Contacts of the helix formed by residues 940 - 975 (chain F) in PDB entry 5EJC
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 GLN 940 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
961C GLU* 4.1 15.5 + - + +
968C ARG* 5.4 5.5 + - - -
966D TYR* 2.6 33.6 + - - +
941E LEU* 3.6 31.7 - - + +
939F GLY* 1.3 75.5 - - - +
941F LEU* 1.3 61.6 + - - +
943F ALA* 3.4 9.0 + - + +
944F ALA* 3.2 20.6 + - - +
947F ARG* 4.9 2.9 + - - +
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Residues in contact with LEU 941 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A LYS* 4.2 16.4 - - - +
80A TYR* 4.1 9.2 - - - +
940E GLN* 3.6 43.1 - - + +
941E LEU* 4.1 13.8 - - + +
944E ALA* 4.8 4.3 - - + -
939F GLY 3.3 4.8 - - - +
940F GLN* 1.3 77.0 - - - +
942F GLN* 1.3 67.1 + - + +
944F ALA* 3.1 8.4 + - - +
945F GLU* 2.9 46.5 + - + +
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Residues in contact with GLN 942 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
939F GLY* 3.4 22.9 + - - +
941F LEU* 1.3 84.1 - - + +
943F ALA* 1.3 57.0 + - - +
945F GLU* 3.3 7.6 + - - +
946F SER* 2.9 27.0 + - - +
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Residues in contact with ALA 943 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
957C VAL* 3.5 23.1 - - + +
961C GLU* 5.4 4.5 - - + +
939F GLY 3.4 8.4 + - - +
940F GLN* 3.4 11.6 + - + +
941F LEU 3.2 0.6 - - - -
942F GLN* 1.3 79.0 - - - +
944F ALA* 1.3 62.1 + - - +
946F SER* 3.3 9.9 - - - -
947F ARG* 3.2 30.4 + - - +
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Residues in contact with ALA 944 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
941E LEU* 5.1 5.4 - - + -
944E ALA* 4.2 25.8 - - + +
945E GLU* 4.4 11.0 - - + +
948E TYR* 4.9 1.0 - - - +
940F GLN 3.2 11.7 + - - +
941F LEU* 3.1 12.9 + - - +
943F ALA* 1.3 75.4 - - - +
945F GLU* 1.3 63.8 + - - +
947F ARG* 3.4 33.4 + - - +
948F TYR* 3.2 19.4 + - - +
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Residues in contact with GLU 945 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A LYS* 5.3 0.3 - - - -
79A MSE 5.5 1.8 - - - +
80A TYR* 2.5 36.9 + - + +
944E ALA* 4.9 2.2 - - + -
947E ARG* 4.3 18.8 + - - +
941F LEU* 2.9 28.5 + - + +
942F GLN* 3.7 9.6 - - - +
944F ALA* 1.3 73.5 - - - +
946F SER* 1.3 67.2 + - - +
948F TYR* 3.2 9.9 + - - +
949F GLU* 3.0 25.6 + - - +
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Residues in contact with SER 946 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
953C ARG* 5.4 8.6 - - - +
957C VAL* 4.4 16.3 - - - +
942F GLN* 2.9 14.9 + - - +
943F ALA* 3.3 15.3 - - - -
945F GLU* 1.3 76.5 - - - +
947F ARG* 1.3 60.4 + - - +
949F GLU* 3.1 36.0 + - - +
950F ALA* 3.1 11.3 + - - +
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Residues in contact with ARG 947 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
954C ILE* 4.0 21.5 - - + +
957C VAL* 4.0 18.5 - - + +
958C PHE* 3.1 51.3 - - - -
961C GLU* 3.6 19.2 + - - -
941E LEU* 6.3 0.2 - - - +
945E GLU* 3.2 36.5 + - - +
948E TYR* 3.8 25.8 - - + +
940F GLN* 4.9 3.6 + - - +
943F ALA* 3.2 10.4 + - - +
944F ALA* 3.5 33.5 + - - +
945F GLU 3.2 0.2 - - - -
946F SER* 1.3 77.7 - - - +
948F TYR* 1.3 64.5 + - - +
950F ALA* 3.4 2.6 + - - +
951F GLN* 3.0 23.7 + - - +
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Residues in contact with TYR 948 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A GLU* 3.5 21.3 + - - +
87A ASP* 2.7 27.2 + - - -
944E ALA 4.8 0.7 - - - +
947E ARG* 2.7 71.1 + - + +
948E TYR* 4.2 15.0 - - - +
951E GLN* 3.5 24.7 - - + -
944F ALA 3.2 10.8 + - - +
945F GLU* 3.2 10.0 + - - +
947F ARG* 1.3 78.9 - - - +
