Contacts of the helix formed by residues 894 - 914 (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 ARG 894 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106E LEU* 3.9 9.6 - - + +
109E ALA* 5.6 3.4 - - + -
110E ASN* 3.6 16.7 + - - +
113E GLU* 3.2 35.9 + - - +
679E PHE* 4.3 3.8 - - - -
835E LYS* 4.5 3.6 - - - +
890E GLY 3.5 12.6 + - - +
891E LEU* 3.0 28.8 + - - +
893E LEU* 1.3 79.6 - - - +
895E ASN* 1.3 64.9 + - - +
896E PRO 3.4 0.9 - - - -
897E TYR* 3.0 24.5 + - - +
898E ILE* 3.2 24.0 + - + +
965E GLY* 3.1 30.1 + - - -
967E GLN* 3.5 23.6 - - - +
1004E FLC 2.6 31.7 + - - -
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Residues in contact with ASN 895 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72E GLU* 3.0 36.6 + - - +
785E ARG* 3.5 22.0 + - - +
834E ALA 4.8 11.0 + - - +
835E LYS* 5.8 2.3 - - - -
891E LEU 3.7 9.1 + - - +
892E VAL* 3.2 25.1 + - - +
894E ARG* 1.3 76.4 - - - +
896E PRO* 1.3 62.6 - - + +
898E ILE* 4.0 16.0 - - - +
899E THR* 2.7 34.5 + - - -
966E MET* 6.1 0.2 - - - +
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Residues in contact with PRO 896 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20E LEU* 4.9 2.2 - - + -
23E LEU* 3.7 23.1 - - + -
65E TYR* 3.5 34.4 - - + +
68E SER* 3.3 17.5 - - - +
69E ALA* 4.0 21.1 - - + +
72E GLU* 4.6 2.5 - - + -
892E VAL 3.4 14.1 - - - +
893E LEU 3.8 8.1 - - - +
894E ARG 3.5 3.8 - - - -
895E ASN* 1.3 91.4 - - + +
897E TYR* 1.3 60.5 + - + +
900E THR* 2.8 23.9 + - - -
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Residues in contact with TYR 897 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16E ILE* 4.7 2.6 - - - +
20E LEU* 4.6 7.8 - - + +
38E ASP* 4.7 6.8 + - - +
42E VAL* 3.7 19.5 - - + +
65E TYR* 3.6 37.9 + + - -
102E ILE* 3.4 30.3 - - + +
105E MET* 3.7 40.6 - - + -
106E LEU* 3.9 31.9 - - + -
109E ALA* 4.0 16.2 - - + +
893E LEU 3.4 20.2 - - - -
894E ARG 3.0 17.8 + - - +
896E PRO* 1.3 74.7 - - + +
898E ILE* 1.3 65.7 + - - +
900E THR 3.6 0.5 + - - -
901E LEU* 3.3 20.5 + - - +
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Residues in contact with ILE 898 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106E LEU* 4.2 15.5 - - + -
785E ARG* 3.7 25.6 - - - +
894E ARG* 3.3 26.9 - - + +
895E ASN* 3.1 17.2 + - - +
897E TYR* 1.3 77.0 - - - +
899E THR* 1.3 57.9 + - - +
901E LEU* 3.0 12.7 + - - +
902E ASN* 2.9 32.8 + - - +
961E GLY 5.0 0.7 - - - +
962E ILE* 4.5 23.0 - - + +
965E GLY* 3.7 31.6 - - - +
966E MET* 4.4 9.0 - - + +
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Residues in contact with THR 899 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68E SER* 3.3 20.2 - - - +
71E TYR* 4.2 9.0 - - + -
72E GLU* 2.7 23.8 + - - -
80E LEU* 4.2 20.6 - - + -
785E ARG* 3.2 13.7 + - - +
840E ILE* 3.4 16.8 - - + +
895E ASN 2.7 18.5 + - - -
898E ILE* 1.3 72.9 - - - +
900E THR* 1.3 62.4 + - - +
902E ASN* 3.1 9.9 + - - +
903E VAL* 3.0 24.1 + - + +
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Residues in contact with THR 900 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64E CYS* 3.7 30.0 + - + -
65E TYR* 4.4 1.6 - - - -
68E SER* 2.9 16.9 + - - -
83E LEU* 4.2 10.3 - - + -
87E LEU* 4.2 12.2 - - + +
98E VAL* 5.7 1.3 - - + -
102E ILE* 4.2 24.9 - - + +
896E PRO 2.8 23.3 + - - -
897E TYR 3.6 6.2 + - - -
898E ILE 3.3 0.6 - - - -
899E THR* 1.3 77.3 - - - +
901E LEU* 1.3 58.2 + - + +
903E VAL* 3.5 2.6 + - - +
904E PHE* 3.1 28.6 + - + +
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Residues in contact with LEU 901 (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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99E ALA* 4.2 30.7 - - + +
