Contacts of the helix formed by residues 864 - 878 (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 864 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
860B ILE* 3.1 7.5 + - - +
861B MET 3.2 2.6 + - - -
863B VAL* 1.3 89.5 - - + +
865B ARG* 1.3 59.9 + - - +
866B PRO* 3.3 23.8 - - - +
867B THR* 3.0 44.8 + - - +
868B PHE* 3.2 11.8 + - - +
871B TRP* 5.6 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 865 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
858B TRP* 4.0 4.9 - - - -
861B MET* 2.9 45.2 + - + +
862B GLN* 3.1 31.5 - - - +
864B ASP* 1.3 69.6 - - - +
866B PRO* 1.3 70.8 - - + +
868B PHE* 3.0 7.1 + - - +
869B CYS* 2.9 39.0 + - - -
903B THR 2.9 27.6 + - - +
904B SER 4.3 1.0 - - - -
905B ALA 2.9 29.6 + - - +
906B GLU* 4.1 14.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 866 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
864B ASP* 3.3 16.6 - - - +
865B ARG* 1.3 95.2 - - + +
867B THR* 1.3 60.9 - - + +
869B CYS* 3.4 21.8 - - + +
870B ARG* 3.6 7.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 867 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
864B ASP* 3.0 41.6 + - - +
866B PRO* 1.3 77.2 - - + +
868B PHE* 1.3 64.6 + - - +
870B ARG* 3.1 8.3 + - - +
871B TRP* 2.9 56.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 868 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
834B VAL* 4.1 16.8 - - + -
857B LEU* 3.8 37.0 - - + -
860B ILE* 3.5 27.4 - - + -
861B MET* 3.3 33.2 - - + -
864B ASP 3.2 11.2 + - - +
865B ARG* 3.0 11.4 + - + +
867B THR* 1.3 82.5 + - - +
869B CYS* 1.3 61.1 + - - +
871B TRP* 3.5 9.8 - - - +
872B LEU* 2.8 46.4 + - + +
902B VAL* 3.8 28.3 - - + -
903B THR* 4.3 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 869 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
865B ARG* 2.9 28.3 + - - -
866B PRO* 3.4 14.1 - - + +
868B PHE* 1.3 76.9 - - - +
870B ARG* 1.3 56.6 + - - +
873B GLU* 2.9 16.1 + - - +
899B HIS* 2.8 33.2 + - + +
903B THR* 3.6 32.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 870 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
866B PRO 3.6 7.0 + - - +
867B THR* 3.1 9.9 + - - +
869B CYS* 1.3 75.5 - - - +
871B TRP* 1.3 63.4 + - + +
873B GLU* 2.6 40.1 + - - +
874B ASN* 2.8 69.4 + - - +
877B LYS* 4.2 10.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 871 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
826B MET* 3.5 40.6 - - + -
827B ASN* 5.1 6.7 - - - -
830B GLY* 3.8 13.2 - - - -
831B GLN* 2.8 62.7 + - + +
834B VAL* 3.9 25.4 - - + -
860B ILE* 3.8 20.4 - - + -
864B ASP* 5.6 2.2 - - + -
867B THR* 2.9 34.7 + - - -
868B PHE* 3.5 19.3 - - + +
870B ARG* 1.3 79.0 - - + +
872B LEU* 1.3 56.4 + - - +
874B ASN* 4.9 1.6 - - - -
875B SER* 2.8 20.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 872 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
834B VAL* 4.1 15.0 - - + +
838B LEU* 4.8 10.8 - - + -
857B LEU* 5.9 4.3 - - + -
868B PHE* 2.8 30.9 + - + +
869B CYS 3.6 4.0 - - - +
871B TRP* 1.3 68.9 - - - +
873B GLU* 1.3 60.3 + - - +
875B SER* 3.2 5.0 + - - -
876B LEU* 2.8 39.2 + - + +
898B PHE* 3.8 24.0 - - + -
899B HIS* 3.5 26.2 - - + -
902B VAL* 3.9 32.5 - - + -
903B THR* 3.9 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 873 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
869B CYS 2.9 11.0 + - - +
870B ARG* 2.6 53.7 + - - +
872B LEU* 1.3 76.5 - - - +
874B ASN* 1.3 58.0 + - - +
876B LEU* 3.1 7.9 + - + +
877B LYS* 2.8 31.6 + - - +
899B HIS* 3.5 31.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 874 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
831B GLN* 2.8 31.3 + - - +
835B SER* 4.9 0.4 - - - -
870B ARG* 2.8 50.1 + - - +
871B TRP* 3.5 2.2 - - - +
873B GLU* 1.3 73.4 - - - +
875B SER* 1.3 62.1 + - - +
877B LYS* 3.1 20.1 + - + +
878B GLY* 3.1 19.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 875 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
831B GLN* 3.3 1.8 + - - +
834B VAL* 3.5 7.5 - - - +
835B SER* 2.8 45.6 + - - -
838B LEU* 3.8 19.4 - - - +
839B HIS* 5.0 3.3 + - - -
871B TRP 2.8 20.2 + - - -
872B LEU* 3.4 12.1 - - - -
873B GLU 3.2 0.2 - - - -
874B ASN* 1.3 75.3 - - - +
876B LEU* 1.3 62.0 + - - +
878B GLY* 3.2 11.8 + - - -
879B LEU* 3.4 13.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 876 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
838B LEU* 3.7 18.4 - - + -
872B LEU* 2.8 20.6 + - + +
873B GLU* 3.5 6.1 - - + +
875B SER* 1.3 74.0 - - - +
877B LYS* 1.3 64.8 + - - +
879B LEU* 3.4 8.5 + - + +
881B LYS* 3.0 25.8 + - - -
895B LEU* 3.9 24.6 - - + +
898B PHE* 3.7 30.1 - - + -
899B HIS* 3.7 34.5 - - + -
918B PHE* 3.8 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 877 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
870B ARG* 4.2 13.9 - - - +
873B GLU* 2.8 11.5 + - - +
874B ASN* 3.1 32.5 + - + +
876B LEU* 1.3 78.7 - - - +
878B GLY* 1.3 56.3 + - - +
879B LEU 3.3 3.3 + - - +
881B LYS* 3.8 7.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 878 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
839B HIS* 3.2 20.2 + - - -
874B ASN 3.1 13.2 + - - -
875B SER 3.2 7.6 + - - -
876B LEU 3.2 0.2 - - - -
877B LYS* 1.3 75.5 - - - +
879B LEU* 1.3 58.5 + - - +
880B PRO* 3.8 2.6 - - - +
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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