Contacts of the helix formed by residues 932 - 963 (chain B) in PDB entry 3U3F
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 PRO 932 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
931B LEU* 1.3 93.6 - - + +
933B SER* 1.3 65.3 + - - +
934B SER* 3.5 17.7 - - - +
935B SER* 3.0 31.7 + - - +
936B ARG 3.1 9.4 + - - -
997B ALA 4.4 5.8 - - - +
1000B LEU* 5.0 6.5 - - + +
1001B ALA* 3.7 25.4 - - + +
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Residues in contact with SER 933 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
931B LEU 3.4 3.2 + - - -
932B PRO* 1.3 71.8 - - - +
934B SER* 1.3 65.3 + - - +
936B ARG* 2.9 22.6 + - - +
937B THR* 3.2 16.4 + - - -
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Residues in contact with SER 934 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
932B PRO* 3.5 16.6 - - - +
933B SER* 1.3 82.6 + - - +
935B SER* 1.3 61.4 + - - +
937B THR* 4.4 11.2 - - - -
938B GLU* 4.5 4.9 + - - +
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Residues in contact with SER 935 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
931B LEU* 3.7 8.5 - - - -
932B PRO* 3.0 22.7 + - - +
933B SER 3.0 0.4 - - - -
934B SER* 1.3 77.8 + - - +
936B ARG* 1.3 67.5 + - - +
937B THR 3.1 1.8 - - - -
938B GLU* 3.0 8.5 + - - +
939B ILE* 3.0 23.4 + - - +
997B ALA* 3.0 37.9 - - - +
1000B LEU* 5.0 6.4 - - - +
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Residues in contact with ARG 936 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
928B LEU* 4.2 20.4 - - + +
931B LEU* 4.0 4.7 - - + +
932B PRO 3.1 7.9 + - - +
933B SER* 2.9 14.7 + - - +
935B SER* 1.3 78.3 - - - +
937B THR* 1.3 66.7 + - - +
939B ILE* 3.0 8.0 + - - -
940B GLU* 2.9 41.8 + - - +
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Residues in contact with THR 937 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
933B SER 3.2 11.3 + - - -
934B SER* 4.4 8.8 + - - -
935B SER 3.0 0.8 + - - -
936B ARG* 1.3 81.2 - - - +
938B GLU* 1.3 62.0 + - + +
940B GLU* 3.4 9.9 + - - +
941B GLY* 2.9 20.6 + - - -
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Residues in contact with GLU 938 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
934B SER 4.5 5.3 + - - +
935B SER* 3.0 9.2 + - - +
937B THR* 1.3 80.2 - - + +
939B ILE* 1.3 60.8 + - - +
941B GLY* 3.3 8.6 + - - -
942B THR* 3.2 31.5 + - + +
993B ALA* 5.2 7.1 - - + +
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Residues in contact with ILE 939 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
924B VAL* 4.3 18.8 - - + -
928B LEU* 3.7 30.3 - - + -
931B LEU* 4.4 13.0 - - + -
935B SER 3.0 14.4 + - - +
936B ARG* 3.5 7.4 - - - +
938B GLU* 1.3 74.2 - - - +
940B GLU* 1.3 61.0 + - - +
941B GLY 2.8 3.8 - - - -
942B THR* 2.8 26.0 + - - -
943B GLN* 3.1 10.8 + - - +
990B LEU* 4.0 5.0 - - + +
993B ALA* 4.1 31.9 - - + +
994B VAL* 4.1 20.0 - - + -
997B ALA* 4.2 13.9 - - + -
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Residues in contact with GLU 940 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
928B LEU* 4.5 13.3 - - + +
936B ARG* 2.9 38.7 + - - +
937B THR* 3.7 6.9 - - - +
939B ILE* 1.3 74.1 - - + +
941B GLY* 1.3 61.8 + - - +
943B GLN* 3.6 23.4 - - - +
944B LYS* 3.0 30.0 + - + +
