
892B CYS* 3.3 15.5 + - - +
923B ALA* 4.1 13.0 - - + +
926B LEU* 4.3 7.5 - - + +
927B TYR* 3.8 22.7 - - + +
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Residues in contact with SER 890 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
770B PRO* 4.1 3.4 - - - -
771B LEU 3.0 26.7 + - - -
772B PRO 3.9 7.9 - - - -
773B PRO* 3.2 18.9 - - - +
836B ARG* 3.0 24.7 + - - -
838B TRP* 3.1 21.1 + - - -
886B ARG 3.1 11.4 + - - -
887B PHE* 2.9 15.4 + - - -
888B MET 3.1 0.8 - - - -
889B ALA* 1.3 74.8 - - - +
891B GLN* 1.3 64.6 + - - +
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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