Contacts of the helix formed by residues 807 - 822 (chain B) in PDB entry 5J3V
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 807 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
804B ILE* 4.3 0.2 - - - +
805B ARG* 2.8 30.4 + - + +
806B ASP* 1.3 75.2 - - - +
808B GLU* 1.3 59.6 + - - +
809B GLU* 3.1 16.7 - - + +
810B LYS* 2.9 32.0 + - - +
811B ASP* 2.9 30.2 + - - +
842B TRP* 4.5 0.3 - - - -
11D THR* 3.1 37.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 808 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
777B ARG* 4.5 2.0 + - - +
807B ASN* 1.3 74.3 - - - +
809B GLU* 1.3 65.8 + - + +
810B LYS 3.2 0.2 - - - -
811B ASP* 3.9 11.7 - - + +
812B SER* 3.0 29.1 + - - -
846B LYS* 5.7 8.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 809 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
730B TRP* 4.8 4.9 + - - -
734B GLU* 4.6 4.6 - - - +
773B ILE* 3.7 36.6 - - + +
777B ARG* 3.5 27.4 + - - +
804B ILE* 5.8 0.2 - - + -
807B ASN* 3.2 14.4 - - + +
808B GLU* 1.3 79.8 - - + +
810B LYS* 1.3 57.6 + - - +
812B SER* 3.3 13.9 + - - -
813B ALA 3.9 3.1 + - - -
11D THR* 4.0 22.7 - - + +
12D GLY* 3.6 15.6 + - - -
13D GLY* 3.9 13.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 810 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
773B ILE* 5.4 2.0 - - - -
801B LEU* 3.3 31.6 + - + +
804B ILE* 2.6 36.8 + - + +
805B ARG 3.5 5.8 - - - +
806B ASP* 2.5 33.1 + - - +
807B ASN* 2.9 16.9 - - - +
809B GLU* 1.3 74.6 - - - +
811B ASP* 1.3 65.1 + - - +
812B SER 3.2 2.2 - - - -
813B ALA* 3.2 4.6 + - - +
814B PHE* 3.1 41.5 + - + -
841B SER* 3.9 18.0 + - - -
842B TRP* 3.6 20.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 811 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
807B ASN 2.9 18.7 + - - +
808B GLU* 3.4 13.5 + - - +
810B LYS* 1.3 78.4 - - - +
812B SER* 1.3 58.8 + - - +
814B PHE* 3.9 1.7 + - - +
815B ARG* 2.3 54.5 + - - +
842B TRP* 3.5 18.4 - - + -
846B LYS* 3.5 32.0 + - - +
849B LEU* 3.4 20.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 812 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
737B ILE* 5.9 0.7 - - - -
773B ILE* 4.9 0.2 - - - +
776B GLY 4.3 4.2 - - - +
777B ARG* 2.9 42.5 + - - -
780B TYR* 4.6 5.0 - - - +
808B GLU* 3.0 19.4 + - - -
809B GLU 3.3 5.0 + - - -
811B ASP* 1.3 78.0 + - - +
813B ALA* 1.3 66.7 + - - +
815B ARG* 3.5 9.4 + - - +
816B GLY* 3.2 17.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 813 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
773B ILE* 4.2 17.7 - - - +
776B GLY* 4.0 12.7 - - - -
777B ARG* 4.8 0.9 - - - +
797B TRP* 3.4 14.0 - - + -
801B LEU* 3.8 28.3 - - + -
809B GLU 3.9 11.0 - - - +
810B LYS* 3.2 9.5 + - - +
812B SER* 1.3 82.7 + - - +
814B PHE* 1.3 57.2 + - - +
816B GLY* 3.3 1.9 + - - -
817B ILE 3.0 20.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 814 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
797B TRP* 4.0 24.5 - + - -
801B LEU* 4.2 10.1 - - + -
810B LYS* 3.1 46.2 + - + +
811B ASP 4.3 0.4 - - - +
813B ALA* 1.3 75.8 - - + +
815B ARG* 1.3 62.7 + - - +
816B GLY 3.1 1.3 - - - -
817B ILE* 3.2 9.6 - - + +
818B CYS* 3.0 31.5 + - - -
835B PHE* 5.3 2.9 - + - -
838B ALA* 3.6 39.7 - - + -
839B VAL* 4.3 6.3 - - + -
842B TRP* 3.4 35.4 - + + -
849B LEU* 4.2 14.6 - - + -
