Contacts of the helix formed by residues 895 - 917 (chain B) in PDB entry 2OOQ
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 ASP 895 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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891B ILE* 4.0 9.2 - - + -
892B ARG* 2.8 62.5 + - + +
894B ALA* 1.3 74.5 - - - +
896B LEU* 1.3 58.5 + - - +
897B LEU 3.4 2.7 - - - -
898B GLN* 3.4 11.1 + - + +
899B HIS* 2.9 28.8 + - + +
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Residues in contact with LEU 896 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
891B ILE* 3.9 13.0 - - + -
892B ARG 3.1 6.8 + - - +
893B VAL* 3.2 16.4 + - - +
894B ALA 3.5 0.2 - - - -
895B ASP* 1.3 75.3 - - - +
897B LEU* 1.3 61.8 + - - +
899B HIS* 3.3 9.7 + - + +
900B ILE* 2.9 55.2 + - + +
1132B VAL* 4.0 23.3 - - + -
1134B ILE* 4.8 9.2 - - + -
1159B HIS* 5.0 0.7 - - + +
1162B ILE* 3.9 28.3 - - + -
1163B LEU* 3.9 24.2 - - + +
1166B CYS* 4.3 11.0 - - - -
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Residues in contact with LEU 897 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
893B VAL 4.7 1.0 + - - -
894B ALA 5.0 3.9 + - - +
895B ASP 3.4 0.4 - - - -
896B LEU* 1.3 76.2 - - - +
898B GLN* 1.3 59.3 + - - +
900B ILE* 3.2 3.3 + - + -
901B THR* 2.9 41.7 + - - +
1163B LEU* 3.7 37.4 - - + +
1167B LEU* 5.5 11.4 - - + -
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Residues in contact with GLN 898 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
894B ALA 5.5 0.6 + - - +
895B ASP* 3.4 12.7 + - + +
896B LEU 3.3 0.4 - - - -
897B LEU* 1.3 79.6 - - - +
899B HIS* 1.3 62.9 + - - +
901B THR* 3.4 8.2 + - + -
902B GLN* 3.0 34.5 + - + +
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Residues in contact with HIS 899 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
891B ILE* 4.1 39.6 - - + +
895B ASP* 2.9 14.7 + - + +
896B LEU* 3.3 19.5 + - + +
898B GLN* 1.3 78.7 - - - +
900B ILE* 1.3 60.5 + - - +
902B GLN* 3.3 6.3 + - - +
903B MET* 2.9 64.3 + - + +
914B GLU* 4.8 8.8 + - - -
1159B HIS* 4.6 17.1 + + - -
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Residues in contact with ILE 900 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
896B LEU* 2.9 36.6 + - + +
897B LEU* 3.7 5.4 - - + +
899B HIS* 1.3 73.5 - - + +
901B THR* 1.3 67.1 + - - +
903B MET* 3.1 9.4 + - - +
904B LYS* 3.0 52.7 + - + +
911B PHE* 4.2 7.4 - - + -
1159B HIS* 3.6 46.2 - - + +
1160B ASP* 4.2 5.4 - - - +
1163B LEU* 3.8 26.7 - - + -
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Residues in contact with THR 901 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
897B LEU* 2.9 29.7 + - - +
898B GLN* 3.5 10.4 - - + -
900B ILE* 1.3 77.5 - - - +
902B GLN* 1.3 66.3 + - + +
904B LYS* 3.0 19.9 + - - +
905B ARG* 3.2 22.0 + - + +
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Residues in contact with GLN 902 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
898B GLN* 3.0 30.3 + - + +
899B HIS* 3.7 7.6 - - - +
901B THR* 1.3 79.1 - - + +
903B MET* 1.3 63.4 + - + +
905B ARG* 3.4 31.8 + - - +
910B GLY* 5.1 2.9 + - - -
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Residues in contact with MET 903 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
899B HIS* 2.9 40.6 - - + +
900B ILE* 3.1 9.1 + - - +
902B GLN* 1.3 80.9 - - + +
904B LYS* 1.3 56.1 + - - +
905B ARG 3.5 0.2 - - - -
908B GLY* 3.4 14.2 - - - -
910B GLY* 3.4 35.5 + - - +
911B PHE* 3.1 55.0 + - + -
914B GLU* 3.7 31.2 - - + +
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Residues in contact with LYS 904 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
900B ILE* 3.0 35.7 + - + +
901B THR* 3.0 10.5 + - - +
903B MET* 1.3 73.4 - - - +
905B ARG* 1.3 63.9 + - - +
907B GLN* 3.6 4.2 + - - -
908B GLY* 2.9 22.5 + - - -
911B PHE* 3.6 17.7 - - + -
1156B VAL* 4.2 11.0 - - + -
1160B ASP* 3.0 29.1 + - - -
1163B LEU* 6.1 0.8 - - - +
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Residues in contact with ARG 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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901B THR* 3.2 23.2 + - + +
902B GLN* 3.4 27.8 + - - +
903B MET 4.2 1.4 - - - +
904B LYS* 1.3 80.4 - - - +
906B GLY* 1.3 65.5 + - - +
909B TYR* 3.2 17.8 + - - +
910B GLY 4.5 0.3 + - - -
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Residues in contact with GLY 906 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
905B ARG* 1.3 73.5 - - - +
907B GLN* 1.3 72.1 + - - +
909B TYR* 3.2 20.2 + - - +
