Contacts of the helix formed by residues 818 - 838 (chain G) in PDB entry 5FUR
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 LYS 818 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61E C 6.5 1.6 - - - -
103F C 3.4 35.5 + - - -
104F G 3.3 38.4 + - - +
816G ASN 3.8 20.2 + - - -
817G SER* 1.3 73.2 - - - +
819G ARG* 1.3 56.8 + - - +
821G ASN* 3.4 10.5 + - + +
822G THR* 2.8 36.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 819 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
810G PHE* 4.2 7.9 - - - -
811G GLU 5.5 1.8 + - - +
813G PRO* 3.7 31.2 - - + +
817G SER* 4.1 8.2 - - - +
818G LYS* 1.3 78.8 - - - +
820G ALA* 1.3 57.2 + - - +
822G THR* 3.2 8.1 + - - -
823G HIS* 2.9 41.6 + - - +
905G GLN* 3.7 49.8 + - - +
908G ALA* 4.1 10.5 - - - +
909G TYR* 5.2 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 820 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
813G PRO* 4.1 5.1 - - + +
814G GLY 3.7 11.0 - - - +
816G ASN* 4.4 5.2 - - - +
817G SER* 3.3 24.1 + - - +
819G ARG* 1.3 87.3 - - - +
821G ASN* 1.3 63.9 + - - +
823G HIS* 3.2 5.0 + - - +
824G ILE* 3.1 29.7 + - + +
909G TYR* 4.1 5.0 - - + -
912G MET* 3.8 22.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 821 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61E C 6.4 2.8 - - - -
62E C 5.1 8.8 + - - +
816G ASN* 3.2 39.7 + - - +
817G SER 3.0 22.1 + - - +
818G LYS* 3.9 11.3 - - + +
820G ALA* 1.3 73.7 - - - +
822G THR* 1.3 65.9 + - - +
824G ILE* 3.7 16.3 + - - +
825G ARG* 3.3 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 822 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
818G LYS* 2.8 26.3 + - - +
819G ARG* 3.6 8.1 - - - -
821G ASN* 1.3 77.8 - - - +
823G HIS* 1.3 57.5 + - - +
825G ARG* 3.5 27.2 + - - +
826G ASP* 3.0 44.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 823 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
819G ARG* 2.9 29.0 + - - +
820G ALA* 3.2 9.4 + - - +
822G THR* 1.3 75.1 - - - +
824G ILE* 1.3 63.9 + - - +
826G ASP* 3.2 4.3 + - - +
827G PHE* 2.8 40.4 + + + +
901G VAL* 3.9 13.0 - - + +
905G GLN* 3.5 34.4 + - + -
906G CYS* 3.5 28.3 + - - -
909G TYR* 3.4 40.5 - + + -
910G TYR* 6.0 1.1 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 824 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
626G THR 5.9 1.3 - - - +
820G ALA* 3.1 19.6 + - + +
821G ASN* 4.3 18.4 - - - +
823G HIS* 1.3 78.3 - - - +
825G ARG* 1.3 58.7 + - - +
827G PHE* 3.7 6.4 - - + +
828G LEU* 2.9 33.1 + - - +
855G PHE* 5.0 8.7 - - + -
858G HIS* 3.7 31.6 - - + +
909G TYR* 3.4 39.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 825 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61E C 5.1 8.7 + - - -
821G ASN 3.3 17.7 + - - +
822G THR* 3.5 22.1 + - - +
824G ILE* 1.3 80.2 - - - +
826G ASP* 1.3 97.1 + - - +
828G LEU* 3.3 8.0 + - - +
829G GLN* 2.9 27.0 + - - +
858G HIS* 5.8 1.1 - - - -
866G ARG* 3.4 43.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 826 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
822G THR* 3.0 34.1 + - - +
823G HIS* 3.8 3.9 - - - +
825G ARG* 1.3 105.6 + - - +
827G PHE* 1.3 56.9 + - - +
829G GLN* 3.1 9.7 + - - +
830G VAL* 2.9 31.5 + - - +
900G MET* 4.6 10.5 - - + +
901G VAL* 3.7 19.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 827 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
619G LEU* 4.4 17.7 - - + -
621G GLN* 4.6 4.0 - - - -
624G PHE* 4.1 11.7 - - + -
625G PRO 3.7 15.9 - - - -
626G THR* 3.7 31.4 - - + -
823G HIS* 2.8 31.7 + + + +
824G ILE* 3.7 9.2 - - + +
826G ASP* 1.3 69.1 - - - +
828G LEU* 1.3 65.9 + - - +
830G VAL* 3.2 7.2 + - + +
831G PHE* 3.0 24.9 + - + +
855G PHE* 3.8 21.8 - + - -
901G VAL* 3.9 12.9 - - + +
906G CYS* 3.7 31.2 - - - -
910G TYR* 4.2 6.1 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 828 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
824G ILE 2.9 18.7 + - - +
825G ARG* 3.4 5.2 - - - +
827G PHE* 1.3 75.7 - - - +
829G GLN* 1.3 64.1 + - - +
831G PHE* 3.3 2.0 + - + +
832G ILE* 3.0 34.0 + - + +
851G ILE* 3.8 20.0 - - + -
855G PHE* 3.8 43.1 - - + -
858G HIS* 3.8 28.3 - - + +
862G SER 4.8 2.0 - - - +
863G ILE* 4.5 13.9 - - + -
