Contacts of the helix formed by residues 974 - 1006 (chain B) in PDB entry 3H2V
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 ASP 974 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
972B CYS* 3.4 10.8 - - - -
973B THR* 1.3 80.3 - - - +
975B LYS* 1.3 55.0 + - - +
976B ARG* 3.1 19.2 + - - +
977B ILE* 3.0 31.2 + - + +
978B ARG* 2.5 38.9 + - - +
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Residues in contact with LYS 975 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
973B THR 3.8 3.0 + - - -
974B ASP* 1.3 74.0 + - - +
976B ARG* 1.3 62.9 + - - +
978B ARG* 3.3 29.7 - - - +
979B THR* 2.8 38.8 + - - +
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Residues in contact with ARG 976 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
974B ASP* 3.1 16.2 + - - +
975B LYS* 1.3 83.8 - - - +
977B ILE* 1.3 70.0 + - + +
979B THR* 3.4 11.9 - - - +
980B ASN* 3.1 59.8 + - - +
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Residues in contact with ILE 977 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
972B CYS* 4.3 3.6 - - - -
974B ASP* 3.0 30.2 + - + +
976B ARG* 1.3 85.7 - - + +
978B ARG* 1.3 59.2 + - - +
979B THR 2.8 11.4 + - - -
980B ASN* 3.1 7.4 + - - +
981B LEU* 2.9 23.2 + - + +
1040B GLU* 3.2 37.2 - - - +
1043B ALA* 4.4 11.4 - - + +
1044B ALA* 3.8 32.1 - - + +
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Residues in contact with ARG 978 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
969B ALA* 3.0 33.4 + - + +
970B LYS* 5.5 0.9 - - - +
972B CYS* 3.0 38.7 + - + -
973B THR* 4.2 7.1 + - - +
974B ASP 2.5 21.3 + - - +
975B LYS* 3.3 40.3 + - - +
977B ILE* 1.3 71.1 - - - +
979B THR* 1.3 59.2 + - - +
981B LEU* 4.1 7.0 - - - +
982B LEU* 3.3 37.3 + - - +
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Residues in contact with THR 979 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
975B LYS* 2.8 34.2 + - - +
976B ARG* 3.4 12.1 - - - +
977B ILE 2.8 1.0 + - - -
978B ARG* 1.3 79.5 + - - +
980B ASN* 1.3 77.0 + - - +
981B LEU 3.1 1.6 - - - -
982B LEU* 3.1 6.2 + - - +
983B GLN* 3.0 23.9 + - + +
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Residues in contact with ASN 980 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
976B ARG* 3.1 54.9 + - - +
977B ILE* 3.1 6.5 + - - +
979B THR* 1.3 79.1 - - - +
981B LEU* 1.3 63.2 + - - +
983B GLN* 3.2 20.6 + - - +
984B VAL* 3.1 27.8 + - + +
1040B GLU* 3.4 33.8 - - + +
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Residues in contact with LEU 981 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
965B ALA* 3.2 31.0 - - + +
968B VAL* 3.6 24.7 - - + -
969B ALA* 3.7 13.7 - - + +
977B ILE 2.9 17.0 + - - +
978B ARG* 4.2 4.9 - - - +
980B ASN* 1.3 79.0 - - - +
982B LEU* 1.3 64.4 + - - +
984B VAL* 3.3 5.5 - - + +
985B CYS* 3.3 22.8 + - - +
1037B THR* 4.1 20.9 - - + +
1040B GLU* 4.0 14.3 + - + +
1041B ALA* 3.9 26.7 - - + +
1044B ALA* 4.1 9.9 - - + -
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Residues in contact with LEU 982 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
966B LYS* 3.8 25.4 - - + -
969B ALA* 3.8 23.8 - - + -
978B ARG* 3.3 29.3 + - - +
979B THR* 3.1 6.5 + - - +
981B LEU* 1.3 76.8 - - - +
983B GLN* 1.3 65.3 + - - +
985B CYS* 3.2 9.1 + - - -
986B GLU* 2.8 43.8 + - + +
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Residues in contact with GLN 983 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
