Contacts of the helix formed by residues 776 - 797 (chain B) in PDB entry 4BIC
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 ASN 776 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
773B LEU* 2.7 33.6 + - + +
774B LYS 3.3 0.2 - - - -
775B ASP* 1.4 71.5 - - - +
777B GLU* 1.3 55.5 + - - +
778B GLN* 3.2 18.3 - - - +
779B THR* 3.2 36.5 + - - +
780B ILE* 3.2 21.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 777 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
774B LYS 3.9 9.1 - - - +
775B ASP 3.9 2.5 + - - -
776B ASN* 1.3 69.7 - - - +
778B GLN* 1.3 59.7 + - - +
780B ILE* 3.8 8.4 - - - +
781B GLY* 2.9 25.6 + - - -
907B MET* 3.5 29.7 - - + +
908B SER* 2.7 49.2 + - - -
910B GLU* 5.1 0.2 - - - +
911B ALA* 3.4 13.6 - - - +
937B PHE* 3.8 19.0 - - + +
941B SER 5.2 1.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 778 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
776B ASN* 3.5 12.2 - - - +
777B GLU* 1.3 77.5 - - - +
779B THR* 1.4 57.1 + - - +
781B GLY* 3.9 0.5 - - - -
782B PHE* 3.0 30.7 + - + +
941B SER* 3.6 49.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 779 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
770B TRP* 5.0 3.4 - - + -
773B LEU* 3.7 32.0 - - + +
776B ASN* 3.2 32.5 + - - -
778B GLN* 1.4 75.6 - - - +
780B ILE* 1.4 65.4 + - - +
782B PHE* 3.2 8.6 + - - +
783B TYR* 3.0 46.9 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 780 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
773B LEU* 3.3 37.9 - - + +
774B LYS 3.9 2.9 - - - +
776B ASN 3.2 13.7 + - - +
777B GLU* 4.0 7.9 - - - +
779B THR* 1.4 74.1 - - - +
781B GLY* 1.3 51.9 + - - +
783B TYR* 3.5 0.9 + - - -
784B THR* 2.6 45.0 + - - +
871B ILE* 3.7 27.6 - - + -
874B MET* 4.1 19.3 - - + +
875B ALA* 4.0 15.0 - - + +
907B MET* 3.7 26.2 - - + -
937B PHE* 4.2 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 781 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
777B GLU 2.9 18.5 + - - -
778B GLN 3.9 0.4 - - - -
780B ILE* 1.3 71.8 - - - +
782B PHE* 1.4 65.4 + - - +
784B THR* 3.0 6.5 + - - -
785B LYS* 2.9 28.3 + - - +
937B PHE* 4.2 17.5 - - - -
938B LEU* 4.0 11.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 782 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
778B GLN* 3.0 19.5 + - + +
779B THR* 3.2 7.2 + - - +
781B GLY* 1.4 73.9 - - - +
783B TYR* 1.4 89.1 + + - +
785B LYS* 4.0 5.7 + - - +
786B GLN* 3.4 38.4 + - - +
815B SER 4.6 4.5 - - - -
816B GLY* 3.4 31.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 783 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
762B LEU* 5.5 2.0 - - + -
770B TRP* 3.8 24.7 - + - -
773B LEU* 5.5 0.2 - - + -
779B THR* 3.0 43.4 + - + +
780B ILE 4.2 2.0 - - - +
782B PHE* 1.4 95.5 - + - +
784B THR* 1.3 65.5 + - - +
786B GLN* 3.4 8.6 + - - +
787B ILE* 3.2 26.4 + - - +
811B ILE* 3.7 31.9 - - + +
813B THR* 5.7 1.4 - - - -
816B GLY* 3.3 27.3 - - - -
818B LEU* 3.6 27.3 - - + +
874B MET* 4.4 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 784 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
780B ILE* 2.6 30.0 + - - +
781B GLY* 3.5 5.4 - - - -
783B TYR* 1.3 75.6 - - - +
785B LYS* 1.3 61.1 + - - +
787B ILE* 3.0 11.6 + - - +
788B LEU* 3.0 25.9 + - + +
867B LEU* 4.5 3.7 - - + +
871B ILE* 3.6 39.2 - - + +
874B MET* 3.6 8.6 - - - +
914B PHE* 3.8 22.9 - - + -
937B PHE* 4.8 2.9 - - + -
938B LEU* 3.9 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 785 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
781B GLY 2.9 18.5 + - - +
782B PHE* 4.0 7.2 - - - +
784B THR* 1.3 72.0 - - - +
786B GLN* 1.4 53.3 + - + +
788B LEU* 3.4 4.3 + - - +
789B GLU* 2.9 54.4 + - - +
933B LEU* 3.9 20.0 - - + -
938B LEU* 4.1 33.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 786 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
736B ASN* 3.1 36.2 + - - +
782B PHE* 3.4 38.8 + - - +
783B TYR* 3.4 11.3 + - - +
784B THR 3.2 0.6 - - - -
785B LYS* 1.4 73.8 - - + +
787B ILE* 1.4 65.9 + - - +
789B GLU* 4.4 4.3 - - - +
790B GLY* 3.1 17.2 + - - -
816B GLY 2.8 23.0 + - - -
817B VAL* 3.5 7.0 - - - +
818B LEU* 2.9 35.9 + - + +
820B ILE* 5.2 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 787 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
762B LEU* 4.6 0.4 - - + -
783B TYR 3.2 13.1 + - - +