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Residues in contact with GLY 941 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
937B THR 2.9 13.7 + - - -
938B GLU* 3.4 15.3 - - - -
939B ILE 2.8 1.8 - - - -
940B GLU* 1.3 79.5 - - - +
942B THR* 1.3 57.9 + - - +
944B LYS* 3.6 7.2 - - - +
945B LEU* 2.9 26.3 + - - +
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Residues in contact with THR 942 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
938B GLU* 3.2 22.6 + - + +
939B ILE* 2.8 8.7 + - - -
941B GLY* 1.3 74.2 - - - +
943B GLN* 1.3 60.2 + - - +
945B LEU* 3.4 15.9 - - + +
946B LEU* 3.1 31.2 + - - +
986B ASP* 4.8 4.8 - - - +
989B ASN* 4.5 16.8 - - + +
990B LEU* 2.8 43.3 - - - +
993B ALA* 4.7 8.4 - - + +
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Residues in contact with GLN 943 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
921B ILE* 3.4 45.6 + - + +
924B VAL* 3.4 24.5 - - + +
925B ASP* 3.7 18.0 + - - +
928B LEU* 4.5 3.2 - - - +
939B ILE* 3.1 11.3 + - - +
940B GLU* 3.6 28.2 + - - +
942B THR* 1.3 73.9 - - - +
944B LYS* 1.3 67.8 + - - +
945B LEU 3.0 1.1 - - - -
946B LEU* 2.8 18.9 + - - +
947B ASN* 3.1 16.4 + - - +
990B LEU* 4.1 16.2 - - + -
263F ALA* 4.3 15.3 - - + +
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Residues in contact with LYS 944 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
940B GLU* 3.0 17.7 + - + +
941B GLY* 3.6 7.4 - - - +
943B GLN* 1.3 79.3 - - - +
945B LEU* 1.3 65.1 + - - +
946B LEU 3.2 0.2 + - - -
947B ASN* 3.2 18.2 + - - +
948B LYS* 3.2 11.8 + - - +
263F ALA* 5.5 2.5 - - - +
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Residues in contact with LEU 945 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
941B GLY 2.9 18.7 + - - +
942B THR* 3.4 18.2 - - + +
943B GLN 3.0 0.4 - - - -
944B LYS* 1.3 76.5 - - - +
946B LEU* 1.3 57.0 + - - +
948B LYS* 3.2 26.2 + - + +
949B ASP* 3.0 34.1 + - - +
986B ASP* 3.1 26.5 - - + +
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Residues in contact with LEU 946 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
887B LEU* 5.6 0.2 - - + -
917B LEU* 4.0 27.1 - - + -
920B LEU* 4.5 3.6 - - + -
921B ILE* 4.8 4.5 - - + -
942B THR 3.1 18.2 + - - +
943B GLN* 2.8 11.9 + - - +
945B LEU* 1.3 72.6 - - - +
947B ASN* 1.3 67.1 + - - +
949B ASP* 2.8 6.9 + - - +
950B LEU* 2.8 23.6 + - - +
983B LEU* 3.3 35.0 - - + +
986B ASP* 3.4 30.7 - - + +
987B ALA* 3.7 17.7 - - + +
990B LEU* 4.3 20.4 - - + -
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Residues in contact with ASN 947 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
921B ILE* 3.2 15.3 - - - +
943B GLN 3.1 8.2 + - - -
944B LYS* 3.2 11.9 + - - +
946B LEU* 1.3 74.2 - - - +
948B LYS* 1.3 59.4 + - - +
950B LEU* 3.2 6.9 + - - +
951B ALA* 2.9 24.4 + - - +
263F ALA* 3.0 33.7 + - - +
266F GLU* 3.7 12.4 - - + +
267F LEU* 3.1 35.7 - - - +
270F LEU* 3.3 18.5 - - + +
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Residues in contact with LYS 948 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
944B LYS 3.2 7.1 + - - +
945B LEU* 3.2 29.5 + - + +
946B LEU 3.1 0.4 - - - -
947B ASN* 1.3 78.9 - - - +
949B ASP* 1.3 64.4 + - - +
951B ALA* 3.1 7.9 + - - +
952B GLU* 2.9 62.4 + - + +
