Contacts of the helix formed by residues 853 - 876 (chain E) in PDB entry 6V3O
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 LEU 853 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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735E GLU* 5.9 1.1 - - - +
737E ARG* 3.6 46.4 - - + +
740E GLU* 3.0 37.9 - - + +
741E TYR* 4.1 25.8 - - + +
744E SER* 5.3 2.2 - - - +
849E VAL* 3.7 17.5 - - + -
850E ALA* 2.9 15.4 + - + +
852E GLU* 1.3 79.3 - - - +
854E LYS* 1.3 65.9 + - - +
855E PRO* 3.4 3.1 - - - -
856E PHE* 3.1 32.2 + - + +
857E GLY 3.3 4.7 + - - -
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Residues in contact with LYS 854 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
845E ASP* 3.6 20.0 - - + +
846E GLU* 3.4 36.0 + - - +
849E VAL* 3.1 34.5 - - + -
850E ALA 3.4 6.3 - - - +
851E GLU* 3.4 42.9 + - - +
853E LEU* 1.3 74.5 - - - +
855E PRO* 1.3 71.0 - - + +
857E GLY* 3.1 4.4 + - - +
858E LYS* 3.0 39.6 + - - +
861E ARG* 4.6 3.4 + - - +
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Residues in contact with PRO 855 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
851E GLU 3.6 13.0 - - - +
852E GLU* 3.9 10.1 - - - +
853E LEU 3.5 4.0 - - - -
854E LYS* 1.3 90.4 - - + +
856E PHE* 1.3 60.9 + - - +
858E LYS* 3.3 14.6 + - + +
859E GLN* 3.1 37.4 + - - +
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Residues in contact with PHE 856 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
731E VAL* 4.2 14.6 - - + -
735E GLU* 4.2 33.9 - - + -
737E ARG 5.0 0.7 - - - -
738E PHE* 4.0 26.9 - + - -
741E TYR* 3.8 34.3 - + + -
852E GLU 5.4 0.4 + - - +
853E LEU* 3.1 23.8 + - + +
855E PRO* 1.3 80.0 - - - +
857E GLY* 1.3 60.3 + - - +
859E GLN* 3.3 21.8 + - + +
860E LEU* 3.2 46.4 + - + +
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Residues in contact with GLY 857 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
741E TYR* 3.3 30.2 + - - -
845E ASP* 3.8 5.4 - - - -
853E LEU 3.3 5.1 + - - -
854E LYS 3.1 6.9 + - - -
856E PHE* 1.3 77.8 - - - +
858E LYS* 1.3 62.5 + - - +
860E LEU* 3.2 5.7 + - - +
861E ARG* 3.0 34.6 + - - +
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Residues in contact with LYS 858 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
854E LYS* 3.0 30.2 + - - +
855E PRO* 3.6 14.1 - - + +
857E GLY* 1.3 75.0 - - - +
859E GLN* 1.3 57.9 + - + +
861E ARG* 3.4 27.7 + - - +
862E ASP* 3.0 36.6 + - - +
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Residues in contact with GLN 859 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
855E PRO* 3.1 28.5 + - - +
856E PHE* 3.5 21.5 - - + +
857E GLY 3.2 0.4 - - - -
858E LYS* 1.3 75.9 - - + +
860E LEU* 1.3 67.0 + - + +
862E ASP* 3.1 15.0 + - - +
863E LYS* 3.0 31.4 + - - +
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Residues in contact with LEU 860 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
731E VAL* 3.7 27.4 - - + -
738E PHE* 4.7 3.6 - - + -
741E TYR* 3.7 31.0 - - + -
786E PHE* 3.8 15.9 - - + -
788E LEU* 4.0 23.6 - - + -
791E TRP* 3.6 10.9 - - + -
792E LEU* 5.1 2.9 - - + -
856E PHE* 3.2 34.8 + - + +
857E GLY* 3.2 6.9 + - - +
859E GLN* 1.3 75.1 - - + +
861E ARG* 1.3 57.6 + - - +
863E LYS* 3.3 24.6 + - + +
864E TYR* 3.0 21.3 + - - +
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Residues in contact with ARG 861 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
741E TYR* 4.0 2.6 + - - -
786E PHE* 3.7 19.9 - - + -
838E PRO* 3.6 34.8 - - + -