949F GLU* 1.3 63.7 + - + +
951F GLN* 3.2 4.6 + - - +
952F LYS* 2.9 49.0 + - + +
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Residues in contact with GLU 949 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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953C ARG* 5.1 5.0 - - - -
945F GLU 3.0 13.3 + - - +
946F SER* 3.1 31.9 + - - +
948F TYR* 1.3 83.1 - - + +
950F ALA* 1.3 66.4 + - + +
952F LYS* 3.1 11.8 + - - +
953F ARG* 3.0 48.7 + - - +
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Residues in contact with ALA 950 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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950C ALA* 4.0 14.3 - - + +
953C ARG* 4.7 14.4 - - + -
954C ILE* 3.7 25.6 - - + -
946F SER 3.1 13.3 + - - +
947F ARG 3.7 0.4 - - - +
949F GLU* 1.3 83.4 - - + +
951F GLN* 1.3 62.5 + - - +
953F ARG* 3.1 18.6 + - - +
954F ILE* 3.1 26.5 + - - +
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Residues in contact with GLN 951 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
951C GLN* 4.4 9.3 + - - +
954C ILE* 3.1 25.8 - - - +
948D TYR* 5.3 1.4 + - - -
952D LYS* 6.3 0.4 - - - +
948E TYR* 3.5 21.1 + - + -
951E GLN* 3.9 23.1 - - + -
952E LYS* 3.8 24.0 - - - +
955E THR* 3.6 26.7 + - - +
947F ARG 3.0 12.6 + - - +
948F TYR 3.2 7.2 + - - +
950F ALA* 1.3 76.2 - - - +
952F LYS* 1.3 60.3 + - - +
954F ILE* 3.2 18.1 + - - +
955F THR* 2.8 28.3 + - - -
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Residues in contact with LYS 952 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A GLU* 5.0 5.1 + - - +
87A ASP* 3.9 18.2 + - - -
951E GLN* 3.4 24.8 + - - +
948F TYR* 2.9 37.4 + - + +
949F GLU* 3.2 14.6 - - - +
951F GLN* 1.3 74.7 - - - +
953F ARG* 1.3 58.9 + - + +
955F THR* 3.3 4.0 + - - -
956F GLN* 2.9 31.8 + - - +
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Residues in contact with ARG 953 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
950C ALA* 5.0 8.6 - - + +
953C ARG* 3.2 49.5 - - - +
949F GLU* 3.0 55.0 + - + +
950F ALA* 3.1 13.1 + - - +
952F LYS* 1.3 77.1 - - + +
954F ILE* 1.3 61.2 + - - +
956F GLN* 3.3 24.0 - - - +
957F VAL* 3.1 28.8 + - + +
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Residues in contact with ILE 954 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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947C ARG* 4.0 19.3 - - + +
950C ALA* 3.7 23.6 - - + -
951C GLN* 3.1 29.2 - - - +
954C ILE* 4.1 4.9 - - + -
948D TYR* 3.9 7.4 - - + +
955E THR* 3.9 12.8 - - + +
950F ALA 3.1 14.8 + - - +
951F GLN* 3.2 24.2 + - - +
953F ARG* 1.3 77.4 - - - +
955F THR* 1.3 63.0 + - - +
957F VAL* 3.2 10.1 + - - +
958F PHE* 3.1 45.1 + - + -
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Residues in contact with THR 955 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
951E GLN* 2.5 29.2 + - - +
954E ILE* 3.4 17.0 - - + -
955E THR* 3.4 14.4 + - - +
958E PHE* 3.3 30.2 - - + -
951F GLN 2.8 9.2 + - - -
952F LYS* 3.4 7.6 - - - -
954F ILE* 1.3 77.5 - - - +
956F GLN* 1.3 53.1 + - - +
958F PHE* 3.1 9.0 + - - +
959F GLU* 2.7 37.6 + - - +
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Residues in contact with GLN 956 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
952F LYS* 2.9 14.4 + - + +
953F ARG* 3.3 36.4 - - - +
955F THR* 1.3 76.5 - - - +
957F VAL* 1.3 62.6 + - + +
959F GLU* 3.4 19.3 - - - +
960F LEU* 3.2 25.5 + - + +
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Residues in contact with VAL 957 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
943C ALA* 3.6 41.1 - - + +
946C SER* 4.4 18.4 - - - +
947C ARG* 4.0 16.4 - - + +
953F ARG* 3.1 19.1 + - + +