979B THR* 3.0 15.5 + - + +
980B ASN* 3.2 23.6 + - - +
982B LEU* 1.3 80.1 - - - +
984B VAL* 1.3 85.9 + - - +
986B GLU* 3.0 20.3 + - - +
987B ARG* 3.5 21.4 + - - +
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Residues in contact with VAL 984 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
980B ASN* 3.2 14.1 - - + +
981B LEU* 3.3 12.8 - - + +
983B GLN* 1.3 93.4 - - - +
985B CYS* 1.3 63.3 + - - +
986B GLU 3.5 0.3 + - - -
987B ARG* 3.4 39.9 + - - +
988B ILE* 3.7 11.6 - - - +
1033B SER* 4.4 3.8 - - - +
1036B GLU* 4.6 22.7 - - + +
1037B THR* 4.0 27.2 + - - +
1040B GLU* 4.8 8.1 - - + -
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Residues in contact with CYS 985 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
962B THR* 3.5 22.9 - - + +
965B ALA* 4.0 27.4 - - + -
966B LYS* 3.2 32.5 - - - -
981B LEU 3.4 18.6 - - - +
982B LEU* 3.2 16.9 + - - -
984B VAL* 1.3 78.8 - - - +
986B GLU* 1.3 63.5 + - - +
987B ARG 3.3 0.9 - - - -
988B ILE* 3.8 12.6 + - + +
989B PRO* 3.6 6.9 - - - +
1037B THR* 3.8 14.6 - - + +
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Residues in contact with GLU 986 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
962B THR* 5.2 0.5 - - - +
966B LYS* 3.5 30.0 + - - -
982B LEU* 2.8 41.4 + - + +
983B GLN* 3.0 11.0 + - - +
985B CYS* 1.3 81.0 - - - +
987B ARG* 1.3 61.0 + - + +
989B PRO* 3.0 21.2 - - - +
990B THR* 3.9 7.4 + - - -
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Residues in contact with ARG 987 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
983B GLN* 3.5 31.9 + - - +
984B VAL* 3.4 38.2 + - - +
986B GLU* 1.3 76.6 - - + +
988B ILE* 1.3 63.6 - - - +
990B THR* 3.2 10.4 + - - -
991B ILE* 2.8 46.5 + - + +
1033B SER* 3.2 26.9 + - - +
1036B GLU* 4.2 13.9 + - - +
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Residues in contact with ILE 988 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
958B SER* 3.5 31.0 - - - +
961B VAL* 4.4 13.0 - - + -
962B THR* 3.6 16.2 - - - +
984B VAL 3.7 14.8 - - - +
985B CYS* 3.8 8.7 - - + +
986B GLU 3.3 0.2 - - - -
987B ARG* 1.3 79.2 - - - +
989B PRO* 1.4 59.5 - - + +
991B ILE* 3.0 7.1 + - - +
992B SER* 2.8 33.7 + - - -
1030B LEU* 4.3 10.1 - - + +
1033B SER* 4.1 22.4 - - - +
1034B VAL* 4.2 12.1 - - + -
1037B THR* 3.6 22.7 - - - +
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Residues in contact with PRO 989 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
958B SER* 5.8 0.9 - - - -
959B ASP* 5.0 12.8 - - - +
962B THR* 4.1 13.2 - - + +
985B CYS 3.6 6.5 - - - +
986B GLU* 3.0 22.9 - - - +
987B ARG 3.3 0.4 - - - -
988B ILE* 1.4 100.4 - - + +
990B THR* 1.3 58.8 + - - +
992B SER* 2.7 21.5 + - - +
993B THR* 2.9 21.4 + - - -
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Residues in contact with THR 990 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
986B GLU 3.9 11.4 + - - -
987B ARG* 3.2 11.4 + - - -
989B PRO* 1.3 75.6 - - - +
991B ILE* 1.3 67.5 + - + +
993B THR* 2.8 17.6 + - - +
994B GLN* 3.0 30.7 + - + +
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Residues in contact with ILE 991 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
987B ARG* 2.8 52.4 + - + +
988B ILE* 3.6 4.7 - - - +
990B THR* 1.3 71.9 - - + +
992B SER* 1.3 64.0 + - - +
994B GLN* 3.3 14.4 + - - +
995B LEU* 3.1 9.4 + - - +