102E ILE* 4.0 15.7 - - + -
103E LEU* 4.9 9.2 - - - -
106E LEU* 5.0 3.4 - - + -
897E TYR 3.3 15.4 + - - +
898E ILE* 3.0 10.1 + - - +
900E THR* 1.3 76.2 - - + +
902E ASN* 1.3 60.6 + - - +
904E PHE* 3.7 8.7 - - + +
905E GLN* 2.9 29.8 + - - +
957E LEU 4.5 2.7 - - - +
958E THR* 3.8 24.5 - - + +
961E GLY* 3.7 35.4 - - - -
962E ILE* 4.0 13.6 - - + +
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Residues in contact with ASN 902 (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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783E GLN 2.8 28.7 + - - -
785E ARG* 3.0 37.5 + - - +
840E ILE* 3.7 23.6 - - + -
843E LEU* 5.6 0.7 - - - -
844E TYR* 3.0 24.2 + - - -
898E ILE* 2.9 15.9 + - - +
899E THR* 3.1 10.5 + - - +
901E LEU* 1.3 74.0 - - - +
903E VAL* 1.3 65.4 + - + +
905E GLN 3.1 1.0 + - - -
906E ALA* 3.0 24.0 + - - +
962E ILE* 3.6 8.1 - - - +
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Residues in contact with VAL 903 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80E LEU* 3.6 36.1 - - + +
83E LEU* 3.8 17.3 - - + -
84E GLY* 3.5 36.6 - - - +
87E LEU* 4.0 7.1 - - + +
840E ILE* 5.8 1.1 - - + -
843E LEU* 4.2 13.4 - - + +
899E THR* 3.0 15.2 + - + +
900E THR 3.8 6.7 - - - +
902E ASN* 1.3 77.1 - - + +
904E PHE* 1.3 63.7 + - - +
906E ALA 3.5 0.3 + - - -
907E TYR* 3.2 31.6 + - + +
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Residues in contact with PHE 904 (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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87E LEU* 3.5 51.3 - - + +
90E LEU* 4.3 3.8 - - + -
95E ALA* 3.7 44.9 - - + -
98E VAL* 4.1 11.4 - - + -
99E ALA* 4.2 17.0 - - + -
102E ILE* 6.6 0.2 - - + -
900E THR* 3.1 19.9 + - + +
901E LEU* 3.7 11.7 - - + +
903E VAL* 1.3 78.2 - - - +
905E GLN* 1.3 54.5 + - - +
907E TYR* 4.2 3.0 - - + -
908E THR* 2.6 44.7 + - + -
954E THR* 3.8 20.2 - - + -
958E THR* 4.3 6.3 - - + -
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Residues in contact with GLN 905 (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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747E PRO* 4.0 20.5 - - - +
783E GLN* 2.9 27.8 + - - +
844E TYR* 2.5 43.3 + - - +
901E LEU 2.9 17.4 + - - +
902E ASN 3.1 0.6 + - - +
904E PHE* 1.3 74.4 - - - +
906E ALA* 1.3 60.0 + - - +
908E THR* 3.3 6.7 + - - -
909E LEU* 2.8 36.9 + - + +
955E LEU* 3.6 14.4 - - + -
958E THR* 3.0 27.1 + - - +
959E MET* 3.5 9.7 - - - +
962E ILE* 3.8 8.1 - - + +
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Residues in contact with ALA 906 (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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843E LEU* 4.7 7.0 - - + -
844E TYR* 4.1 35.1 - - + -
847E LEU* 3.6 22.4 - - + +
848E LEU* 3.9 7.0 - - + +
902E ASN 3.0 15.7 + - - +
903E VAL 4.0 4.0 - - - +
904E PHE 3.4 0.2 - - - -
905E GLN* 1.3 77.4 - - - +
907E TYR* 1.3 62.7 + - + +
909E LEU* 3.3 6.8 + - - +
910E LYS* 3.2 21.0 + - - +
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Residues in contact with TYR 907 (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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80E LEU 4.8 0.9 - - - -
81E GLY* 3.6 22.7 + - - -
84E GLY* 3.9 23.8 - - - +
85E ALA* 4.8 1.1 - - - -
87E LEU* 6.2 2.5 - - + -
88E THR* 3.6 30.1 - - + -
843E LEU* 4.4 13.2 - - + +
847E LEU* 3.5 39.6 - - + +
903E VAL* 3.2 32.3 + - + +
904E PHE* 4.3 4.7 - - + +
906E ALA* 1.3 80.9 - - + +
908E THR* 1.3 63.3 + - + +
910E LYS* 3.4 12.1 + - + +
911E ARG* 3.1 27.1 + - - +