954F ILE* 3.2 8.7 + - - +
956F GLN* 1.3 76.9 - - + +
958F PHE* 1.3 65.0 + - - +
960F LEU* 3.3 14.1 + - + +
961F GLU* 3.0 23.1 + - - +
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Residues in contact with PHE 958 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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947C ARG* 3.1 44.2 - - - -
945D GLU* 5.2 4.7 - - - -
948D TYR* 3.8 13.0 - + - -
955E THR* 3.6 35.4 - - + -
958E PHE* 4.0 17.9 - - + -
959E GLU* 3.7 27.4 - - + -
962E ILE* 3.2 26.4 - - + +
954F ILE* 3.1 20.0 + - + -
955F THR* 3.5 6.7 - - - +
957F VAL* 1.3 73.1 - - - +
959F GLU* 1.3 60.9 + - - +
961F GLU* 3.2 8.8 + - - +
962F ILE* 2.8 36.0 + - - +
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Residues in contact with GLU 959 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A HIS* 2.7 38.2 + - - -
94A VAL* 3.9 22.3 - - + +
958E PHE* 4.3 8.9 - - + -
955F THR* 2.7 22.0 + - - +
956F GLN* 3.4 20.8 - - - +
958F PHE* 1.3 74.8 - - - +
960F LEU* 1.3 57.8 + - - +
962F ILE* 3.4 9.3 + - - +
963F LEU* 3.1 41.6 + - + +
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Residues in contact with LEU 960 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
943C ALA* 5.3 7.9 - - + -
956F GLN* 3.2 15.1 + - + +
957F VAL* 3.3 21.1 + - + +
958F PHE 3.3 0.2 - - - -
959F GLU* 1.3 76.4 - - - +
961F GLU* 1.3 67.0 + - + +
963F LEU* 3.4 10.5 + - + +
964F ASP* 2.9 30.2 + - + +
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Residues in contact with GLU 961 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
940C GLN* 5.1 8.2 + - + +
943C ALA* 5.2 4.7 - - + +
947C ARG* 3.3 27.9 + - - -
945D GLU* 4.9 3.6 - - - +
962E ILE* 4.1 16.5 - - + +
966E TYR* 3.3 29.8 + - - +
957F VAL* 3.0 16.0 + - + +
958F PHE* 3.2 19.3 + - - +
960F LEU* 1.3 82.6 - - + +
962F ILE* 1.3 55.6 + - - +
964F ASP* 3.4 8.0 + - + +
965F LEU* 2.9 42.5 + - + +
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Residues in contact with ILE 962 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A VAL* 4.2 19.5 - - + +
95A VAL* 4.8 0.2 - - + -
958E PHE* 3.6 50.7 - - + +
961E GLU* 4.5 9.2 - - + -
962E ILE* 3.5 19.3 - - + +
965E LEU* 4.2 8.5 - - + -
958F PHE 2.8 19.9 + - - +
959F GLU* 3.5 4.0 - - - +
961F GLU* 1.3 73.0 - - - +
963F LEU* 1.3 62.8 + - + +
965F LEU* 3.0 9.5 + - - +
966F TYR* 2.8 57.1 + - + -
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Residues in contact with LEU 963 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A VAL* 4.6 21.3 - - + +
96A ARG* 6.0 3.6 - - - +
959F GLU* 3.1 25.3 + - + +
960F LEU* 3.7 13.5 - - + +
961F GLU 3.4 0.2 - - - -
962F ILE* 1.3 80.6 - - + +
964F ASP* 1.3 62.2 + - - +
966F TYR* 3.8 9.1 - - + +
967F GLY* 3.0 20.1 + - - -
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Residues in contact with ASP 964 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
940C GLN* 5.6 5.9 - - - +
960F LEU* 2.9 18.3 + - + +
961F GLU* 3.5 9.2 - - - +
963F LEU* 1.3 75.4 - - - +
965F LEU* 1.3 59.2 + - + +
967F GLY* 3.3 3.6 + - - -
968F ARG* 3.0 45.1 + - - +
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Residues in contact with LEU 965 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
962E ILE* 3.8 35.9 - - + +
965E LEU* 3.9 28.7 - - + -
966E TYR* 3.7 37.0 - - + +
969E LEU* 4.9 9.0 - - + +
961F GLU* 2.9 23.1 + - + +
962F ILE 3.0 6.3 + - - +
964F ASP* 1.3 75.4 - - + +
966F TYR* 1.3 65.5 + - - +
968F ARG* 3.2 23.3 + - - +
969F LEU* 3.1 26.4 + - - +
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Residues in contact with TYR 966 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A VAL 3.8 13.2 - - - -
