Contacts of the helix formed by residues 940 - 969 (chain E) 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 E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A PRO* 5.2 0.2 - - - +
72A GLU* 5.8 1.4 - - - +
73A SER* 2.6 40.0 + - - +
76A LYS* 4.0 31.4 - - + +
77A VAL* 4.2 12.5 - - + +
80A TYR* 3.9 6.5 - - + -
939E GLY* 1.3 78.8 + - - +
941E LEU* 1.3 62.3 + - - +
943E ALA* 3.4 4.5 + - - +
944E ALA* 3.2 19.9 + - - +
941F LEU* 3.6 19.5 - - + +
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Residues in contact with LEU 941 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
939E GLY 3.2 5.0 - - - +
940E GLN* 1.3 77.7 - - - +
942E GLN* 1.3 71.6 + - + +
944E ALA* 3.1 5.8 + - - +
945E GLU* 2.9 39.4 + - + +
940F GLN* 3.6 58.3 - - + +
941F LEU* 4.1 15.7 - - + +
944F ALA* 5.1 6.1 - - + -
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Residues in contact with GLN 942 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A GLY 5.2 5.4 - - - +
81A ARG* 4.6 3.1 - - - +
157A ARG* 5.8 2.0 + - - -
939E GLY* 3.5 23.3 + - - +
940E GLN 3.4 0.2 - - - -
941E LEU* 1.3 85.6 - - + +
943E ALA* 1.3 57.1 + - - +
945E GLU* 3.3 6.4 + - - +
946E SER* 2.9 28.5 + - - -
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Residues in contact with ALA 943 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A VAL* 3.9 21.3 - - + -
80A TYR* 3.7 22.5 - - + +
81A ARG* 3.4 25.9 + - - +
939E GLY 3.5 6.5 + - - +
940E GLN 3.4 9.3 + - - +
941E LEU 3.2 0.2 - - - -
942E GLN* 1.3 79.4 - - - +
944E ALA* 1.3 62.6 + - - +
946E SER* 3.3 4.2 - - - -
947E ARG* 3.1 26.2 + - - +
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Residues in contact with ALA 944 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A TYR* 4.2 9.1 - - + -
940E GLN 3.2 12.6 + - - +
941E LEU* 3.1 12.7 + - - +
943E ALA* 1.3 74.9 - - - +
945E GLU* 1.3 61.0 + - - +
947E ARG* 3.4 27.0 + - - +
948E TYR* 3.3 19.1 + - - +
941F LEU* 4.8 7.0 - - + -
944F ALA* 4.2 25.4 - - + +
945F GLU* 4.9 6.7 - - + -
948F TYR* 4.8 1.0 - - - +
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Residues in contact with GLU 945 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
958C PHE* 5.3 3.6 - - - -
961C GLU* 5.4 2.1 - - - +
941E LEU* 2.9 36.5 + - + +
942E GLN* 3.7 6.5 - - - +
944E ALA* 1.3 73.9 - - - +
946E SER* 1.3 66.1 + - - +
948E TYR* 3.2 17.0 + - - +
949E GLU* 3.0 34.2 + - + +
944F ALA* 4.4 6.7 - - + +
947F ARG* 3.2 38.1 + - - +
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Residues in contact with SER 946 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A ARG* 3.6 18.7 + - - -
84A GLN* 2.6 33.6 + - - -
153A TRP* 4.4 3.8 - - - -
156A ARG* 5.1 3.5 + - - -
157A ARG* 4.8 5.7 + - - -
942E GLN 2.9 14.5 + - - -
943E ALA 3.3 11.2 - - - -
944E ALA 3.3 0.2 - - - -
945E GLU* 1.3 77.5 - - - +
947E ARG* 1.3 56.5 + - - +
949E GLU* 3.4 5.8 + - - +
950E ALA* 3.1 15.2 + - - +
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Residues in contact with ARG 947 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A TYR* 3.1 71.5 - - + +
83A GLU* 3.7 17.6 + - - -
84A GLN* 3.1 15.5 - - + +
87A ASP* 5.4 0.2 - - - +
943E ALA 3.1 10.6 + - - +
944E ALA* 3.5 22.8 + - - +
945E GLU 3.2 0.4 - - - -
946E SER* 1.3 79.1 - - - +
948E TYR* 1.3 62.3 + - - +
