Contacts of the helix formed by residues 722 - 748 (chain R) in PDB entry 4UJ3
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 722 (chain R).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
720R LEU 3.3 6.6 - - - +
721R MET* 1.3 78.3 - - + +
723R ALA* 1.3 59.1 + - - +
724R ILE 3.2 2.7 - - - -
725R GLN* 3.1 14.1 + - + +
726R LYS* 3.1 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 723 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
720R LEU* 3.7 16.4 + - - +
721R MET 3.2 0.8 - - - -
722R GLU* 1.3 78.8 - - - +
724R ILE* 1.3 58.8 + - + +
726R LYS* 3.4 6.3 + - - +
727R GLN* 2.9 29.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 724 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
720R LEU 5.4 1.8 - - - +
721R MET* 3.8 16.1 + - + +
722R GLU 3.2 0.4 - - - -
723R ALA* 1.3 79.0 - - + +
725R GLN* 1.3 61.8 + - - +
727R GLN* 3.8 7.6 - - + +
728R GLU* 3.4 21.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 725 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
721R MET 4.2 2.3 + - - +
722R GLU* 3.1 22.0 + - + +
724R ILE* 1.3 80.9 - - - +
726R LYS* 1.3 61.1 + - - +
728R GLU* 3.7 7.0 + - - +
729R GLU* 3.7 15.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 726 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
722R GLU 3.1 13.8 + - - +
723R ALA* 4.0 6.7 - - - +
724R ILE 3.4 0.2 - - - -
725R GLN* 1.3 75.8 - - - +
727R GLN* 1.3 63.0 + - - +
728R GLU 3.3 0.9 - - - -
729R GLU* 3.3 17.3 + - - +
730R ILE* 3.4 17.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 727 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
723R ALA 2.9 18.7 + - - +
724R ILE* 4.0 10.3 - - + +
725R GLN 3.3 0.4 - - - -
726R LYS* 1.3 76.7 - - - +
728R GLU* 1.3 60.1 + - - +
730R ILE* 3.6 26.4 + - - +
731R ASN* 3.4 20.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 728 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
724R ILE 3.4 15.1 + - - +
725R GLN* 4.0 7.6 - - - +
726R LYS 3.3 0.4 - - - -
727R GLN* 1.3 74.6 - - - +
729R GLU* 1.3 59.7 + - - +
730R ILE 3.2 0.7 - - - -
731R ASN* 3.7 8.0 - - - +
732R PHE* 3.0 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 729 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
725R GLN 3.7 10.2 + - - +
726R LYS* 3.3 12.8 + - - +
727R GLN 3.3 0.4 - - - -
728R GLU* 1.3 76.9 - - - +
730R ILE* 1.3 64.0 + - + +
732R PHE* 3.9 6.7 - - - +
733R ARG* 3.3 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 730 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
726R LYS 3.4 14.0 + - - +
727R GLN* 3.8 29.8 - - - +
728R GLU 3.2 0.4 - - - -
729R GLU* 1.3 76.1 - - + +
731R ASN* 1.3 54.9 + - - +
733R ARG* 3.2 5.3 + - - +
734R LEU* 2.7 55.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 731 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
727R GLN* 3.4 12.2 + - - +
728R GLU* 3.7 10.5 - - - +
730R ILE* 1.3 81.6 - - - +
732R PHE* 1.3 55.9 + - - +
734R LEU* 4.3 9.1 - - - +
735R GLN* 2.8 51.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 732 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
728R GLU 3.0 18.5 + - - +
729R GLU* 3.9 9.6 - - - +
730R ILE 3.3 0.2 - - - -
731R ASN* 1.3 74.7 - - - +
733R ARG* 1.3 58.7 + - - +
735R GLN* 4.1 2.7 - - - +
736R ASP* 2.9 31.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 733 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
729R GLU 3.3 13.8 + - - +
730R ILE* 3.2 5.7 + - - +
732R PHE* 1.3 76.8 - - - +
734R LEU* 1.3 62.0 + - - +
736R ASP* 3.5 5.6 + - - +
737R TYR* 2.9 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 734 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
730R ILE* 2.7 41.2 + - + +
731R ASN* 3.7 10.8 - - - +
733R ARG* 1.3 75.1 - - + +
735R GLN* 1.3 56.5 + - - +
737R TYR* 3.4 14.3 - - + +
738R ILE* 3.0 35.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 735 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44P ILE* 5.2 13.0 - - - +
731R ASN* 2.8 34.7 + - - +
732R PHE* 4.2 3.4 - - - +
734R LEU* 1.3 72.5 - - - +
736R ASP* 1.3 61.6 + - - +
737R TYR 3.1 1.8 - - - -
738R ILE* 3.0 15.6 + - + +