1026B ASN* 2.7 56.5 - - - +
1029B ASN* 4.3 11.0 - - + +
1030B LEU* 3.7 22.9 - - + +
1033B SER* 3.8 20.4 - - - +
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Residues in contact with SER 992 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
951B ALA 5.3 0.2 - - - +
954B ILE* 5.2 0.4 - - - -
955B ALA* 4.3 17.2 + - - +
958B SER* 3.8 27.6 - - - -
959B ASP* 5.1 3.3 + - - -
988B ILE 2.8 11.1 + - - -
989B PRO* 2.7 27.2 + - - +
991B ILE* 1.3 77.1 - - - +
993B THR* 1.3 60.4 + - - +
995B LEU* 3.4 20.1 - - - +
996B LYS* 3.4 18.2 + - - +
1030B LEU* 4.3 11.6 - - - +
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Residues in contact with THR 993 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
989B PRO 2.9 17.0 + - - -
990B THR* 2.8 8.7 + - - -
992B SER* 1.3 75.3 + - - +
994B GLN* 1.3 64.9 + - + +
995B LEU 3.1 1.6 - - - -
996B LYS* 3.2 29.3 + - - +
997B ILE* 3.2 34.8 + - + +
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Residues in contact with GLN 994 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
990B THR* 3.0 33.2 + - + +
991B ILE* 3.6 14.1 - - - +
993B THR* 1.3 77.6 - - + +
995B LEU* 1.3 53.3 + - - +
997B ILE* 3.2 11.6 + - + +
998B LEU* 2.6 44.7 + - + +
1026B ASN* 2.5 34.6 + - - +
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Residues in contact with LEU 995 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
930B MET* 5.2 2.7 - - + -
933B MET* 4.7 7.9 - - - -
951B ALA* 4.6 11.9 - - + +
954B ILE* 3.8 41.5 - - + -
991B ILE 3.1 12.1 + - - +
992B SER* 3.4 12.8 - - - +
993B THR 3.1 0.2 - - - -
994B GLN* 1.3 79.6 - - - +
996B LYS* 1.3 48.9 + - - +
998B LEU* 3.5 2.7 + - - +
999B SER* 2.4 38.3 + - - -
1023B LEU* 3.4 28.5 - - + +
1026B ASN* 3.7 22.0 - - + +
1027B ALA* 4.2 14.1 - - + +
1030B LEU* 4.0 10.5 - - + -
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Residues in contact with LYS 996 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
951B ALA* 4.1 18.6 - - + +
952B LYS* 4.5 20.2 - - + +
955B ALA* 4.1 21.8 - - + +
959B ASP* 5.7 1.8 + - - -
992B SER* 3.4 14.2 + - - +
993B THR* 3.2 35.1 + - - +
994B GLN 3.3 0.4 - - - -
995B LEU* 1.3 73.9 - - - +
997B ILE* 1.3 61.9 + - + +
999B SER* 2.8 17.8 + - - -
1000B THR* 3.0 24.6 + - - -
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Residues in contact with ILE 997 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
993B THR* 3.2 29.8 - - + +
994B GLN* 3.2 12.3 + - + +
996B LYS* 1.3 75.7 - - + +
998B LEU* 1.3 69.5 + - + +
1000B THR* 3.1 13.9 + - - -
1001B VAL* 3.0 23.9 + - + +
----------------------------------------------------------
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Residues in contact with LEU 998 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
994B GLN* 2.6 23.4 + - + +
995B LEU* 3.9 0.9 - - - +
997B ILE* 1.3 77.3 - - + +
999B SER* 1.3 57.6 + - - +
1001B VAL* 3.4 14.4 + - + +
1002B LYS* 3.2 26.0 + - - +
1019B ALA 5.0 3.5 - - - +
1022B MET* 3.1 62.4 - - + +
1023B LEU* 3.7 19.7 - - + +
1026B ASN* 3.3 31.9 - - + +
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Residues in contact with SER 999 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
933B MET* 4.7 4.3 - - - -
947B LEU* 4.2 22.4 - - - +
948B ILE* 4.8 4.2 - - - +
951B ALA* 3.3 18.5 - - - +
995B LEU 2.4 23.7 + - - -
996B LYS* 2.8 17.8 + - - -
998B LEU* 1.3 75.2 - - - +
1000B THR* 1.3 58.0 + - - +