950E ALA* 3.4 2.4 + - - +
951E GLN* 3.0 24.6 + - - +
945F GLU* 4.3 16.0 + - - +
948F TYR* 2.7 60.9 - - + +
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Residues in contact with TYR 948 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
951C GLN* 5.3 1.4 + - - -
954C ILE* 4.0 6.0 - - + +
958C PHE* 3.9 16.9 - + - -
955D THR* 3.7 19.6 - - - +
959D GLU* 3.2 27.9 + - - -
944E ALA 3.3 10.4 + - - +
945E GLU* 3.2 24.6 + - - +
947E ARG* 1.3 79.1 - - - +
949E GLU* 1.3 69.7 + - + +
951E GLN* 3.2 5.7 + - - +
952E LYS* 2.9 39.9 + - - +
944F ALA 4.9 0.4 - - - +
947F ARG* 3.8 39.0 - - + +
948F TYR* 4.1 15.8 - - + +
951F GLN* 3.5 29.5 + - + -
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Residues in contact with GLU 949 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
959D GLU* 4.5 2.3 - - - +
945E GLU* 3.0 26.1 + - + +
946E SER* 3.8 6.3 - - - +
948E TYR* 1.3 83.0 - - + +
950E ALA* 1.3 62.0 + - - +
952E LYS* 3.1 38.8 + - - +
953E ARG* 3.0 37.2 + - + +
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Residues in contact with ALA 950 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A GLN* 2.9 39.9 - - + +
87A ASP* 6.2 1.3 - - + -
88A VAL* 4.4 13.9 - - + -
114A LEU* 4.6 1.2 - - - +
115A GLU* 4.8 10.1 - - + +
946E SER 3.1 6.0 + - - +
947E ARG 3.7 1.6 - - - +
949E GLU* 1.3 76.8 - - - +
951E GLN* 1.3 62.4 + - + +
953E ARG* 3.1 11.4 + - - +
954E ILE* 3.1 27.1 + - + +
----------------------------------------------------------
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Residues in contact with GLN 951 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A ASP* 3.3 31.5 + - + +
947E ARG 3.0 9.6 + - - +
948E TYR 3.5 8.1 - - - +
950E ALA* 1.3 76.2 - - - +
952E LYS* 1.3 61.7 - - - +
954E ILE* 3.2 14.8 + - + +
955E THR* 2.9 28.4 + - - -
948F TYR* 3.5 26.5 - - + -
951F GLN* 3.8 16.7 - - + +
952F LYS* 3.4 28.3 - - - +
955F THR* 2.5 37.9 + - - +
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Residues in contact with LYS 952 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
956D GLN* 6.4 1.3 - - + -
959D GLU* 2.6 36.8 + - - +
948E TYR* 2.9 32.9 + - - +
949E GLU* 3.1 40.1 + - - +
951E GLN* 1.3 76.7 - - - +
953E ARG* 1.3 62.7 + - + +
955E THR* 3.3 5.9 + - - -
956E GLN* 3.1 36.4 + - + +
951F GLN* 3.8 27.7 - - - +
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Residues in contact with ARG 953 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A LEU* 3.6 22.7 - - + +
115A GLU* 3.1 22.6 + - - +
116A SER* 2.9 38.8 + - - +
117A GLY* 3.0 9.6 - - - +
949E GLU* 3.0 28.7 + - + +
950E ALA* 3.1 9.4 + - - +
952E LYS* 1.3 74.6 - - + +
954E ILE* 1.3 64.8 + - - +
956E GLN* 3.3 27.8 + - - +
957E VAL* 3.1 28.0 + - - +
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Residues in contact with ILE 954 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A ASP* 3.8 39.7 - - + +
88A VAL* 4.0 4.7 - - + +
91A ALA* 3.5 20.6 - - + -
114A LEU* 3.9 14.1 - - + -
950E ALA 3.1 16.7 + - - +
951E GLN* 3.2 22.6 + - - +
953E ARG* 1.3 75.6 - - - +
955E THR* 1.3 63.4 + - - +
957E VAL* 3.1 10.1 + - - +
958E PHE* 3.0 35.3 + - + -
955F THR* 3.4 25.6 - - + -
----------------------------------------------------------
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Residues in contact with THR 955 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
