Contacts of the helix formed by residues 907 - 922 (chain B) in PDB entry 4OL0
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 907 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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858B TRP* 3.3 16.4 - - - -
905B ALA* 3.8 4.7 - - - +
906B GLU* 1.3 83.0 - - - +
908B CYS* 1.3 68.0 + - + +
909B LYS* 3.6 40.7 + - + +
910B GLN* 3.1 32.2 + - + +
911B VAL* 3.6 3.5 + - - +
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Residues in contact with CYS 908 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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851B PRO* 4.3 0.9 - - - -
854B ALA* 3.4 14.1 - - - -
855B GLU* 3.3 48.5 - - + -
858B TRP* 3.9 30.0 - - + -
907B GLU* 1.3 76.1 - - + +
909B LYS* 1.3 57.7 + - - +
911B VAL* 3.0 6.6 + - - +
912B CYS* 2.8 27.5 + - - +
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Residues in contact with LYS 909 (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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907B GLU* 3.2 33.1 + - + +
908B CYS* 1.3 77.8 - - - +
910B GLN* 1.3 56.3 + - + +
912B CYS* 3.2 9.0 + - + +
913B TRP* 2.9 50.8 + - + +
916B ARG* 6.2 2.5 - - - +
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Residues in contact with GLN 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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901B GLN* 4.6 7.0 + - + +
904B SER* 4.4 2.6 + - - +
905B ALA* 3.5 21.2 - - + -
906B GLU* 3.6 27.2 + - - +
907B GLU* 3.1 26.0 + - + +
909B LYS* 1.3 73.4 - - + +
911B VAL* 1.3 62.4 + - - +
913B TRP* 3.3 8.7 + - - +
914B ALA* 2.8 30.8 + - - +
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Residues in contact with VAL 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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854B ALA* 4.0 24.5 - - + +
857B LEU* 4.2 17.5 - - + -
858B TRP* 4.3 6.7 - - + -
861B MET* 3.5 25.6 - - + -
902B VAL* 4.2 20.8 - - + +
905B ALA* 3.7 18.6 - - + -
907B GLU 3.9 6.7 - - - +
908B CYS* 3.0 12.3 + - - +
910B GLN* 1.3 75.6 - - - +
912B CYS* 1.3 58.0 + - - +
914B ALA* 3.4 6.5 + - - +
915B LEU* 2.8 31.3 + - + +
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Residues in contact with CYS 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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850B LEU* 4.0 3.3 - - - +
851B PRO* 3.7 33.7 - - + -
854B ALA* 3.7 13.4 - - + +
908B CYS* 2.8 12.8 + - - +
909B LYS* 3.4 14.8 - - + +
910B GLN 3.2 0.2 - - - -
911B VAL* 1.3 74.0 - - - +
913B TRP* 1.3 60.7 + - - +
915B LEU* 3.1 6.9 + - - +
916B ARG* 2.8 66.8 + - - +
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Residues in contact with TRP 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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901B GLN* 5.6 1.3 - - - +
909B LYS* 2.9 47.4 + - + +
910B GLN* 3.7 6.7 - - - +
912B CYS* 1.3 72.7 - - + +
914B ALA* 1.3 58.1 + - - +
916B ARG* 3.2 39.8 + - + +
917B ASP* 2.9 45.0 + - - +
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Residues in contact with ALA 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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898B PHE* 3.9 6.7 - - + +
901B GLN* 3.4 37.1 - - + +
902B VAL* 3.7 23.3 - - + +
910B GLN 2.8 17.1 + - - +
911B VAL* 3.5 5.6 - - - +
913B TRP* 1.3 75.9 - - - +
915B LEU* 1.3 56.6 + - - +
917B ASP* 3.3 2.9 + - - +
918B PHE* 2.8 31.5 + - - +
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Residues in contact with LEU 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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838B LEU* 5.0 7.0 - - + -
841B CYS* 4.5 20.6 - - + -
850B LEU* 3.6 33.9 - - + +
853B VAL* 4.3 7.9 - - + -
854B ALA* 3.9 16.2 - - - +
857B LEU* 4.0 25.1 - - + -