841E ALA* 4.4 2.9 + - - +
842E GLY* 3.9 20.9 + - - +
845E ASP* 2.9 34.6 + - - +
854E LYS* 4.6 3.4 + - - +
857E GLY 3.0 19.5 + - - +
858E LYS* 3.4 38.1 - - - +
860E LEU* 1.3 73.2 - - - +
862E ASP* 1.3 67.7 + - - +
864E TYR* 3.2 8.4 + - - +
865E VAL* 3.2 29.2 + - + +
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Residues in contact with ASP 862 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
858E LYS* 3.0 22.6 + - - +
859E GLN* 3.3 17.0 - - - +
861E ARG* 1.3 77.5 - - - +
863E LYS* 1.3 62.7 + - + +
864E TYR 3.3 0.2 + - - -
865E VAL* 3.3 5.1 + - - +
866E GLU* 3.0 25.4 + - - +
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Residues in contact with LYS 863 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
727E GLU* 2.6 32.7 + - - +
731E VAL* 4.2 17.3 - - - -
791E TRP* 3.9 11.0 - - + -
792E LEU* 4.4 11.4 - - + -
859E GLN* 3.0 18.9 + - - +
860E LEU* 3.3 24.4 + - + +
862E ASP* 1.3 75.7 - - + +
864E TYR* 1.3 57.8 + - - +
866E GLU* 3.9 6.1 - - - +
867E THR* 2.8 37.8 + - - +
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Residues in contact with TYR 864 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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785E ARG 4.7 4.3 - - - -
786E PHE* 3.5 32.5 - + + -
787E HIS* 5.3 1.8 - - + -
791E TRP* 3.6 36.3 - + + -
833E PHE* 3.5 33.1 + + - -
836E GLY* 3.5 28.8 + - - -
838E PRO* 3.5 31.8 - - + +
860E LEU 3.0 13.2 + - - +
861E ARG* 3.3 13.7 - - + +
862E ASP 3.2 0.2 - - - -
863E LYS* 1.3 76.9 - - - +
865E VAL* 1.3 65.0 + - + +
867E THR* 3.2 3.3 + - - -
868E GLN* 2.9 43.1 + - - +
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Residues in contact with VAL 865 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
838E PRO* 4.6 12.3 - - + -
861E ARG* 3.2 17.3 + - + +
862E ASP* 4.2 3.6 - - - +
864E TYR* 1.3 86.7 - - + +
866E GLU* 1.3 66.1 + - - +
868E GLN* 3.9 11.4 - - + +
869E GLN* 3.1 30.5 + - + +
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Residues in contact with GLU 866 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
795E GLY* 5.5 4.0 - - - +
799E LYS* 4.9 11.0 - - + +
862E ASP 3.0 18.1 + - - +
863E LYS* 3.9 6.7 - - - +
865E VAL* 1.3 76.2 - - - +
867E THR* 1.3 64.1 + - - +
869E GLN* 4.4 3.8 - - - +
870E LEU* 3.2 45.0 + - + +
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Residues in contact with THR 867 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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791E TRP* 4.0 15.1 + - + -
793E GLY 5.6 0.3 + - - -
794E VAL* 3.4 31.4 - - + -
795E GLY* 3.3 25.2 + - - +
798E PHE* 5.1 1.2 - - - -
833E PHE* 3.5 22.9 - - + -
863E LYS* 2.8 26.2 + - - +
864E TYR 3.5 4.5 - - - -
866E GLU* 1.3 79.2 - - - +
868E GLN* 1.3 61.3 + - - +
870E LEU* 3.5 2.1 + - - +
871E LEU* 3.0 22.8 + - + +
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Residues in contact with GLN 868 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
833E PHE* 3.7 38.7 - - + +
864E TYR* 2.9 37.7 + - + +
865E VAL* 3.4 14.0 + - + +
867E THR* 1.3 77.8 - - - +
869E GLN* 1.3 60.1 + - - +
871E LEU* 3.3 4.3 + - - +
872E LEU* 3.0 44.3 + - + +
880E ILE* 4.2 23.0 - - + +
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Residues in contact with GLN 869 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
865E VAL* 3.1 23.0 + - + +
866E GLU* 4.4 4.9 - - - +
868E GLN* 1.3 76.7 - - - +
870E LEU* 1.3 66.5 + - - +
872E LEU* 3.3 17.0 + - + +
