Contacts of the helix formed by residues 814 - 828 (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 ASP 814 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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764B PRO* 4.9 6.2 - - - +
765B VAL* 3.9 20.8 - - + +
812B GLU* 2.8 35.0 - - - +
813B GLU* 1.3 76.4 + - - +
815B PHE* 1.3 57.7 + - - +
816B GLU 3.4 1.1 - - - -
817B LEU* 3.3 14.2 + - + +
818B ARG* 2.8 49.0 + - - +
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Residues in contact with PHE 815 (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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805B THR 5.0 0.4 - - - -
806B GLY 3.8 22.4 - - - -
807B VAL* 4.0 8.3 - - + -
808B ALA 3.1 33.4 - - - -
809B ASN 3.5 10.1 - - - +
810B ASP* 3.6 28.7 - - + +
812B GLU 3.4 16.5 + - - +
813B GLU 3.1 3.0 - - - -
814B ASP* 1.3 77.4 - - - +
816B GLU* 1.3 73.0 + - - +
818B ARG* 3.3 14.1 + - - +
819B LYS* 2.7 67.3 + - + +
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Residues in contact with GLU 816 (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 ASP 4.7 5.0 - - - +
812B GLU 5.1 1.7 - - - +
813B GLU 4.4 11.3 - - - +
814B ASP 3.4 0.4 - - - -
815B PHE* 1.3 96.4 - - - +
817B LEU* 1.3 63.6 + - - +
819B LYS* 3.3 14.0 + - + +
820B GLU* 3.1 28.2 + - - +
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Residues in contact with LEU 817 (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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765B VAL* 3.3 35.0 - - + -
769B ARG* 3.7 26.5 - - - +
813B GLU 5.2 0.6 + - - +
814B ASP* 3.3 15.8 + - + +
816B GLU* 1.3 80.8 - - - +
818B ARG* 1.3 57.7 + - - +
820B GLU* 3.8 2.7 - - - +
821B LEU* 2.9 50.3 + - + +
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Residues in contact with ARG 818 (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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764B PRO* 4.0 25.1 - - + -
765B VAL* 3.8 15.9 - - + -
768B LEU* 4.3 9.2 - - + -
805B THR* 3.3 28.3 + - - +
806B GLY* 4.6 0.7 - - - -
808B ALA* 2.2 40.0 + - - +
809B ASN* 3.7 8.0 + - - +
812B GLU* 3.5 22.0 - - - +
814B ASP* 2.8 43.9 + - - +
815B PHE* 3.5 25.4 - - - +
817B LEU* 1.3 73.6 - - - +
819B LYS* 1.3 56.9 + - - +
821B LEU* 3.2 8.4 + - - +
822B ILE* 2.9 36.5 + - - +
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Residues in contact with LYS 819 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
805B THR 4.9 0.2 + - - -
806B GLY* 3.8 27.0 - - - +
815B PHE* 2.7 49.8 + - + +
816B GLU* 3.4 15.5 + - + +
817B LEU 3.2 0.2 - - - -
818B ARG* 1.3 73.1 - - - +
820B GLU* 1.3 77.3 + - + +
822B ILE* 3.5 3.6 + - - +
823B GLY* 3.1 21.7 + - - -
863B VAL* 5.8 1.7 - - - +
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Residues in contact with GLU 820 (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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816B GLU* 3.1 14.6 + - + +
817B LEU* 4.1 3.1 - - - +
819B LYS* 1.3 96.0 - - + +
821B LEU* 1.3 60.9 + - - +
823B GLY* 3.1 6.3 + - - +
824B GLN* 2.8 40.8 + - - +
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Residues in contact with LEU 821 (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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765B VAL* 4.3 14.1 - - + -
768B LEU* 3.8 43.1 - - + +
769B ARG* 4.1 20.6 - - + -
817B LEU* 2.9 52.7 + - + +
818B ARG* 3.5 8.3 - - - +
820B GLU* 1.3 76.3 - - - +
822B ILE* 1.3 56.9 + - - +
824B GLN* 3.1 21.8 + - + +
825B VAL* 3.0 33.6 + - + +
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Residues in contact with ILE 822 (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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768B LEU* 3.8 16.6 - - + -
802B LEU* 3.1 34.5 - - + +
803B ILE* 4.3 18.4 - - + +
805B THR* 3.5 13.5 - - + -
806B GLY* 3.6 22.0 - - - +
818B ARG 2.9 20.0 + - - +
819B LYS 3.7 4.3 - - - +
821B LEU* 1.3 75.5 - - - +
823B GLY* 1.3 52.1 + - - +
825B VAL* 3.2 9.2 + - + +
826B MET* 2.7 55.9 + - + +
863B VAL* 4.6 11.2 - - + -
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Residues in contact with GLY 823 (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 3.1 15.6 + - - -
820B GLU* 3.1 11.4 + - - -
822B ILE* 1.3 77.5 - - - +
824B GLN* 1.3 52.0 + - - +
826B MET* 3.2 7.8 + - - +
827B ASN* 2.5 42.5 + - - -
863B VAL* 5.5 5.4 - - - +
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Residues in contact with GLN 824 (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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820B GLU* 2.8 24.2 + - + +
821B LEU* 3.1 24.5 + - + +
823B GLY* 1.3 71.0 - - - +
825B VAL* 1.3 65.0 + - + +
826B MET 3.0 5.8 + - - -
827B ASN* 3.2 24.1 + - - +
828B GLN* 3.5 19.2 + - - +
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Residues in contact with VAL 825 (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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768B LEU* 4.7 19.1 - - + +
773B VAL* 4.7 24.9 - - + -
774B ILE* 5.4 11.4 - - + -
777B LEU* 3.4 33.3 - - + +
802B LEU* 5.2 7.4 - - + -
803B ILE* 6.5 1.1 - - + -
821B LEU* 3.0 17.8 + - + +
822B ILE* 3.2 11.6 + - + +
824B GLN* 1.3 78.0 - - + +
826B MET* 1.3 55.8 + - + +
828B GLN* 2.7 28.3 - - + +
829B LEU* 4.2 1.5 - - + +
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Residues in contact with MET 826 (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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777B LEU* 6.1 3.1 - - + -
803B ILE* 3.4 37.5 - - + -
822B ILE* 2.7 36.1 + - + +
823B GLY* 3.5 8.3 - - - +
824B GLN 3.0 0.2 - - - -
825B VAL* 1.3 80.7 - - + +
827B ASN* 1.3 65.0 + - - +
828B GLN 2.9 10.0 - - - +
829B LEU 5.2 0.7 - - - +
830B GLY* 3.3 34.9 + - - -
833B LEU* 4.4 11.9 - - + -
860B ILE* 4.5 13.0 - - + -
863B VAL* 4.6 14.8 - - + -
871B TRP* 3.5 29.1 - - + -
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Residues in contact with ASN 827 (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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823B GLY* 2.5 34.1 + - - -
824B GLN* 3.4 13.5 - - - +
826B MET* 1.3 76.7 - - - +
828B GLN* 1.3 59.0 + - + +
830B GLY 5.0 0.3 + - - -
871B TRP* 5.1 6.7 - - - -
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Residues in contact with GLN 828 (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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774B ILE* 3.8 33.4 - - + +
824B GLN* 3.7 20.5 + - - +
825B VAL* 2.7 34.3 - - + +
826B MET 2.9 1.6 - - - +
827B ASN* 1.3 78.1 - - - +
829B LEU* 1.3 72.4 + - + +
830B GLY 2.8 11.3 + - - -
832B GLN* 5.1 2.0 - - - +
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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