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Residues in contact with THR 908 (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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904E PHE* 2.6 36.9 + - + +
905E GLN* 3.3 7.8 + - - -
907E TYR* 1.3 75.5 - - + +
909E LEU* 1.3 59.3 + - - +
911E ARG* 3.7 20.8 - - - +
912E ILE* 2.8 40.0 + - - +
951E LEU* 4.1 17.0 - - + -
954E THR* 4.2 27.0 - - + +
955E LEU* 4.2 9.9 - - - +
958E THR* 4.9 0.3 - - - +
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Residues in contact with LEU 909 (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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747E PRO* 4.1 24.0 - - + -
750E GLU* 3.6 34.1 - - + +
844E TYR* 4.1 18.4 - - + -
848E LEU* 3.7 29.4 - - + -
905E GLN* 2.8 24.8 + - + +
906E ALA 3.3 4.9 + - - +
908E THR* 1.3 77.7 + - - +
910E LYS* 1.3 62.2 + - - +
912E ILE* 3.3 4.1 + - + +
913E ARG* 3.0 36.8 + - - +
955E LEU* 3.9 24.7 - - + -
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Residues in contact with LYS 910 (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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847E LEU* 4.3 27.1 - - + +
848E LEU* 3.6 13.4 - - + +
906E ALA 3.2 12.0 + - - +
907E TYR* 3.5 16.2 - - + +
908E THR 3.3 0.2 - - - -
909E LEU* 1.3 76.7 - - - +
911E ARG* 1.3 70.1 + - + +
913E ARG* 3.6 3.3 + - - +
914E ASP* 3.3 41.2 + - - +
917E PHE* 5.4 4.6 - - - -
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Residues in contact with ARG 911 (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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88E THR* 2.7 53.9 + - - +
90E LEU 5.3 5.1 + - - -
907E TYR 3.1 17.7 + - - +
908E THR* 3.3 15.0 + - - +
910E LYS* 1.3 83.4 - - + +
912E ILE* 1.3 66.0 + - - +
914E ASP* 3.3 18.9 + - - +
917E PHE* 3.4 63.0 - - + +
919E VAL* 5.7 2.6 - - - +
948E PRO* 5.7 0.5 - - - +
951E LEU* 4.0 21.1 - - + +
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Residues in contact with ILE 912 (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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750E GLU* 4.6 17.0 - - + +
754E MET* 4.0 10.8 - - + -
908E THR* 2.8 29.8 + - - +
909E LEU* 3.3 6.5 + - - +
911E ARG* 1.3 73.5 - - - +
913E ARG* 1.3 62.2 + - + +
914E ASP 3.5 3.6 + - - +
947E TYR* 4.0 27.9 - - + -
948E PRO* 5.8 3.4 - - - +
951E LEU* 3.7 42.6 - - + +
955E LEU* 3.6 31.2 - - + -
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Residues in contact with ARG 913 (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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743E ARG 3.4 12.5 + - - -
744E SER* 2.8 30.9 + - - +
746E THR 3.0 27.7 + - - -
747E PRO* 4.2 1.2 - - - +
749E THR* 5.0 1.4 - - - -
750E GLU* 3.0 39.4 + - - +
848E LEU* 3.6 26.9 + - - +
909E LEU* 3.0 25.4 + - - +
910E LYS* 4.2 3.8 - - - +
911E ARG 3.2 0.2 - - - -
912E ILE* 1.3 76.7 - - + +
914E ASP* 1.3 62.9 + - - +
915E PRO* 3.2 11.6 - - - +
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Residues in contact with ASP 914 (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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910E LYS* 3.3 37.5 + - - +
911E ARG* 3.3 10.4 + - - +
912E ILE 4.3 3.1 - - - +
913E ARG* 1.3 74.1 - - - +
915E PRO* 1.3 70.2 - - - +
916E ASN* 2.9 26.6 + - - +
917E PHE* 3.3 29.2 + - + +
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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
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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) + - + + + + + -
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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