95A VAL 4.2 7.8 + - - -
96A ARG* 3.3 56.7 - - - +
961E GLU* 2.6 27.5 + - - +
965E LEU* 3.9 23.5 - - + +
968E ARG* 5.0 8.1 - - - -
962F ILE* 2.8 49.9 + - + +
963F LEU* 3.8 10.1 - - + +
965F LEU* 1.3 71.5 - - - +
967F GLY* 1.3 63.4 + - - +
968F ARG 3.3 0.2 + - - -
969F LEU* 3.3 19.3 + - + +
970F GLU* 3.0 24.2 + - - +
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Residues in contact with GLY 967 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
963F LEU 3.0 15.1 + - - -
964F ASP* 3.6 5.2 - - - -
965F LEU 3.3 0.4 - - - -
966F TYR* 1.3 76.5 - - - +
968F ARG* 1.3 59.4 + - - +
970F GLU* 3.5 13.7 + - - +
971F LYS* 3.2 20.4 + - - +
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Residues in contact with ARG 968 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
940C GLN* 5.0 12.5 + - - -
966E TYR* 5.8 4.8 - - - -
969E LEU* 3.8 30.3 - - + +
964F ASP* 3.0 37.8 + - - +
965F LEU* 3.2 21.7 + - - +
967F GLY* 1.3 76.7 - - - +
969F LEU* 1.3 58.4 + - - +
970F GLU 3.2 0.4 - - - -
971F LYS* 3.3 17.6 + - - +
972F ASP* 3.1 24.8 + - - +
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Residues in contact with LEU 969 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
965E LEU* 3.6 39.5 - - + +
968E ARG* 3.9 31.4 - - + +
969E LEU* 4.6 17.7 - - + +
965F LEU 3.1 13.6 + - - +
966F TYR* 3.4 23.8 - - + +
968F ARG* 1.3 74.2 - - - +
970F GLU* 1.3 69.2 + - + +
972F ASP* 3.9 10.3 - - + +
973F GLY* 3.7 12.3 + - - -
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Residues in contact with GLU 970 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
966F TYR 3.0 15.5 + - - +
967F GLY* 3.6 12.9 - - - +
969F LEU* 1.3 80.5 - - + +
971F LYS* 1.3 63.3 + - - +
972F ASP 3.2 0.2 - - - -
973F GLY* 3.2 12.4 + - - -
974F LEU* 3.4 9.4 + - - +
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Residues in contact with LYS 971 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
967F GLY 3.2 11.1 + - - +
968F ARG* 3.3 17.5 + - - +
970F GLU* 1.3 80.4 - - - +
972F ASP* 1.3 55.8 + - - +
974F LEU* 3.1 26.1 + - + +
975F LEU* 3.2 26.6 + - + +
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Residues in contact with ASP 972 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
969E LEU* 3.1 29.8 - - + +
968F ARG 3.1 14.8 + - - +
969F LEU* 4.2 7.0 - - - +
970F GLU 3.2 0.6 - - - -
971F LYS* 1.3 76.4 - - - +
973F GLY* 1.3 60.5 + - - +
974F LEU 3.3 0.2 - - - -
975F LEU* 3.8 25.8 + - - +
976F LYS* 3.8 9.9 + - - +
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Residues in contact with GLY 973 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
969F LEU 3.7 7.4 + - - -
970F GLU 3.2 10.8 + - - -
972F ASP* 1.3 78.8 - - - +
974F LEU* 1.3 57.2 + - - +
976F LYS* 3.2 28.5 - - - +
977F LYS* 4.2 6.8 - - - +
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Residues in contact with LEU 974 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
970F GLU 3.4 6.1 + - - +
971F LYS* 3.1 20.5 + - + +
973F GLY* 1.3 74.7 - - - +
975F LEU* 1.3 59.4 + - - +
976F LYS 3.0 5.2 - - - -
977F LYS* 3.2 34.8 + - + +
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Residues in contact with LEU 975 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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971F LYS* 3.2 30.3 + - + +
972F ASP* 4.0 24.2 - - - +
973F GLY 3.5 0.2 - - - -
974F LEU* 1.3 75.1 - - - +
976F LYS* 1.3 60.1 + - - +
977F LYS 3.3 6.7 + - - +
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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
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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