739R ASP* 2.8 45.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 736 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
732R PHE 2.9 20.6 + - - +
733R ARG* 3.9 6.3 - - - +
735R GLN* 1.3 76.0 - - - +
737R TYR* 1.3 60.5 + - - +
739R ASP* 3.7 9.8 + - - +
740R ARG* 3.5 20.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 737 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
733R ARG 2.9 17.9 + - - +
734R LEU* 3.4 16.2 - - + +
736R ASP* 1.3 75.0 - - - +
738R ILE* 1.3 70.4 + - + +
739R ASP 3.3 0.2 + - - -
740R ARG* 3.3 6.0 + - + +
741R ILE* 3.0 53.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 738 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44P ILE* 5.3 20.0 - - + -
45P GLY* 4.3 25.8 - - - +
734R LEU* 3.0 20.2 - - + +
735R GLN* 3.0 17.8 + - + +
737R TYR* 1.3 80.9 - - + +
739R ASP* 1.3 68.0 + - - +
741R ILE* 3.1 22.8 - - + +
742R ILE* 3.2 14.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 739 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76P ILE* 2.8 38.0 - - + +
735R GLN* 2.8 33.4 + - - +
736R ASP* 3.8 9.5 - - - +
737R TYR 3.2 0.2 - - - -
738R ILE* 1.3 81.9 - - - +
740R ARG* 1.3 63.7 + - - +
743R VAL* 3.1 9.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 740 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
736R ASP 3.5 10.2 + - - +
737R TYR* 3.3 10.9 + - + +
739R ASP* 1.3 79.3 - - - +
741R ILE* 1.3 63.4 + - - +
743R VAL* 3.1 13.8 + - - +
744R ALA* 3.1 20.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 741 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
737R TYR* 3.0 49.1 + - + +
738R ILE* 3.1 21.5 - - + +
740R ARG* 1.3 74.1 - - - +
742R ILE* 1.3 68.7 + - + +
744R ALA* 3.2 8.7 + - + +
745R ILE* 3.0 47.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 742 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45P GLY* 4.4 9.0 - - - -
46P VAL* 3.9 35.0 - - + +
76P ILE* 3.9 15.3 - - + -
738R ILE* 3.2 26.1 + - + +
739R ASP* 3.2 4.7 + - - +
741R ILE* 1.3 85.7 - - + +
743R VAL* 1.3 64.1 + - - +
745R ILE* 3.1 9.8 + - + +
746R MET* 3.0 38.6 + - + +
753R LEU* 3.7 29.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 743 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76P ILE* 3.2 34.1 - - + -
79P ALA* 6.0 1.7 - - + +
739R ASP 3.1 18.8 + - - +
740R ARG* 3.1 12.1 - - - +
742R ILE* 1.3 77.2 - - - +
744R ALA* 1.3 57.2 + - - +
746R MET* 3.4 3.5 + - - +
747R GLU* 3.0 32.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 744 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
740R ARG 3.1 11.2 + - - +
741R ILE* 3.5 13.0 - - + +
742R ILE 3.2 0.2 - - - -
743R VAL* 1.3 76.0 - - - +
745R ILE* 1.3 65.1 + - + +
747R GLU* 3.3 12.9 + - - +
748R THR* 3.3 24.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 745 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
741R ILE* 3.0 36.3 + - + +
742R ILE* 3.1 13.4 + - + +
744R ALA* 1.3 76.0 - - + +
746R MET* 1.3 57.2 + - - +
748R THR* 4.6 2.9 - - - -
749R ASN 2.9 50.4 + - - +
750R PRO* 4.4 0.7 - - + -
752R ILE* 3.6 37.0 - - + -
753R LEU* 3.9 31.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 746 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13P LYS* 4.6 2.0 - - - +
46P VAL* 4.8 5.8 - - - -
65P TRP* 3.3 37.5 - - + -
76P ILE* 4.4 6.1 - - - -
79P ALA* 3.3 49.6 - - + +
80P TYR* 4.2 2.7 - - - +
742R ILE* 3.0 31.0 + - - +
743R VAL* 4.0 3.8 - - - +
745R ILE* 1.3 74.7 - - - +
747R GLU* 1.3 60.5 + - - +
748R THR 3.0 7.2 + - - +
750R PRO* 3.3 25.0 - - + +
753R LEU* 3.7 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 747 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
743R VAL* 3.0 22.8 + - + +
744R ALA* 3.3 7.8 + - - +
746R MET* 1.3 75.6 - - - +
748R THR* 1.3 63.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 748 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
744R ALA* 3.3 18.8 + - + +
745R ILE* 3.9 2.8 + - - -
746R MET 3.0 1.4 - - - +
747R GLU* 1.3 89.0 - - + +
749R ASN* 1.3 80.0 + - - +
750R PRO* 3.3 10.0 - - - +
752R ILE* 6.1 0.3 - - - +
----------------------------------------------------------
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