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Residues in contact with GLN 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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904B LYS 3.6 4.0 + - - -
905B ARG 3.3 0.6 - - - -
906B GLY* 1.3 80.1 - - - +
908B GLY* 1.3 58.9 + - - +
909B TYR* 3.5 0.3 + - - -
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Residues in contact with GLY 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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903B MET 3.4 16.4 - - - -
904B LYS* 2.9 18.0 + - - -
907B GLN* 1.3 76.1 - - - +
909B TYR* 1.3 66.3 + - - +
910B GLY 3.3 2.5 - - - -
911B PHE* 3.2 8.6 + - - +
912B LYS* 2.9 24.2 + - - +
1152B GLU* 4.6 4.1 - - - +
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Residues in contact with TYR 909 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
905B ARG 3.2 9.6 + - - +
906B GLY* 3.2 18.3 + - - +
907B GLN 3.4 0.2 - - - -
908B GLY* 1.3 77.0 - - - +
910B GLY* 1.3 62.8 + - - +
912B LYS* 3.2 7.1 + - + +
913B GLU* 3.0 64.2 + - + +
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Residues in contact with GLY 910 (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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902B GLN 5.1 2.3 + - - -
903B MET* 3.4 30.9 + - - +
905B ARG 4.5 1.0 + - - -
908B GLY 3.3 0.6 - - - -
909B TYR* 1.3 85.8 - - - +
911B PHE* 1.3 55.7 + - - +
913B GLU* 3.5 4.3 + - - +
914B GLU* 3.0 31.2 + - - +
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Residues in contact with PHE 911 (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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900B ILE* 3.9 11.2 - - + -
903B MET* 3.1 51.1 + - + +
904B LYS* 3.6 29.4 - - + -
908B GLY* 3.2 8.9 + - - +
910B GLY* 1.3 71.7 - - - +
912B LYS* 1.3 60.4 + - - +
914B GLU* 3.4 0.5 + - - +
915B TYR* 2.8 33.7 + - - +
1152B GLU* 4.5 5.8 - - + +
1155B TYR* 4.1 12.4 - + - -
1156B VAL* 3.6 40.2 - - + -
1159B HIS* 3.5 52.5 - + + -
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Residues in contact with LYS 912 (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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908B GLY 2.9 13.5 + - - +
909B TYR* 3.6 11.9 - - + +
911B PHE* 1.3 76.6 - - - +
913B GLU* 1.3 59.3 + - - +
915B TYR* 3.8 1.4 - - - +
916B GLU* 3.0 53.3 + - - +
1152B GLU* 3.9 27.1 + - - +
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Residues in contact with GLU 913 (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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909B TYR* 3.0 53.2 + - + +
910B GLY* 3.9 6.0 - - - +
912B LYS* 1.3 79.5 - - - +
914B GLU* 1.3 62.3 + - - +
916B GLU* 3.4 9.6 + - - +
917B ALA* 3.2 19.9 + - - +
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Residues in contact with GLU 914 (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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889B MET* 6.0 1.6 - - - +
899B HIS* 4.8 9.9 + - - -
903B MET* 3.7 22.5 - - + +
910B GLY 3.0 18.3 + - - +
911B PHE 3.9 2.2 - - - +
913B GLU* 1.3 77.9 - - - +
915B TYR* 1.3 61.9 + - - +
917B ALA* 3.0 20.6 + - - +
918B LEU* 3.6 3.5 + - - +
1135B PHE* 3.5 31.5 + - + +
1155B TYR* 2.5 35.0 + - + +
1159B HIS* 4.3 6.6 + - - -
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Residues in contact with TYR 915 (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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911B PHE 2.8 23.3 + - - +
912B LYS 3.8 3.4 - - - +
914B GLU* 1.3 72.2 - - - +
916B GLU* 1.3 70.3 + - + +
918B LEU* 3.1 37.5 + - + +
1142B ARG* 3.1 27.0 + - - -
1149B VAL 3.9 3.4 - - - -
1150B GLN 3.0 32.3 + - - -
1151B THR* 3.4 17.3 - - - -
1152B GLU* 3.6 32.5 - - + -
1155B TYR* 3.5 28.8 - + + -
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Residues in contact with GLU 916 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
912B LYS* 3.0 40.8 + - - +
913B GLU* 3.8 8.4 - - - +
914B GLU 3.2 0.2 - - - -
915B TYR* 1.3 85.4 - - + +
917B ALA* 1.3 58.7 + - - +
918B LEU 3.3 7.1 + - - +
1152B GLU* 5.3 0.9 - - - +
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Residues in contact with ALA 917 (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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913B GLU 3.2 10.8 + - - +
914B GLU* 3.0 15.9 + - - +
916B GLU* 1.3 76.3 - - - +
918B LEU* 1.3 62.6 + - - +
919B PRO* 3.8 2.8 - - - +
1135B PHE* 4.1 21.1 - - + -
1139B ARG* 6.0 0.2 - - - -
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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