Contacts of the helix formed by residues 809 - 828 (chain B) in PDB entry 5C0V
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 THR 809 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
899A GLU* 3.5 16.6 - - + +
801B GLU* 5.2 1.3 + - - +
802B LEU* 3.8 4.0 - - - +
806B ASN 5.9 0.4 - - - +
807B GLY 3.7 7.8 + - - +
808B PHE* 1.3 87.1 - - - +
810B GLN* 1.3 64.9 + - - +
811B HIS* 4.1 4.9 - - - +
812B VAL* 3.2 31.9 + - + +
813B TYR* 3.0 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 810 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
899A GLU* 2.7 40.3 + - - +
902A VAL* 4.2 8.5 - - + +
903A LYS* 3.8 24.7 - - + +
906A GLU* 4.0 13.7 - - - +
931A ASP* 3.9 5.4 - - - +
808B PHE* 3.5 26.9 - - - -
809B THR* 1.3 72.3 - - - +
811B HIS* 1.3 57.2 + - - +
813B TYR* 3.7 3.7 - - - -
814B HIS* 2.8 61.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 811 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
895A LYS* 4.5 18.4 + - - +
898A GLN* 4.0 12.1 + - + +
899A GLU* 4.2 2.1 + - - +
929A ASP* 3.2 42.4 + - + -
930A ILE 3.7 3.8 + - - -
931A ASP* 3.4 50.6 + - + +
932A PRO* 3.8 7.6 - - + +
809B THR* 3.2 6.1 + - - +
810B GLN* 1.3 78.9 - - - +
812B VAL* 1.3 65.7 + - + +
814B HIS* 3.2 2.1 + - - +
815B LYS* 3.0 40.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 812 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
895A LYS* 5.9 5.4 - - - +
798B PRO* 4.6 10.3 - - + -
801B GLU* 3.8 28.7 - - - +
802B LEU* 3.7 24.9 - - + -
809B THR* 3.2 19.8 + - + +
811B HIS* 1.3 78.1 - - + +
813B TYR* 1.3 62.1 + - - +
815B LYS* 3.5 18.4 + - - +
816B TYR* 3.1 22.9 + - - +
819B ARG* 5.4 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 813 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
802B LEU* 3.8 13.9 - - + +
808B PHE* 3.6 24.7 - + + -
809B THR 3.0 19.2 + - - +
810B GLN* 3.7 4.0 - - - +
812B VAL* 1.3 78.7 - - - +
814B HIS* 1.3 76.6 + + - +
816B TYR* 3.8 3.5 - + - +
817B ARG* 2.8 57.3 + - + +
838B LEU* 4.4 5.4 - - + -
841B PHE* 3.7 33.0 - + - -
842B TRP* 3.0 31.5 + - - -
854B MSE 3.5 26.9 - - + +
857B GLU* 4.6 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 814 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
902A VAL* 4.0 9.2 - - + -
906A GLU* 4.5 4.8 + - - -
931A ASP* 2.8 41.3 + - - +
932A PRO* 4.2 11.8 - - + +
933A LYS* 3.4 32.1 - - + +
810B GLN* 2.8 43.9 + - + +
811B HIS 3.2 2.4 + - - +
813B TYR* 1.3 92.9 - + - +
815B LYS* 1.3 57.6 + - - +
817B ARG* 3.8 11.2 + - - +
818B ARG* 2.9 32.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 815 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
895A LYS* 5.8 2.6 - - - +
929A ASP* 3.5 22.4 + - - +
932A PRO* 4.4 11.7 - - + -
811B HIS* 3.0 45.8 + - + +
812B VAL* 3.9 20.0 - - - +
814B HIS* 1.3 76.0 - - - +
816B TYR* 1.3 57.5 + - - +
818B ARG* 3.5 5.2 + - - +
819B ARG* 3.0 38.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 816 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
797B HIS* 3.5 23.6 - + - -
798B PRO* 3.9 18.8 - - + -
799B SER* 3.6 19.2 - - - -
802B LEU* 3.8 16.8 - - + -
812B VAL 3.1 17.9 + - - +
813B TYR* 3.8 6.5 - + - +
815B LYS* 1.3 74.9 - - - +
817B ARG* 1.3 67.1 + - - +
819B ARG* 3.3 27.0 + - - +
820B CYS* 3.0 49.6 + - - -
834B GLU* 4.3 1.1 - - - -
837B THR* 2.7 27.8 + - - -
838B LEU* 3.1 32.8 + - + -
841B PHE* 4.4 8.5 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 817 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
933A LYS* 5.4 12.4 - - - +
813B TYR* 2.8 54.4 + - + +
814B HIS* 3.8 10.7 + - - +
816B TYR* 1.3 73.4 - - - +
818B ARG* 1.3 72.9 + - - +
820B CYS* 3.3 2.3 + - - +
821B LEU* 3.0 50.0 + - + +
