Contacts of the helix formed by residues 887 - 908 (chain B) in PDB entry 4QUN
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 THR 887 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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650B PHE* 3.7 11.9 - - - -
812B HIS* 3.5 29.5 + - + +
885B VAL* 4.1 0.3 - - - +
886B GLN* 1.3 96.2 - - + +
888B SER* 1.3 63.5 + - - +
889B SER* 2.8 24.6 + - - -
890B GLN* 3.1 17.3 + - - +
891B TYR 3.2 15.9 + - - -
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Residues in contact with SER 888 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
647B LEU* 4.3 16.5 - - - +
650B PHE* 3.8 20.1 - - - -
651B GLU* 3.5 26.2 + - - -
887B THR* 1.3 73.9 - - - +
889B SER* 1.3 59.1 + - - +
891B TYR* 3.3 1.6 + - - +
892B LYS* 2.8 31.9 + - - +
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Residues in contact with SER 889 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
812B HIS 3.7 10.7 + - - -
813B GLY* 4.6 1.6 - - - -
814B VAL* 3.5 17.9 - - - +
887B THR* 2.8 20.4 + - - -
888B SER* 1.3 81.2 + - - +
890B GLN* 1.3 56.4 + - - +
892B LYS* 3.8 9.7 - - - +
893B PHE* 2.9 28.8 + - - +
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Residues in contact with GLN 890 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
809B TRP* 4.6 0.4 - - + +
812B HIS* 3.5 23.6 - - - +
813B GLY 3.1 30.0 + - - +
814B VAL* 4.3 5.6 - - + -
847B GLY* 3.8 22.9 - - - +
848B ARG* 4.1 7.5 - - - +
851B VAL* 3.6 21.3 - - + +
885B VAL* 4.1 4.7 - - + -
886B GLN* 2.9 29.8 + - - +
887B THR* 3.1 21.7 + - - +
889B SER* 1.3 79.1 + - - +
891B TYR* 1.3 58.9 + - - +
893B PHE* 3.3 3.2 + - - +
894B VAL* 3.0 30.7 + - - +
1001B PO4 4.9 0.4 + - - -
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Residues in contact with TYR 891 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
646B VAL* 3.5 29.6 + - + +
647B LEU* 4.0 14.4 - - + -
650B PHE* 3.4 54.5 - + + -
870B PRO* 3.4 20.9 - - + +
871B LEU* 3.1 32.4 + - + +
874B VAL* 3.9 22.9 - - + -
885B VAL* 3.9 5.7 - - + +
887B THR 3.2 9.4 + - - +
888B SER 3.7 6.1 - - - +
890B GLN* 1.3 74.2 - - - +
892B LYS* 1.3 66.8 + - - +
894B VAL* 3.2 13.6 - - + +
895B CYS* 2.9 36.3 + - - -
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Residues in contact with LYS 892 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
641B LEU* 4.3 12.8 - - + -
647B LEU* 4.0 28.9 - - + -
888B SER 2.8 17.6 + - - +
889B SER* 3.8 8.5 - - - +
891B TYR* 1.3 77.2 - - - +
893B PHE* 1.3 64.8 + - - +
895B CYS* 3.3 5.1 + - - +
896B GLU* 2.8 61.5 + - - +
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Residues in contact with PHE 893 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
814B VAL* 3.8 21.5 - - + -
815B PRO* 3.5 38.8 - - + -
818B SER* 3.8 29.6 - - - -
821B PHE* 3.5 40.6 - + - -
851B VAL* 4.2 11.7 - - + -
889B SER 2.9 20.2 + - - +
890B GLN* 3.5 3.8 - - - +
891B TYR 3.2 0.2 - - - -
892B LYS* 1.3 78.2 - - - +
894B VAL* 1.3 62.1 + - - +
896B GLU* 3.2 13.3 + - + +
897B ALA* 2.9 36.9 + - + +
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Residues in contact with VAL 894 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
851B VAL* 3.7 34.3 - - + +
854B THR* 3.8 28.9 - - + -
855B MET* 3.2 29.7 - - + +
885B VAL* 5.7 3.1 - - + -
890B GLN 3.0 14.8 + - - +
891B TYR* 3.2 28.0 - - + +
893B PHE* 1.3 80.5 - - - +
895B CYS* 1.3 63.8 + - - +
897B ALA 3.3 0.3 + - - -
898B ILE* 2.9 36.0 + - + +
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Residues in contact with CYS 895 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
637B LEU* 3.8 25.7 - - + +
641B LEU* 4.0 15.0 - - + -
646B VAL* 4.1 3.4 - - - -
870B PRO* 3.9 16.4 - - - -
891B TYR* 2.9 53.7 + - - +
892B LYS 3.7 4.0 - - - +
894B VAL* 1.3 79.7 - - - +
896B GLU* 1.3 61.5 + - - +
898B ILE* 3.2 10.3 + - - +
899B LEU* 3.1 25.1 + - - +
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Residues in contact with GLU 896 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
641B LEU* 4.2 19.3 - - + +
892B LYS* 2.8 59.2 + - + +
893B PHE* 3.6 13.2 - - + +
895B CYS* 1.3 75.7 - - - +
897B ALA* 1.3 57.8 - - - +
899B LEU* 3.3 8.7 + - + +
900B ARG* 3.0 26.9 + - - +
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Residues in contact with ALA 897 (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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818B SER* 5.9 2.7 - - - -
821B PHE* 4.8 0.2 - - + -
822B LEU* 4.3 14.8 - - + -
855B MET* 3.4 28.0 - - + -
893B PHE* 2.9 30.7 + - + +
894B VAL* 4.3 0.7 - - - -
896B GLU* 1.3 72.7 - - - +
898B ILE* 1.3 61.0 + - - +
900B ARG* 3.3 7.9 + - - +