853B PHE* 3.5 24.0 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 815 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
780B TYR* 3.6 27.5 - - + -
811B ASP* 2.3 50.6 + - - +
812B SER* 3.7 9.6 - - - +
813B ALA 3.4 0.2 - - - -
814B PHE* 1.3 77.9 - - - +
816B GLY* 1.3 61.4 + - - +
818B CYS* 3.7 4.0 + - - +
819B THR* 3.3 27.5 + - - +
846B LYS* 3.6 23.6 - - - +
848B ASP* 2.7 43.5 + - - +
849B LEU* 4.1 15.9 - - + +
852B MET* 5.1 8.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 816 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
776B GLY 3.2 25.8 - - - -
780B TYR* 3.5 15.6 + - - +
812B SER 3.2 9.5 + - - -
813B ALA 3.3 1.3 + - - -
814B PHE 3.1 0.6 - - - -
815B ARG* 1.3 74.4 - - - +
817B ILE* 1.3 61.0 + - - +
818B CYS 3.0 4.6 + - - -
819B THR* 2.7 19.9 + - - -
820B MET* 3.0 15.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 817 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
776B GLY* 4.6 3.9 + - - -
790B LEU* 3.7 28.5 - - + -
793B PHE* 3.8 22.7 - - + -
794B ILE* 4.5 6.3 - - + -
797B TRP* 3.6 46.7 - - + +
798B CYS* 6.1 0.2 - - - -
813B ALA 3.0 7.4 + - - +
814B PHE* 3.2 22.9 - - + +
816B GLY* 1.3 72.6 - - - +
818B CYS* 1.3 62.9 + - - +
820B MET* 3.4 12.8 - - + +
821B ILE* 3.2 25.8 - - + +
828B VAL* 6.4 0.4 - - + -
835B PHE* 4.4 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 818 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
814B PHE 3.0 23.0 + - - +
815B ARG 3.9 3.8 - - - +
816B GLY 3.0 0.2 - - - -
817B ILE* 1.3 78.3 - - - +
819B THR* 1.3 65.0 + - - +
820B MET 3.1 1.6 - - - -
821B ILE* 3.2 12.3 + - - +
822B SER* 3.2 13.9 + - - -
835B PHE* 5.4 0.4 - - - -
849B LEU* 4.1 4.9 - - - -
852B MET* 3.6 37.7 - - + +
853B PHE* 3.7 28.5 - - - -
856B ILE* 4.0 25.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 819 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
779B GLY 3.5 16.6 + - - -
780B TYR* 3.6 22.9 - - + +
783B PRO* 4.0 14.2 - - - +
815B ARG 3.3 13.5 - - - +
816B GLY 2.7 17.7 + - - -
818B CYS* 1.3 73.8 - - - +
820B MET* 1.3 63.3 + - - +
822B SER* 3.0 20.9 + - - +
823B VAL* 3.3 18.4 - - - +
852B MET* 4.8 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 820 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
775B ILE 5.3 1.6 - - - +
776B GLY* 6.0 1.1 - - - -
779B GLY* 3.6 17.9 - - - +
783B PRO* 4.5 4.9 - - - +
786B VAL* 3.3 49.1 - - + +
787B ALA* 3.6 17.4 - - - +
790B LEU* 3.6 23.8 - - + +
793B PHE* 3.5 28.5 - - + -
816B GLY 3.0 21.9 + - - +
817B ILE* 3.4 20.6 - - + +
819B THR* 1.3 79.6 - - - +
821B ILE* 1.3 56.1 + - - +
823B VAL 3.5 0.7 + - - -
824B ASN* 3.0 26.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 821 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
790B LEU* 4.3 2.7 - - + -
817B ILE* 3.2 18.8 - - + +
818B CYS 3.2 7.0 + - - +
820B MET* 1.3 73.9 - - - +
822B SER* 1.3 57.0 - - - +
823B VAL 3.0 7.1 + - - -
824B ASN 3.8 5.4 - - - -
825B PRO* 2.9 44.5 - - + +
828B VAL* 3.6 30.1 - - + -
835B PHE* 3.9 18.8 - - + -
856B ILE* 3.6 50.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 822 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
818B CYS 3.2 6.9 + - - -
819B THR* 3.0 24.4 + - - +
821B ILE* 1.3 78.1 - - - +
823B VAL* 1.3 62.0 + - - +
825B PRO* 4.6 6.3 - - - +
852B MET* 6.4 1.3 - - - -
----------------------------------------------------------
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