898B PHE* 3.9 27.6 - - + -
902B VAL* 5.4 0.2 - - + -
911B VAL* 2.8 26.1 + - + +
912B CYS* 3.4 4.9 - - - +
914B ALA* 1.3 72.8 - - - +
916B ARG* 1.3 55.3 + - - +
918B PHE* 3.7 2.5 - - + +
919B THR* 2.5 40.0 + - - +
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Residues in contact with ARG 916 (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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847B PRO* 5.0 7.2 + - + +
850B LEU* 3.6 24.4 - - + +
851B PRO* 4.3 17.8 - - - +
909B LYS* 6.2 1.8 - - - +
912B CYS* 2.8 43.8 + - - +
913B TRP* 3.5 48.3 - - + +
915B LEU* 1.3 75.7 - - - +
917B ASP* 1.3 64.3 + - - +
919B THR* 3.1 1.0 + - - -
920B ARG* 2.9 34.8 + - + +
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Residues in contact with ASP 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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901B GLN* 4.0 17.9 + - - +
913B TRP* 2.9 33.9 + - - +
914B ALA* 3.6 5.4 - - - +
916B ARG* 1.3 75.8 - - - +
918B PHE* 1.3 61.7 + - - +
920B ARG* 3.7 11.9 + - - +
921B LEU* 3.7 17.5 - - - +
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Residues in contact with PHE 918 (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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838B LEU* 3.9 12.3 - - + -
842B CYS* 3.7 18.2 - - - -
876B LEU* 3.8 7.0 - - + -
879B LEU* 3.7 12.1 - - + -
890B VAL* 4.4 7.4 - - + -
894B GLN 3.7 15.0 - - - -
895B LEU* 3.7 33.0 - - + -
898B PHE* 3.5 40.6 - + + -
914B ALA 2.8 17.0 + - - +
915B LEU* 3.9 4.3 - - + +
917B ASP* 1.3 73.9 - - - +
919B THR* 1.3 66.2 + - - +
921B LEU* 3.4 26.6 + - + +
922B PHE* 3.4 34.5 - + - -
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Residues in contact with THR 919 (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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841B CYS* 3.6 29.1 + - - +
842B CYS* 4.8 7.8 - - - +
845B LEU 5.6 1.6 - - - +
846B PRO 6.4 0.2 - - - -
847B PRO* 5.8 5.2 - - + -
850B LEU* 3.7 27.0 - - + +
915B LEU* 2.5 32.2 + - - +
916B ARG* 3.7 2.9 - - - -
918B PHE* 1.3 72.5 - - - +
920B ARG* 1.3 65.6 + - - +
921B LEU 3.0 4.0 + - - -
922B PHE* 3.1 21.4 + - - +
923B ARG 3.7 9.4 + - - -
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Residues in contact with ARG 920 (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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916B ARG* 2.9 26.7 + - + +
917B ASP* 3.9 9.2 - - - +
918B PHE 3.4 0.2 - - - -
919B THR* 1.3 76.6 - - + +
921B LEU* 1.3 64.3 + - + +
923B ARG* 3.0 20.7 + - - +
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Residues in contact with LEU 921 (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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890B VAL* 3.9 31.1 - - + +
894B GLN* 3.2 50.5 - - + +
917B ASP 3.7 13.0 - - - +
918B PHE* 3.4 27.4 - - + +
919B THR 3.0 0.6 + - - -
920B ARG* 1.3 79.7 - - + +
922B PHE* 1.3 58.8 + - + +
923B ARG* 3.1 11.0 + - - -
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Residues in contact with PHE 922 (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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842B CYS* 3.5 30.7 - - + +
843B PHE* 3.7 22.9 - + + -
879B LEU* 3.6 22.9 - - + -
880B PRO 3.8 20.6 - - - -
881B LYS* 4.7 6.1 - - + -
882B GLU 5.8 2.5 - - - -
883B THR 6.5 0.7 - - - -
890B VAL* 3.6 29.6 - - + -
918B PHE* 3.4 44.6 - + - -
919B THR* 3.1 10.0 + - - +
921B LEU* 1.3 74.3 - - + +
923B ARG* 1.3 73.0 + - - +
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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
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Atomic class I II III IV V VI VII VIII
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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