Contacts of the helix formed by residues 724 - 741 (chain B) in PDB entry 5JO3
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 724 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
662B ASN* 3.9 10.7 + - - -
680B SER* 2.6 33.5 + - - +
682B GLU* 3.5 28.4 - - + +
721B LEU 3.1 16.0 + - - +
722B ALA 3.5 3.0 - - - +
723B THR* 1.3 75.0 + - - +
725B LEU* 1.3 60.1 + - - +
726B ALA* 3.1 28.0 + - - +
727B LEU* 2.9 28.7 + - + +
728B TYR 3.2 8.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 725 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
723B THR 3.2 8.7 + - - +
724B ASP* 1.3 73.2 + - - +
726B ALA* 1.3 56.3 + - - +
728B TYR* 3.2 27.1 + - + +
729B ILE* 2.9 38.5 + - + +
761B THR* 4.3 14.4 - - + -
765B LEU* 4.3 11.9 - - + -
820B PHE* 4.1 24.5 - - + -
824B ILE* 4.1 21.8 - - + -
903B 6LK 4.3 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 726 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
663B GLN* 6.2 2.2 - - - +
724B ASP* 3.1 19.6 + - - +
725B LEU* 1.3 78.3 - - - +
727B LEU* 1.3 60.0 + - + +
729B ILE* 3.5 10.9 + - - +
730B LYS* 3.0 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 727 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
680B SER* 3.4 24.7 - - - +
721B LEU* 3.3 37.7 - - + +
722B ALA* 4.7 6.5 - - - +
724B ASP* 2.9 13.7 + - + +
726B ALA* 1.3 78.1 - - + +
728B TYR* 1.3 66.2 + - - +
730B LYS* 4.1 20.9 - - + +
731B ARG* 3.0 39.6 + - - +
758B MET* 5.1 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 728 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
722B ALA 4.4 3.6 + - - +
724B ASP 3.2 6.7 + - - +
725B LEU* 3.4 29.4 - - + +
727B LEU* 1.3 75.7 - - - +
729B ILE* 1.3 63.9 + - + +
732B ARG* 2.9 80.0 + - + +
736B PHE* 3.9 5.4 - + - -
758B MET* 3.8 29.2 - - + -
761B THR* 3.7 26.2 - - + +
824B ILE* 2.6 41.4 + - + -
828B LEU* 3.4 29.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 729 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
725B LEU* 2.9 30.2 + - + +
726B ALA* 3.8 7.9 - - - +
728B TYR* 1.3 79.2 - - + +
730B LYS* 1.3 62.7 + - - +
732B ARG* 3.8 27.9 + - - +
733B GLY 4.7 1.2 + - - -
824B ILE* 3.8 31.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 730 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
726B ALA 3.0 17.4 + - - +
727B LEU* 3.6 23.4 - - + +
728B TYR 3.2 0.4 - - - -
729B ILE* 1.3 78.9 - - - +
731B ARG* 1.3 68.8 + - + +
733B GLY* 4.7 2.9 + - - -
734B GLU 5.5 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 731 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
722B ALA* 6.0 0.2 - - - +
727B LEU* 3.0 27.3 + - - +
730B LYS* 1.3 90.5 - - + +
732B ARG* 1.3 66.7 + - - +
733B GLY 3.2 2.7 - - - -
734B GLU* 3.2 29.0 + - - +
735B PHE 3.5 3.5 + - - -
750B HIS* 3.9 21.8 - - - -
753B GLU* 2.7 44.1 + - - -
754B LEU* 3.7 37.3 - - + +
757B ALA* 3.9 17.4 - - - +
758B MET* 4.3 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 732 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
728B TYR* 2.9 71.8 + - + +
729B ILE* 3.8 22.5 + - - +
730B LYS 3.6 0.2 - - - -
731B ARG* 1.3 78.8 - - - +
733B GLY* 1.3 60.2 + - - +
735B PHE* 3.0 3.3 + - - +
736B PHE* 2.9 50.0 + - + -
758B MET* 3.9 13.0 - - - +
823B ALA* 2.8 31.1 + - - +