866G ARG* 4.0 28.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 829 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
825G ARG 2.9 13.2 + - - +
826G ASP* 3.1 14.1 + - - +
828G LEU* 1.3 78.0 - - - +
830G VAL* 1.3 61.3 + - + +
832G ILE* 3.3 11.8 + - - +
833G TYR* 3.1 68.6 + - + +
866G ARG* 3.0 61.2 + - + +
870G CYS* 5.0 1.0 - - - -
900G MET* 5.1 4.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 830 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
619G LEU* 4.9 18.4 - - + -
826G ASP 2.9 17.6 + - - +
827G PHE* 3.6 10.5 - - + +
829G GLN* 1.3 73.7 - - - +
831G PHE* 1.3 65.8 + - - +
833G TYR* 3.3 8.3 + - - +
834G ARG* 3.0 36.3 + - + +
897G ILE* 3.7 24.7 - - + +
900G MET* 3.8 35.4 - - + -
901G VAL* 3.9 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 831 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621G GLN* 3.6 26.7 - - + -
626G THR* 3.8 15.3 - - + -
827G PHE* 3.0 15.4 + + + +
828G LEU 3.6 7.9 - - - +
830G VAL* 1.3 76.3 - - - +
832G ILE* 1.3 61.7 + - - +
834G ARG* 3.4 7.0 + - + +
835G LEU* 2.9 55.0 + - + +
838G LYS* 5.9 4.5 - - - -
850G ASP* 4.3 4.7 - - + -
851G ILE* 4.2 17.9 - - + -
854G ALA* 3.5 29.6 - - + -
855G PHE* 3.6 19.3 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 832 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
828G LEU* 3.0 32.3 + - + +
829G GLN* 3.5 17.9 - - - +
830G VAL 3.2 0.2 - - - -
831G PHE* 1.3 75.0 - - + +
833G TYR* 1.3 68.3 + - + +
835G LEU* 2.9 19.1 + - - +
836G PHE* 3.1 35.3 + - + -
846G ILE* 5.5 0.9 - - + -
851G ILE* 4.0 22.2 - - + -
863G ILE* 4.7 2.9 - - + +
866G ARG* 3.5 34.1 - - + -
867G LEU* 3.9 23.1 - - + -
870G CYS* 4.7 4.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 833 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
829G GLN* 3.1 53.7 + - + +
830G VAL* 3.7 5.6 - - - +
832G ILE* 1.3 77.2 - - + +
834G ARG* 1.3 58.7 + - - +
836G PHE* 3.2 9.6 + + - +
837G TRP* 3.0 31.2 + - + -
870G CYS* 4.6 9.7 - - - +
889G PHE* 3.8 31.3 - + - -
891G LEU* 4.1 10.0 - - + +
892G PRO* 3.7 23.2 - - + +
897G ILE* 4.3 17.0 - - + -
900G MET* 3.6 36.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 834 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
617G VAL 4.7 0.2 + - - -
618G GLU* 3.3 33.8 + - - +
619G LEU 5.6 1.6 - - - -
620G ARG* 3.4 37.2 + - - +
830G VAL* 3.0 28.7 + - + +
831G PHE* 3.8 7.2 - - - +
833G TYR* 1.3 76.1 - - - +
835G LEU* 1.3 62.4 + - - +
837G TRP* 3.3 10.7 + - + +
838G LYS* 3.1 27.1 + - - +
894G GLU* 2.8 43.4 + - - -
897G ILE* 3.4 35.2 - - + +
898G ARG* 3.9 9.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 835 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
831G PHE* 2.9 34.1 + - + +
832G ILE* 2.9 11.9 + - - +
834G ARG* 1.3 76.6 - - - +
836G PHE* 1.3 62.6 + - - +
838G LYS* 3.1 39.3 + - - +
839G SER* 3.1 10.2 + - - -
846G ILE* 3.5 31.4 - - + +
847G ARG 4.6 0.2 - - - +
850G ASP* 4.3 23.8 - - + +
851G ILE* 3.8 30.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 836 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
832G ILE* 3.1 41.4 + - + -
833G TYR* 3.5 9.6 - + - +
835G LEU* 1.3 76.4 - - - +
837G TRP* 1.3 61.1 + - - +
839G SER* 3.2 14.6 + - - -
844G ARG* 3.0 32.9 + - + -
845G ARG* 4.0 0.7 - - - -
846G ILE* 3.5 30.1 - - + -
867G LEU* 4.3 2.0 - - + -
870G CYS* 3.9 16.2 - - - -
871G ALA* 3.6 24.0 - - + -
883G TRP 3.6 18.4 - - - -
885G LEU* 3.6 36.8 - - + -
891G LEU* 3.9 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 837 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
833G TYR 3.0 21.0 + - - -
834G ARG* 3.7 13.0 - - + +
835G LEU 3.2 0.4 - - - -
836G PHE* 1.3 77.3 - - - +
838G LYS* 1.3 59.0 + - - +
839G SER 3.9 0.5 - - - +
844G ARG* 3.1 44.8 + - - +
891G LEU* 3.7 32.8 - - + +
892G PRO 2.8 29.7 + - - -
893G THR* 4.7 7.5 - - + -
894G GLU* 5.0 3.1 - - - +
897G ILE* 3.6 18.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 838 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620G ARG* 6.0 4.4 - - - +
621G GLN* 6.0 0.4 + - - -
831G PHE* 5.9 4.9 - - - -
834G ARG* 3.1 17.3 + - - +
835G LEU* 3.1 30.4 + - - +
837G TRP* 1.3 76.2 - - - +
839G SER* 1.3 65.5 + - - +
840G LYS* 3.4 23.2 + - - +
----------------------------------------------------------
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