1002B LYS* 3.7 1.7 - - - +
1003B ALA* 2.9 29.8 + - - +
1023B LEU* 4.1 17.7 - - - +
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Residues in contact with THR1000 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
948B ILE* 4.0 21.5 - - + +
996B LYS 3.0 18.8 + - - -
997B ILE* 3.1 7.4 + - - -
999B SER* 1.3 74.2 - - - +
1001B VAL* 1.3 63.2 + - - +
1003B ALA* 3.5 6.4 + - - +
1004B THR* 2.7 40.3 + - + +
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Residues in contact with VAL1001 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
997B ILE* 3.0 26.0 - - + +
998B LEU* 3.5 16.8 - - + +
1000B THR* 1.3 72.5 - - - +
1002B LYS* 1.3 71.8 + - - +
1004B THR* 3.4 9.4 + - - -
1005B MET* 3.0 35.2 + - + +
1019B ALA* 4.1 21.5 - - + -
1022B MET* 5.7 5.8 - - + -
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Residues in contact with LYS1002 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
937B VAL* 4.7 14.6 - - + -
947B LEU* 4.0 14.1 - - + -
998B LEU 3.2 14.2 + - - +
999B SER 3.7 4.9 - - - +
1001B VAL* 1.3 85.1 - - + +
1003B ALA* 1.3 62.1 + - - +
1005B MET* 3.1 15.0 + - - +
1006B LEU* 3.0 52.1 + - + +
1016B SER* 3.4 26.3 + - - +
1019B ALA* 3.9 9.9 - - + +
1020B THR* 3.2 40.3 + - - +
1023B LEU* 3.7 20.2 - - + -
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Residues in contact with ALA1003 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
944B LYS* 4.0 27.0 - - + +
947B LEU* 4.3 8.5 - - + +
948B ILE* 3.5 29.2 - - + -
999B SER 2.9 18.2 + - - +
1000B THR 3.6 3.4 - - - +
1002B LYS* 1.3 76.2 - - - +
1004B THR* 1.3 63.4 + - + +
1006B LEU* 3.1 28.4 + - - +
----------------------------------------------------------
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Residues in contact with THR1004 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
948B ILE* 6.1 0.4 - - + -
1000B THR* 2.7 31.4 - - + +
1001B VAL* 3.5 7.0 + - - +
1003B ALA* 1.3 74.0 - - + +
1005B MET* 1.3 69.1 + - - +
1006B LEU 3.4 5.6 - - - +
1008B ARG* 3.2 38.5 + - - -
----------------------------------------------------------
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Residues in contact with MET1005 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1001B VAL* 3.0 19.1 + - + +
1002B LYS* 3.1 17.0 + - - +
1004B THR* 1.3 80.2 + - - +
1006B LEU* 1.3 67.5 + - - +
1007B GLY 3.3 0.3 + - - -
1008B ARG* 3.1 27.2 + - - +
1011B ILE* 4.3 22.2 - - + +
1015B GLU* 4.2 34.1 - - + +
1016B SER* 4.1 17.7 - - - -
1019B ALA* 3.7 30.5 - - + -
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Residues in contact with LEU1006 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
936B LEU 4.5 7.0 - - - +
937B VAL* 5.4 5.2 - - - +
938B ARG 5.3 1.6 - - - +
940B GLY* 3.4 22.7 - - - +
941B SER* 5.2 5.2 + - - +
943B THR* 3.0 31.0 - - - +
944B LYS* 4.8 7.4 - - + +
947B LEU* 4.7 11.2 - - + -
1002B LYS* 3.0 53.7 + - + +
1003B ALA* 3.2 16.3 - - - +
1004B THR 3.4 8.5 - - - +
1005B MET* 1.3 78.8 - - - +
1007B GLY* 1.3 58.0 + - - +
1008B ARG* 3.3 4.2 + - - -
----------------------------------------------------------
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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
------------------------------------------------------------
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).
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