948D TYR* 3.8 13.7 - - - +
951E GLN 2.9 14.9 + - - -
952E LYS 3.4 8.1 - - - -
954E ILE* 1.3 76.9 - - - +
956E GLN* 1.3 52.3 + - + +
958E PHE* 3.2 8.4 + - - +
959E GLU* 2.7 41.3 + - - +
951F GLN* 3.6 19.4 + - - +
954F ILE* 3.9 8.5 - - + -
955F THR* 3.4 14.8 + - - +
958F PHE* 3.6 30.5 - - + -
----------------------------------------------------------
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Residues in contact with GLN 956 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
952D LYS* 6.5 1.1 - - + -
952E LYS* 3.1 27.1 + - + +
953E ARG* 3.4 37.8 + - - +
954E ILE 3.3 0.2 - - - -
955E THR* 1.3 80.5 - - - +
957E VAL* 1.3 61.6 + - + +
959E GLU* 3.6 16.8 - - - +
960E LEU* 3.2 33.1 + - + +
----------------------------------------------------------
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Residues in contact with VAL 957 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A VAL* 4.2 22.9 - - + -
114A LEU* 3.8 30.1 - - + +
119A LEU* 4.0 29.4 - - + -
121A ARG* 5.6 5.0 + - - +
953E ARG 3.1 15.9 + - - +
954E ILE* 3.1 6.7 + - + +
956E GLN* 1.3 74.9 - - + +
958E PHE* 1.3 63.8 + - + +
960E LEU* 3.3 8.8 + - - +
961E GLU* 2.9 26.1 + - + +
----------------------------------------------------------
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Residues in contact with PHE 958 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A HIS* 6.1 0.4 - + - -
91A ALA* 3.6 31.9 - - + -
94A VAL* 3.6 29.8 - - + -
95A VAL* 3.5 15.7 - - + -
954E ILE* 3.0 23.7 + - + -
955E THR* 3.6 7.6 - - - +
957E VAL* 1.3 75.9 - - + +
959E GLU* 1.3 60.8 + - - +
961E GLU* 3.1 2.7 + - - +
962E ILE* 2.8 36.9 + - - +
955F THR* 3.3 47.3 - - + -
958F PHE* 4.0 15.7 - - + -
959F GLU* 4.3 8.7 - - + -
962F ILE* 3.6 17.9 - - + -
----------------------------------------------------------
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Residues in contact with GLU 959 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
948D TYR* 2.9 28.5 + - - -
949D GLU* 5.2 2.0 - - - -
952D LYS* 2.9 32.6 + - - +
955E THR* 2.7 24.2 + - - +
956E GLN* 3.6 20.9 - - - +
958E PHE* 1.3 73.2 - - - +
960E LEU* 1.3 57.2 + - + +
962E ILE* 3.3 9.4 + - - +
963E LEU* 3.1 27.5 + - - +
958F PHE* 3.7 20.1 - - + -
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Residues in contact with LEU 960 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A ARG* 5.4 11.0 - - - +
956E GLN* 3.2 25.2 + - + +
957E VAL* 3.7 8.5 - - - +
958E PHE 3.3 0.4 - - - -
959E GLU* 1.3 77.3 - - + +
961E GLU* 1.3 60.9 + - - +
963E LEU* 3.4 13.7 + - + +
964E ASP* 2.9 28.9 + - - +
----------------------------------------------------------
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Residues in contact with GLU 961 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A VAL* 4.1 30.3 - - + +
121A ARG* 2.5 48.5 + - - +
957E VAL* 2.9 14.4 + - + +
958E PHE* 3.5 9.4 - - - +
960E LEU* 1.3 75.7 - - - +
962E ILE* 1.3 58.4 + - - +
964E ASP* 3.3 7.4 + - - +
965E LEU* 2.9 47.4 + - + +
968E ARG* 5.6 1.9 + - - -
962F ILE* 4.5 8.7 - - + -
966F TYR* 2.6 30.0 + - - +
----------------------------------------------------------
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Residues in contact with ILE 962 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
