Contacts of the helix formed by residues 724 - 742 (chain B) in PDB entry 4Z7I
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 SER 724 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
694B ILE* 5.5 0.7 - - - -
695B ASN* 2.7 28.8 + - - -
723B LEU* 1.3 79.3 - - - +
725B ASP* 1.3 64.7 + - - +
726B LYS* 3.5 2.7 + - - +
727B ASP* 3.1 21.0 + - - +
728B ARG* 3.1 28.5 + - - +
761B HIS* 5.9 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 725 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508B TYR* 2.6 37.7 + - - -
509B GLU* 4.7 0.3 - - - +
724B SER* 1.3 72.8 - - - +
726B LYS* 1.3 81.0 + - - +
728B ARG* 3.2 14.0 + - - +
729B ALA* 2.8 31.5 + - - +
761B HIS* 3.4 37.5 + - + +
763B ALA* 3.5 12.1 + - - +
764B PRO* 3.3 9.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 726 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499B GLU* 5.2 6.1 + - - -
508B TYR* 3.6 42.0 - - + +
512B LEU* 4.1 25.3 - - + +
515B ARG* 4.2 18.1 - - - +
557B LEU* 5.6 2.4 - - - +
694B ILE 4.4 2.0 - - - -
695B ASN* 3.6 55.6 + - + +
696B MET 4.9 0.2 + - - -
697B ASN* 4.0 8.9 + - - -
724B SER* 3.3 0.8 + - - +
725B ASP* 1.3 93.3 + - - +
727B ASP* 1.3 53.4 + - - +
729B ALA* 3.6 0.9 - - - +
730B ASN* 2.8 37.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 727 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
659B VAL* 5.0 3.8 - - - +
691B LYS* 4.0 13.6 - - + +
693B ASN 3.6 4.0 - - - +
694B ILE* 2.7 58.2 + - - +
723B LEU* 3.5 23.2 - - + +
724B SER* 3.1 33.4 + - - +
726B LYS* 1.3 75.8 - - - +
728B ARG* 1.3 62.6 + - - +
730B ASN* 3.2 4.6 + - - +
731B LEU* 3.0 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 728 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
716B LEU* 4.0 10.8 - - + +
720B PRO* 3.0 28.2 + - - -
721B TYR* 4.6 11.9 - - - -
723B LEU* 2.8 40.2 + - + +
724B SER* 3.1 19.5 + - - +
725B ASP* 3.4 7.6 - - - +
727B ASP* 1.3 79.8 - - - +
729B ALA* 1.3 62.5 + - - +
731B LEU* 3.5 8.4 + - - +
732B ILE* 3.2 29.4 + - - +
755B TYR* 3.6 20.8 + - + +
759B GLU* 2.4 44.5 + - - -
761B HIS* 3.0 34.7 + - - +
764B PRO* 4.0 6.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 729 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512B LEU* 3.8 18.8 - - + -
516B PHE* 3.9 9.5 - - + -
725B ASP 2.8 16.8 + - - +
726B LYS 3.6 3.8 - - - +
728B ARG* 1.3 73.9 - - - +
730B ASN* 1.3 65.9 + - - +
732B ILE* 3.2 7.2 + - - +
733B ASN* 3.2 21.8 + - - +
763B ALA 3.8 8.7 - - - +
764B PRO* 3.5 28.6 - - + +
767B GLU* 4.5 3.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 730 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512B LEU* 5.5 0.2 - - + -
516B PHE* 3.9 10.2 - - + -
691B LYS* 2.9 25.5 + - - +
693B ASN* 3.8 12.7 + - - +
694B ILE 4.5 1.1 - - - +
696B MET* 2.9 47.3 - - + +
700B TYR 5.4 0.6 + - - -
726B LYS 2.8 21.6 + - - +
727B ASP* 3.4 7.2 - - - +
729B ALA* 1.3 74.1 - - - +
731B LEU* 1.3 61.2 + - - +
733B ASN* 3.4 1.6 + - - +
734B ASN* 3.0 49.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 731 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
691B LYS* 3.4 40.2 - - + +
702B VAL* 6.1 0.4 - - + -
704B TYR* 4.4 10.5 - - + -
709B TRP* 3.8 30.4 - - + -
712B LEU* 4.5 16.8 - - + -
716B LEU* 4.7 18.2 - - + -
723B LEU* 4.3 11.7 - - + -
727B ASP 3.0 14.0 + - - +
728B ARG* 3.7 12.3 - - - +
730B ASN* 1.3 74.7 - - - +
732B ILE* 1.3 64.5 + - - +
734B ASN* 3.4 4.6 + - + +
735B ILE* 3.2 27.1 + - - +
752B LEU* 4.3 15.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 732 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
728B ARG 3.2 17.9 - - - +
729B ALA* 3.2 7.5 + - - +
731B LEU* 1.3 75.4 - - - +
733B ASN* 1.3 62.7 + - - +
735B ILE* 3.3 10.9 - - - +
736B PHE* 3.1 34.0 - - + -
752B LEU* 4.2 15.9 - - + -
753B ILE* 3.6 25.8 - - + -
755B TYR* 3.9 13.2 - - + +
756B LEU* 4.7 12.8 - - + -
764B PRO* 3.8 33.0 - - + +
765B ILE 5.0 0.2 - - - +
767B GLU 3.3 21.5 - - - +
768B ALA* 4.4 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 733 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516B PHE* 3.5 48.5 + - + +
517B LYS* 5.3 1.2 - - - +