901B VAL* 2.9 34.7 + - - +
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Residues in contact with ILE 898 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634B MET* 4.0 26.7 - - + -
637B LEU* 4.2 4.0 - - + -
854B THR* 4.3 17.7 - - + -
855B MET* 3.9 10.1 - - + -
858B ALA* 3.5 27.6 - - + -
868B ILE* 4.1 20.2 - - + -
870B PRO* 3.9 26.0 - - + -
873B ILE* 5.4 0.2 - - + -
894B VAL 2.9 22.5 + - - +
895B CYS* 3.2 7.8 + - - +
897B ALA* 1.3 74.3 - - - +
899B LEU* 1.3 65.5 + - - +
901B VAL* 3.2 10.3 - - + +
902B TYR* 2.9 22.3 + - - +
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Residues in contact with LEU 899 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634B MET* 3.6 43.7 - - + +
637B LEU* 4.0 9.6 - - + -
638B LYS* 3.9 24.9 - - + +
641B LEU* 3.6 28.0 - - + -
895B CYS 3.1 13.9 + - - +
896B GLU* 3.3 9.2 + - + +
898B ILE* 1.3 76.0 - - - +
900B ARG* 1.3 62.7 + - - +
902B TYR* 3.4 7.2 + - + +
903B GLU* 3.0 35.4 + - + +
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Residues in contact with ARG 900 (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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818B SER* 3.4 22.4 + - - -
819B SER* 2.8 40.6 + - - +
822B LEU* 3.6 25.1 - - + +
896B GLU 3.0 14.5 + - - +
897B ALA* 3.6 10.8 - - - +
898B ILE 3.2 0.2 - - - -
899B LEU* 1.3 77.6 - - - +
901B VAL* 1.3 59.1 + - - +
903B GLU* 3.3 7.0 + - - +
904B GLU* 3.0 61.2 + - + +
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Residues in contact with VAL 901 (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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822B LEU* 3.7 33.4 - - + -
855B MET* 4.6 3.1 - - - -
858B ALA 5.4 1.6 - - - +
859B MET* 4.2 24.9 - - + +
862B THR* 4.4 22.9 + - + +
897B ALA 2.9 20.3 + - - +
898B ILE* 3.2 19.3 - - + +
900B ARG* 1.3 75.6 - - - +
902B TYR* 1.3 60.9 + - - +
904B GLU* 3.9 9.3 - - - +
905B GLY* 2.9 26.7 + - - -
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Residues in contact with TYR 902 (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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630B LEU* 3.7 36.6 - - + -
631B GLU* 3.4 30.1 + - - +
634B MET* 3.5 41.5 - - + -
862B THR* 3.6 15.4 + - - +
898B ILE* 2.9 17.9 + - + +
899B LEU* 3.5 5.4 - - + +
901B VAL* 1.3 78.8 - - - +
903B GLU* 1.3 82.9 + - + +
905B GLY* 3.2 3.1 + - - -
906B LEU* 3.1 61.7 + - + +
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Residues in contact with GLU 903 (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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638B LYS* 5.8 5.2 - - - +
899B LEU* 3.0 27.1 + - + +
900B ARG* 3.7 6.3 - - - +
902B TYR* 1.3 96.3 - - + +
904B GLU* 1.3 64.9 + - + +
906B LEU* 3.2 25.5 + - - +
907B VAL* 3.4 15.9 + - - +
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Residues in contact with GLU 904 (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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822B LEU* 5.4 2.9 - - - +
900B ARG* 3.0 59.3 + - + +
901B VAL* 4.0 8.8 - - - +
903B GLU* 1.3 74.6 - - + +
905B GLY* 1.3 65.4 + - - +
907B VAL* 3.2 15.2 + - - +
908B GLN* 3.1 31.6 + - - +
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Residues in contact with GLY 905 (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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862B THR* 5.6 4.0 - - - -
901B VAL 2.9 15.6 + - - -
902B TYR* 3.2 5.6 + - - -
904B GLU* 1.3 77.2 - - - +
906B LEU* 1.3 60.4 + - - +
907B VAL 3.5 0.2 + - - -
908B GLN* 3.5 28.2 + - - +
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Residues in contact with LEU 906 (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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630B LEU* 6.2 0.2 - - + -
902B TYR* 3.1 59.8 + - + +
903B GLU* 3.5 21.5 - - - +
904B GLU 3.2 0.4 - - - -
905B GLY* 1.3 75.6 - - - +
907B VAL* 1.3 67.3 + - + +
908B GLN 4.0 4.0 - - - -
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Residues in contact with VAL 907 (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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903B GLU 3.4 12.7 + - - +
904B GLU* 3.2 11.9 + - - +
906B LEU* 1.3 79.1 - - + +
908B GLN* 1.3 64.7 + - + +
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Residues in contact with GLN 908 (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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904B GLU* 3.1 32.1 + - - +
905B GLY* 3.6 19.9 - - - +
906B LEU 3.3 4.4 - - - -
907B VAL* 1.3 82.9 - - + +
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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