784B THR 3.0 5.6 + - - +
786B GLN* 1.4 74.3 - - - +
788B LEU* 1.4 52.6 + - - +
790B GLY* 3.3 1.7 + - - -
791B LEU* 2.8 43.9 + - + +
804B ILE* 4.2 13.2 - - + -
809B VAL* 4.5 13.0 - - + -
818B LEU* 3.8 23.6 - - + -
820B ILE* 3.8 20.1 - - + +
867B LEU* 3.8 22.9 - - + -
870B THR* 4.1 17.7 - - + -
874B MET* 3.8 29.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 788 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
784B THR* 3.0 19.1 + - + +
785B LYS 3.4 7.6 - - - +
787B ILE* 1.4 72.7 - - - +
789B GLU* 1.3 55.3 + - - +
791B LEU* 3.2 6.8 + - + +
792B LYS* 2.7 35.5 + - - +
864B ILE* 5.1 2.9 - - + -
867B LEU* 3.7 24.5 - - + -
914B PHE* 3.7 20.4 - - + -
929B ALA* 3.9 26.0 - - + +
932B LEU* 3.9 24.5 - - + -
933B LEU* 3.8 12.1 - - + +
938B LEU* 3.6 29.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 789 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
734B HIS* 3.5 17.8 + - + +
735B LYS* 3.5 29.4 + - - -
736B ASN* 3.7 14.1 - - - +
785B LYS* 2.9 49.6 + - - +
786B GLN* 4.0 4.8 - - - +
788B LEU* 1.3 72.0 - - - +
790B GLY* 1.3 62.2 + - - +
792B LYS* 3.5 10.7 - - + +
793B TYR* 3.2 17.7 + - - +
933B LEU* 3.8 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 790 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
734B HIS* 4.0 1.3 - - - -
736B ASN* 3.8 20.3 - - - +
737B ILE* 3.5 20.1 - - - +
786B GLN 3.1 10.8 + - - -
787B ILE 3.6 3.4 - - - -
789B GLU* 1.3 76.4 - - - +
791B LEU* 1.3 60.1 + - - +
793B TYR* 3.4 6.8 + - - +
794B LEU* 3.2 18.9 + - - +
820B ILE* 4.1 9.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 791 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
787B ILE* 2.8 37.7 + - + +
788B LEU* 3.2 8.9 + - + +
790B GLY* 1.3 70.3 - - - +
792B LYS* 1.3 53.0 + - - +
794B LEU* 3.2 10.8 + - + +
795B HIS* 2.8 54.0 + - + +
801B HIS* 4.4 6.1 - - + -
804B ILE* 3.7 34.1 - - + -
820B ILE* 4.0 1.5 - - + +
863B ASP* 3.9 39.9 - - + +
864B ILE* 5.1 4.3 - - + +
867B LEU* 4.4 14.6 - - + -
929B ALA* 5.0 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 792 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
788B LEU 2.7 20.4 + - - +
789B GLU* 3.5 8.7 - - + +
791B LEU* 1.3 71.2 - - - +
793B TYR* 1.3 53.0 + - - +
795B HIS* 3.1 4.6 + - - -
796B ASP* 2.7 67.4 + - - +
929B ALA* 4.1 16.1 - - + +
930B ASN* 2.7 34.4 + - - +
933B LEU* 3.8 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 793 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
731B HIS 3.7 5.7 + - - -
732B LEU* 3.4 32.8 - - + +
733B LYS* 2.8 41.6 + - - +
734B HIS* 3.7 30.5 - + + -
737B ILE* 3.7 18.2 - - + -
789B GLU 3.2 9.8 + - - +
790B GLY 3.5 7.4 - - - +
792B LYS* 1.3 78.2 - - - +
794B LEU* 1.3 65.7 + - + +
796B ASP* 3.6 6.1 + - - +
797B ASN* 3.1 51.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 794 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
732B LEU* 4.0 27.1 - - + -
737B ILE* 4.4 7.2 - - + -
790B GLY 3.2 14.1 + - - +
791B LEU* 3.2 16.4 + - + +
793B TYR* 1.3 82.8 - - + +
795B HIS* 1.3 60.3 + - + +
797B ASN* 3.2 10.8 + - - -
798B GLN 3.2 0.2 + - - -
799B ILE* 2.8 58.4 + - + +
801B HIS* 4.3 24.9 - - + +
820B ILE* 5.0 4.0 - - + -
823B PHE* 4.1 30.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 795 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
791B LEU* 2.8 35.2 + - + +
792B LYS* 3.7 4.5 - - - +
794B LEU* 1.3 74.4 - - + +
796B ASP* 1.4 58.5 + - - +
798B GLN* 2.9 16.8 + - - +
799B ILE 3.2 19.3 - - - -
800B VAL* 4.2 1.1 - - + -
860B LYS* 3.2 76.2 + - + +
863B ASP* 2.7 31.9 + - + +
864B ILE* 3.6 19.5 - - + +
929B ALA* 4.7 8.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 796 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
792B LYS* 2.7 61.5 + - - +
793B TYR* 4.0 5.9 + - - +
795B HIS* 1.4 74.0 - - - +
797B ASN* 1.3 62.7 + - - +
798B GLN* 3.0 18.2 + - - +
860B LYS* 5.0 2.9 + - - +
930B ASN* 4.5 8.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 797 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
856A ARG* 5.6 6.1 - - - +
732B LEU* 5.8 0.4 - - - -
793B TYR* 3.1 50.3 + - + +
794B LEU 3.2 4.5 + - - +
796B ASP* 1.3 80.6 - - - +
798B GLN* 1.4 65.4 + - - +
799B ILE* 3.2 28.0 + - + +
828B ARG* 5.7 0.5 - - - +
----------------------------------------------------------
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