958E PHE 2.8 20.1 + - - +
959E GLU* 3.5 5.8 - - - +
961E GLU* 1.3 73.4 - - - +
963E LEU* 1.3 60.8 + - - +
965E LEU* 3.0 5.3 + - - +
966E TYR* 2.8 58.0 + - + -
958F PHE* 3.2 46.2 - - + +
961F GLU* 4.1 13.5 - - - +
962F ILE* 3.5 25.8 - - + +
965F LEU* 3.8 14.8 - - + +
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Residues in contact with LEU 963 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
959E GLU 3.1 13.1 + - - +
960E LEU* 3.7 13.7 - - + +
962E ILE* 1.3 81.6 - - - +
964E ASP* 1.3 62.5 + - - +
966E TYR* 3.5 11.3 + - + +
967E GLY* 3.0 19.8 + - - -
----------------------------------------------------------
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Residues in contact with ASP 964 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A ARG* 3.7 34.0 + - - +
960E LEU 2.9 18.5 + - - +
961E GLU* 3.5 12.0 - - - +
963E LEU* 1.3 74.7 - - - +
965E LEU* 1.3 58.3 + - + +
967E GLY* 3.3 3.2 + - - -
968E ARG* 3.0 46.5 + - - +
----------------------------------------------------------
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Residues in contact with LEU 965 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
961E GLU* 2.9 29.3 + - + +
962E ILE* 3.5 7.0 - - - +
964E ASP* 1.3 75.0 - - + +
966E TYR* 1.3 65.6 + - - +
968E ARG* 3.2 21.0 + - - +
969E LEU* 3.1 24.3 + - - +
962F ILE* 4.2 12.8 - - + +
965F LEU* 3.9 35.2 - - + -
966F TYR* 3.9 39.9 - - + +
969F LEU* 3.6 29.4 - - + +
----------------------------------------------------------
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Residues in contact with TYR 966 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
940C GLN* 3.0 28.5 + - - -
941D LEU* 5.7 2.9 - - + +
962E ILE* 2.8 50.6 + - + +
963E LEU* 3.8 11.0 - - + +
965E LEU* 1.3 71.7 - - - +
967E GLY* 1.3 60.1 + - - +
969E LEU* 2.9 34.8 + - + +
970E GLU* 3.8 6.3 - - - +
961F GLU* 3.3 18.4 + - - +
965F LEU* 3.7 27.7 - - + +
968F ARG* 5.8 5.8 - - - -
----------------------------------------------------------
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Residues in contact with GLY 967 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
963E LEU 3.0 14.9 + - - -
964E ASP* 3.6 5.4 - - - -
966E TYR* 1.3 76.6 - - - +
968E ARG* 1.3 59.7 + - - +
970E GLU* 3.8 15.3 - - - +
----------------------------------------------------------
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Residues in contact with ARG 968 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
961E GLU* 5.6 2.2 + - - -
964E ASP* 3.0 41.9 + - - +
965E LEU* 3.2 22.8 + - - +
967E GLY* 1.3 77.3 - - - +
969E LEU* 1.3 58.6 + - - +
970E GLU 3.2 8.5 + - - +
966F TYR* 5.0 7.5 + - - -
969F LEU* 3.9 31.0 - - + +
----------------------------------------------------------
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Residues in contact with LEU 969 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
965E LEU 3.1 14.2 + - - +
966E TYR* 2.9 21.9 + - + +
968E ARG* 1.3 73.1 - - - +
970E GLU* 1.3 68.2 + - - +
965F LEU* 4.9 12.6 - - + +
968F ARG* 3.8 45.8 - - + +
969F LEU* 4.6 19.1 - - + +
972F ASP* 3.1 37.0 - - + +
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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