982B THR* 6.2 0.4 - - - +
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Residues in contact with ASP 949 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
945B LEU* 3.0 28.4 + - - +
946B LEU* 2.8 10.1 + - - +
948B LYS* 1.3 86.0 + - - +
950B LEU* 1.3 58.0 + - - +
952B GLU* 3.6 7.3 + - - +
953B LEU* 3.1 24.8 + - - +
979B ALA 4.0 8.1 - - - +
982B THR* 3.5 21.3 - - + +
983B LEU* 3.3 23.4 - - + +
986B ASP* 2.6 39.4 - - - +
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Residues in contact with LEU 950 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
910B VAL* 4.6 4.7 - - + -
913B VAL* 4.7 0.2 - - + -
914B GLY* 4.2 28.9 - - - +
917B LEU* 4.0 11.7 - - + -
946B LEU 2.8 10.5 + - - +
947B ASN* 3.4 9.2 - - - +
949B ASP* 1.3 74.9 - - - +
951B ALA* 1.3 54.3 + - - +
953B LEU* 2.9 23.9 + - + +
954B ILE* 2.8 53.5 + - + +
983B LEU* 4.2 13.2 - - + +
267F LEU* 3.7 27.8 - - + -
270F LEU* 4.3 11.7 - - + -
271F MET* 4.5 10.3 - - + -
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Residues in contact with ALA 951 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
947B ASN 2.9 13.4 + - - +
948B LYS* 3.5 10.8 - - - +
950B LEU* 1.3 75.9 - - - +
952B GLU* 1.3 57.3 + - - +
954B ILE* 3.7 2.0 - - - +
955B ASN* 2.7 43.3 + - - +
270F LEU* 3.6 29.8 - - + +
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Residues in contact with GLU 952 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
948B LYS* 2.9 53.5 + - + +
949B ASP* 3.6 7.0 - - - +
951B ALA* 1.3 76.6 - - + +
953B LEU* 1.3 54.0 + - - +
955B ASN* 3.6 5.6 - - - +
956B LYS* 2.7 55.5 + - + +
979B ALA* 4.4 8.7 - - + -
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Residues in contact with LEU 953 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
894B LEU* 4.8 4.3 - - + -
910B VAL* 4.0 29.6 - - + -
913B VAL* 4.4 15.7 - - + -
949B ASP 3.1 13.9 + - - +
950B LEU* 2.9 20.1 + - + +
952B GLU* 1.3 75.5 - - - +
954B ILE* 1.3 60.3 + - - +
956B LYS* 3.1 3.6 + - - +
957B MET* 2.8 27.7 + - - +
976B MET* 3.1 43.1 - - + +
979B ALA* 3.6 14.3 - - + +
980B SER* 3.7 22.0 - - - -
983B LEU* 4.8 2.7 - - + -
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Residues in contact with ILE 954 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
910B VAL* 4.0 17.9 - - + -
950B LEU* 2.8 33.3 + - + +
951B ALA* 3.7 4.7 - - - +
953B LEU* 1.3 71.0 - - - +
955B ASN* 1.3 63.0 + - - +
957B MET* 2.8 28.4 + - + +
958B ARG* 2.8 27.1 + - + +
270F LEU* 3.8 42.6 - - + +
273F SER* 4.6 6.7 - - - +
274F LEU* 3.8 32.5 - - + -
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Residues in contact with ASN 955 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
951B ALA* 2.7 39.1 + - - +
952B GLU* 3.6 8.1 - - - +
954B ILE* 1.3 79.9 - - - +
956B LYS* 1.3 73.0 + - - +
958B ARG* 3.5 6.4 + - - +
959B LEU* 3.1 25.3 + - - +
270F LEU* 5.6 2.0 - - - +
----------------------------------------------------------
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Residues in contact with LYS 956 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
952B GLU* 2.7 42.0 + - + +
953B LEU 3.5 4.0 - - - +
955B ASN* 1.3 81.5 - - - +
957B MET* 1.3 58.5 + - - +
959B LEU* 3.8 23.6 - - + +
960B ALA* 3.4 15.1 + - - +
972B CYS* 3.8 5.5 - - - +