838B LEU* 4.2 17.5 - - + -
842B TRP* 4.8 1.1 - - + -
857B GLU* 2.7 43.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 818 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
932A PRO* 5.7 5.6 - - + -
814B HIS 2.9 19.8 + - - +
815B LYS* 3.8 5.4 - - - +
817B ARG* 1.3 85.0 - - - +
819B ARG* 1.3 58.6 + - - +
821B LEU* 3.8 4.3 - - - +
822B ASN* 2.8 33.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 819 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
797B HIS* 5.1 1.2 + - - -
798B PRO* 3.7 31.7 - - - +
812B VAL 5.4 0.4 + - - -
815B LYS* 3.0 22.7 + - - +
816B TYR* 3.3 37.2 + - - +
818B ARG* 1.3 75.9 - - - +
820B CYS* 1.3 61.1 + - - +
822B ASN* 3.4 6.5 + - - +
823B GLU* 2.9 28.5 + - + +
834B GLU* 4.7 18.5 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 820 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
816B TYR* 3.0 46.8 + - - +
817B ARG 3.7 0.2 - - - +
819B ARG* 1.3 76.8 - - - +
821B LEU* 1.3 65.4 + - - +
823B GLU* 3.2 7.1 + - - +
824B ARG* 3.0 22.7 + - - +
832B SER* 4.2 2.1 + - - -
834B GLU* 3.3 37.9 - - - +
835B MSE 4.1 9.8 - - - +
838B LEU* 3.7 27.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 821 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
817B ARG* 3.0 60.5 + - + +
818B ARG* 4.0 4.0 - - - +
820B CYS* 1.3 75.5 - - - +
822B ASN* 1.3 58.1 + - - +
824B ARG* 3.3 10.5 + - - +
825B LYS* 2.9 30.2 + - - +
835B MSE 3.8 15.3 - - + -
838B LEU* 4.6 3.8 - - + -
842B TRP* 5.2 0.7 - - + -
857B GLU* 3.5 7.6 - - - +
861B LEU* 3.6 30.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 822 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
818B ARG 2.8 20.5 + - - +
819B ARG* 3.7 6.0 - - - +
821B LEU* 1.3 78.9 - - - +
823B GLU* 1.3 56.1 + - - +
825B LYS* 3.5 11.4 + - - +
826B ARG* 3.0 46.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 823 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
819B ARG* 2.9 18.6 + - + +
820B CYS* 3.2 6.5 + - - +
822B ASN* 1.3 75.9 + - - +
824B ARG* 1.3 54.3 + - - +
826B ARG* 3.1 9.1 + - + +
827B LEU* 2.8 60.0 + - + +
832B SER* 2.5 28.3 + - - +
833B GLN* 3.7 1.9 + - - +
834B GLU* 3.2 31.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 824 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
820B CYS 3.0 13.0 + - - +
821B LEU* 3.5 14.9 - - - +
823B GLU* 1.3 76.3 - - - +
825B LYS* 1.3 58.5 + - - +
828B GLY* 2.8 43.7 + - - +
829B ILE* 3.8 20.5 + - + +
830B GLY 5.1 1.8 - - - +
832B SER* 3.9 11.0 - - - -
835B MSE 3.7 32.0 - - + +
861B LEU* 3.7 24.3 + - - +
864B GLU* 2.8 37.8 + - - +
865B ASP* 2.8 32.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 825 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
821B LEU 2.9 17.4 + - - +
822B ASN* 3.7 11.2 - - - +
824B ARG* 1.3 77.1 - - - +
826B ARG* 1.3 62.3 + - + +
828B GLY* 4.3 2.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 826 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
822B ASN* 3.0 38.0 + - - +
823B GLU* 3.1 9.8 + - - +
825B LYS* 1.3 77.6 - - + +
827B LEU* 1.3 81.3 + - + +
828B GLY 3.8 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 827 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
823B GLU* 2.8 47.0 + - + +
826B ARG* 1.3 97.1 - - + +
828B GLY* 1.3 59.5 + - - +
831B GLN* 3.1 45.0 - - + +
832B SER* 4.5 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 828 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
824B ARG* 2.8 25.9 + - - +
825B LYS 4.3 2.8 + - - -
826B ARG 3.5 2.0 - - - -
827B LEU* 1.3 79.5 - - - +
829B ILE* 1.3 69.7 + - - -
830B GLY 3.2 0.7 + - - -
831B GLN* 3.1 17.6 + - - +
832B SER 4.3 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