873E GLN* 2.9 28.0 + - - +
878E LYS* 3.4 30.7 + - - +
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Residues in contact with LEU 870 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
795E GLY* 3.6 28.5 - - - +
798E PHE* 4.1 20.6 - - + -
799E LYS* 4.1 17.5 - - + +
802E ILE* 5.0 10.3 - - + -
866E GLU* 3.2 40.4 + - + +
867E THR* 3.7 3.6 - - - +
869E GLN* 1.3 78.3 - - - +
871E LEU* 1.3 63.3 + - - +
873E GLN* 2.9 26.5 + - + +
874E ILE* 2.9 30.4 + - + +
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Residues in contact with LEU 871 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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794E VAL* 5.8 1.3 - - + -
798E PHE* 4.2 17.5 - - + -
816E TYR* 6.1 0.4 - - + -
826E LEU* 4.0 20.1 - - + +
829E LEU* 3.6 37.2 - - + -
830E GLU* 4.0 39.9 - - + +
833E PHE* 3.9 17.5 - - + -
867E THR* 3.0 15.8 + - + +
868E GLN* 3.5 9.2 - - - +
869E GLN 3.3 0.2 - - - -
870E LEU* 1.3 75.0 - - - +
872E LEU* 1.3 71.5 + - + +
873E GLN 3.2 0.3 + - - -
874E ILE* 3.2 4.0 + - - +
875E ALA* 3.0 24.5 + - + +
880E ILE* 5.1 2.0 - - + -
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Residues in contact with LEU 872 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
830E GLU* 4.0 9.9 - - - +
868E GLN* 3.0 36.4 + - - +
869E GLN* 3.7 25.8 - - + +
870E LEU 3.3 0.2 - - - -
871E LEU* 1.3 80.9 - - + +
873E GLN* 1.3 55.8 + - - +
875E ALA* 4.6 2.9 - - - -
876E GLY* 3.1 21.5 + - - -
877E HIS* 2.9 28.0 + - + +
878E LYS* 4.2 19.1 - - - +
879E ASP* 3.8 19.1 - - - +
880E ILE* 3.6 32.5 - - + +
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Residues in contact with GLN 873 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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802E ILE* 5.5 8.0 - - - +
809E PHE* 3.5 43.5 - - + -
813E LYS* 4.1 4.3 - - - +
869E GLN* 2.9 21.2 + - - +
870E LEU* 2.9 29.2 + - - +
872E LEU* 1.3 76.5 - - - +
874E ILE* 1.3 65.4 + - + +
876E GLY* 4.0 5.7 + - - -
877E HIS 4.8 0.4 - - - -
878E LYS* 5.0 8.7 - - - +
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Residues in contact with ILE 874 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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798E PHE* 3.7 40.4 - - + -
802E ILE* 4.9 3.1 - - + -
809E PHE* 4.2 11.2 - - + -
812E LEU* 3.7 55.6 - - + +
813E LYS* 3.0 27.8 - - - +
816E TYR* 4.3 3.4 - - + +
822E PHE* 4.3 2.9 - - + -
826E LEU* 4.3 18.4 - - + -
870E LEU* 2.9 19.8 + - + +
871E LEU 3.2 5.6 + - - +
873E GLN* 1.3 76.4 - - + +
875E ALA* 1.3 68.0 + - - +
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Residues in contact with ALA 875 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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813E LYS* 4.7 5.2 - - - -
816E TYR* 3.4 54.9 - - + +
817E ASN* 4.7 7.4 + - - +
826E LEU* 5.2 0.4 - - + +
830E GLU* 4.6 4.3 - - - +
871E LEU* 3.0 18.0 + - + +
872E LEU* 3.9 4.3 - - - +
874E ILE* 1.3 81.2 - - - +
876E GLY* 1.3 58.8 + - - +
877E HIS* 3.8 19.0 - - + +
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Residues in contact with GLY 876 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
813E LYS* 5.1 9.2 - - - -
872E LEU 3.1 5.8 + - - -
873E GLN* 4.4 6.3 - - - -
874E ILE 3.5 1.0 - - - -
875E ALA* 1.3 77.3 - - - +
877E HIS* 1.3 70.2 + - - +
878E LYS* 4.1 5.4 + - - +
882E GLU* 4.0 5.4 - - - +
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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