975B GLN* 3.3 49.4 - - + +
976B MET* 3.3 25.0 - - - +
979B ALA* 4.3 6.1 - - + -
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Residues in contact with MET 957 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
906B TYR* 3.7 17.9 - - + +
907B VAL* 4.0 19.1 - - - -
910B VAL* 4.0 15.9 - - + -
953B LEU 2.8 10.7 + - - +
954B ILE* 2.8 13.5 + - + +
956B LYS* 1.3 75.6 - - - +
958B ARG* 1.3 85.4 + - - +
959B LEU 3.0 0.9 - - - -
960B ALA* 2.6 22.9 + - - +
961B GLN* 2.9 31.5 + - - +
976B MET* 3.4 30.5 - - + -
274F LEU* 3.6 32.1 - - + -
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Residues in contact with ARG 958 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
907B VAL* 4.0 13.5 - - - +
954B ILE* 2.8 27.6 + - + +
955B ASN* 3.7 11.7 - - - +
957B MET* 1.3 83.8 - - - +
959B LEU* 1.3 62.2 + - - +
961B GLN* 2.9 52.2 + - - +
962B GLN* 3.1 34.3 + - - +
273F SER* 3.2 28.1 + - - -
274F LEU* 4.3 14.4 - - - +
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Residues in contact with LEU 959 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
955B ASN 3.1 14.0 + - - +
956B LYS* 3.8 31.4 - - + +
957B MET 3.0 0.4 - - - -
958B ARG* 1.3 81.3 - - - +
960B ALA* 1.3 58.4 + - - +
962B GLN* 4.0 15.2 - - - +
963B ASN* 3.2 46.3 + - - +
968B LEU* 6.1 0.4 - - + -
972B CYS* 3.9 10.8 - - + +
975B GLN* 4.9 7.6 - - - +
----------------------------------------------------------
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Residues in contact with ALA 960 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
906B TYR* 4.5 13.5 - - + -
956B LYS 3.4 12.4 + - - +
957B MET 2.6 16.8 + - - +
959B LEU* 1.3 73.2 - - - +
961B GLN* 1.3 62.3 + - - +
963B ASN 3.8 1.5 - - - -
964B ALA* 3.1 20.8 + - - +
969B SER* 4.5 4.0 + - - +
972B CYS* 3.6 29.1 - - + +
973B LYS* 4.3 11.6 - - + +
976B MET* 4.3 13.0 - - - -
----------------------------------------------------------
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Residues in contact with GLN 961 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
903B PRO* 3.2 37.4 + - + +
904B GLU* 4.4 3.2 - - - +
906B TYR* 4.4 4.0 - - + -
907B VAL* 3.0 33.7 - - - +
957B MET* 2.9 24.3 + - - +
958B ARG* 2.9 36.7 + - - +
960B ALA* 1.3 72.6 - - - +
962B GLN* 1.3 66.4 + - + +
963B ASN 2.8 5.6 + - - -
964B ALA* 2.9 19.9 + - - +
----------------------------------------------------------
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Residues in contact with GLN 962 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
958B ARG* 3.1 33.9 + - - +
959B LEU* 4.0 20.2 - - - +
961B GLN* 1.3 77.2 - - + +
963B ASN* 1.3 64.8 + - - +
964B ALA 3.8 4.9 + - - +
966B THR* 4.1 6.1 - - - +
----------------------------------------------------------
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Residues in contact with ASN 963 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
959B LEU* 3.2 42.5 + - - +
960B ALA 3.8 3.1 - - - +
961B GLN 2.8 2.8 + - - -
962B GLN* 1.3 84.6 + - - +
964B ALA* 1.3 64.8 - - - +
966B THR* 2.9 37.9 + - - +
968B LEU* 2.8 41.5 - - + +
969B SER* 3.2 12.1 - - - -
972B CYS* 4.5 2.5 - - + -
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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