519B MET* 4.3 9.7 - - - +
701B ILE* 4.5 2.3 - - - +
729B ALA 3.2 6.7 + - - +
730B ASN 3.6 7.6 - - - +
732B ILE* 1.3 81.6 - - - +
734B ASN* 1.3 73.0 + - - +
736B PHE* 3.4 2.3 + - - +
737B GLU* 3.3 37.4 + - - +
767B GLU* 3.1 32.9 + - + +
771B GLN* 3.9 7.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 734 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519B MET* 4.9 1.0 - - - +
691B LYS* 4.6 1.2 - - - +
693B ASN* 5.1 0.2 - - - +
700B TYR 4.8 1.4 + - - -
701B ILE* 3.6 30.5 - - + +
702B VAL* 3.6 38.8 - - - +
709B TRP* 4.9 4.7 - - + -
730B ASN* 3.0 42.7 + - - +
731B LEU* 3.9 6.0 - - + +
732B ILE 3.4 0.2 - - - -
733B ASN* 1.3 89.1 - - - +
735B ILE* 1.3 61.2 + - - +
737B GLU* 3.6 4.1 + - - +
738B LEU* 3.2 29.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 735 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
709B TRP* 3.9 29.8 - - + -
713B ILE* 4.5 4.7 - - + -
731B LEU 3.2 12.6 + - - +
732B ILE* 3.3 17.3 - - - +
734B ASN* 1.3 76.3 - - - +
736B PHE* 1.3 72.3 + - + +
738B LEU* 3.3 6.5 + - - +
739B ALA* 2.8 26.9 + - - +
744B VAL* 3.9 19.6 - - + +
748B ARG* 4.0 17.7 - - + +
749B ALA* 3.8 18.8 - - - +
752B LEU* 3.6 31.6 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
732B ILE* 3.1 30.3 + - + +
733B ASN 3.4 1.7 + - - +
735B ILE* 1.3 84.8 - - + +
737B GLU* 1.3 58.8 + - - +
739B ALA* 3.4 6.6 + - - +
740B GLY* 3.1 21.3 + - - -
746B LEU* 4.5 3.8 - - + -
749B ALA* 4.2 23.6 - - + -
750B PHE* 4.3 16.2 - + - -
753B ILE* 3.5 39.0 - - + -
768B ALA* 5.7 0.2 - - - -
771B GLN* 3.5 35.0 - - + +
772B THR* 4.5 14.4 - - + -
775B ILE* 3.9 30.5 - - + -
1013B TRP* 4.8 4.3 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
520B LYS* 3.5 45.6 + - - +
635B PHE* 4.6 16.6 - - + -
701B ILE* 5.1 8.1 - - + -
733B ASN* 3.3 31.5 + - - +
734B ASN* 4.0 5.2 - - - +
735B ILE 3.3 0.6 - - - -
736B PHE* 1.3 77.2 - - - +
738B LEU* 1.3 61.9 + - + +
740B GLY* 3.4 8.4 + - - +
741B LEU* 3.6 21.1 - - - +
770B PHE* 5.3 2.1 - - - -
771B GLN* 3.3 24.1 + - - +
774B LEU* 5.9 0.9 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
618B LEU* 4.6 5.8 - - + -
635B PHE* 4.4 19.1 - - + -
701B ILE* 5.0 6.1 - - + -
702B VAL 4.2 4.0 - - - +
703B HIS* 3.3 42.0 - - + +
709B TRP* 3.8 18.8 - - + -
734B ASN 3.2 20.8 + - - +
735B ILE 3.5 4.9 - - - +
737B GLU* 1.3 75.5 - - + +
739B ALA* 1.3 60.1 + - - +
740B GLY 3.0 4.7 - - - -
741B LEU* 3.1 13.2 + - + +
743B LYS* 3.1 50.2 + - + +
744B VAL* 4.1 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 739 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
735B ILE 2.8 17.9 + - - +
736B PHE* 3.4 7.6 + - - +
738B LEU* 1.3 74.8 - - - +
740B GLY* 1.3 59.2 + - - +
742B GLY 3.5 6.1 + - - -
744B VAL* 3.2 23.4 - - + +
746B LEU* 3.9 28.9 - - + -
749B ALA* 4.0 11.2 - - + -
1013B TRP* 4.6 1.1 - - - +
1017B ASN* 2.9 27.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 740 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
736B PHE 3.1 10.5 + - - -
737B GLU* 3.4 6.7 + - - -
738B LEU 3.0 1.4 - - - -
739B ALA* 1.3 80.2 - - - +
741B LEU* 1.3 63.8 + - - +
742B GLY 3.1 1.5 + - - -
1012B GLN* 3.8 8.5 - - - +
1013B TRP* 3.4 38.8 - - - -
1016B LYS* 4.3 4.9 - - - +
1017B ASN* 4.1 5.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 741 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
635B PHE* 3.9 27.6 - - + -
636B PHE 3.7 22.0 - - - +
637B LEU* 3.9 33.0 - - + -
737B GLU 3.6 14.8 - - - +
738B LEU* 3.1 9.4 + - + +
740B GLY* 1.3 78.1 - - - +
742B GLY* 1.3 57.3 + - - +
743B LYS* 3.1 30.0 + - + +
1009B LEU* 5.6 0.7 - - + -
1012B GLN* 3.7 15.1 - - - +
1016B LYS* 3.2 22.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 742 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
738B LEU 3.2 2.8 + - - -
739B ALA 3.5 8.6 + - - -
740B GLY 3.1 5.3 + - - -
741B LEU* 1.3 78.4 - - - +
743B LYS* 1.3 56.5 + - - +
744B VAL* 2.9 19.3 + - - +
745B PRO* 5.4 0.3 - - - +
1016B LYS* 3.7 25.3 + - - -
1017B ASN* 5.2 1.1 - - - -
----------------------------------------------------------
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