824B ILE* 3.8 8.9 + - - +
827B GLN* 3.6 19.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 733 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
729B ILE 4.7 2.4 + - - -
730B LYS 4.7 2.5 + - - -
731B ARG 3.2 1.4 - - - -
732B ARG* 1.3 83.6 - - - +
734B GLU* 1.3 56.4 + - - +
736B PHE* 3.4 7.4 + - - +
737B GLU* 3.0 38.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 734 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
730B LYS 5.5 0.6 + - - -
731B ARG* 3.2 18.5 + - - +
732B ARG 3.2 0.4 - - - -
733B GLY* 1.3 77.9 - - - +
735B PHE* 1.3 57.8 + - - +
737B GLU* 3.7 5.1 - - - +
738B LEU* 3.0 43.4 + - + +
750B HIS* 2.7 38.1 + - - -
754B LEU* 3.8 20.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 735 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
731B ARG 3.5 1.6 + - - -
732B ARG 3.0 9.5 + - - +
734B GLU* 1.3 78.7 - - - +
736B PHE* 1.3 74.8 + + - +
738B LEU* 3.3 5.0 + - - +
739B ILE* 3.2 33.2 + - + +
744B PHE* 3.6 38.4 - + - -
754B LEU* 3.7 27.0 - - + +
755B PHE* 4.1 22.9 - + - -
758B MET* 3.4 36.6 - - + -
828B LEU* 4.8 4.0 - - + -
831B ALA* 3.4 30.7 - - + -
832B LEU* 4.9 1.8 - - - -
835B VAL* 4.2 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 736 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
728B TYR* 3.9 14.8 - + - -
732B ARG* 2.9 50.6 + - + +
733B GLY* 3.9 6.1 - - - +
735B PHE* 1.3 87.4 - + - +
737B GLU* 1.3 58.5 + - + +
739B ILE* 3.4 7.8 + - - +
740B ARG* 2.9 30.0 + - - +
758B MET* 5.2 0.2 - - - -
827B GLN* 3.6 60.6 - - + -
828B LEU* 3.9 5.4 - - + -
831B ALA* 3.7 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 737 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
733B GLY* 3.0 23.1 + - - +
734B GLU* 3.7 6.1 - - - +
735B PHE 3.2 0.2 - - - -
736B PHE* 1.3 76.0 - - + +
738B LEU* 1.3 64.0 + - - +
740B ARG* 2.4 37.0 + - - +
741B LYS* 2.9 50.0 + - + +
743B GLN* 5.2 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 738 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
734B GLU* 3.0 34.5 + - + +
735B PHE* 3.3 4.7 + - - +
737B GLU* 1.3 77.3 - - - +
739B ILE* 1.3 61.6 + - - +
741B LYS 3.6 0.2 + - - -
742B ASN 3.2 2.3 + - - -
743B GLN* 2.7 61.9 + - + +
744B PHE* 3.2 18.4 + - + -
751B GLU* 3.7 36.8 - - + +
754B LEU* 3.9 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 739 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
735B PHE* 3.2 26.3 + - + +
736B PHE* 3.6 9.4 - - - +
738B LEU* 1.3 77.0 - - - +
740B ARG* 1.3 64.3 + - - +
742B ASN* 3.1 20.1 + - - +
744B PHE* 3.6 36.6 - - + -
831B ALA* 4.8 8.7 - - + +
834B HIS* 3.3 52.9 + - + +
835B VAL* 4.1 11.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 740 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
736B PHE 2.9 17.6 + - - +
737B GLU* 2.4 44.1 + - - +
739B ILE* 1.3 78.0 - - - +
741B LYS* 1.3 78.8 + - - +
742B ASN* 3.3 9.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 741 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
737B GLU* 2.9 35.5 + - + +
738B LEU 4.3 0.2 - - - +
740B ARG* 1.3 105.5 - - - +
742B ASN* 1.3 72.8 + - - +
743B GLN* 3.2 38.1 + - + +
----------------------------------------------------------
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