Contacts of the helix formed by residues 984 - 1014 (chain J) in PDB entry 4XLN
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 THR 984 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
978J TYR* 3.4 6.8 - - - -
981J GLY 5.3 3.8 - - - +
982J PHE 5.2 1.1 - - - +
983J LEU* 1.3 78.5 - - - +
985J ASP* 1.3 66.0 + - - +
986J ARG* 3.4 18.5 - - - +
987J GLU* 3.0 31.8 + - - +
988J ARG* 3.2 19.8 + - - +
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Residues in contact with ASP 985 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
978J TYR* 3.6 26.8 + - + +
984J THR* 1.3 78.4 - - - +
986J ARG* 1.3 63.0 + - - +
988J ARG* 3.4 19.3 + - - +
989J TYR* 2.9 29.1 + - - +
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Residues in contact with ARG 986 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
984J THR* 3.4 12.8 - - - +
985J ASP* 1.3 82.8 + - + +
987J GLU* 1.3 63.7 + - - +
989J TYR* 3.1 8.7 + - - +
990J ASP* 2.9 37.4 + - - +
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Residues in contact with GLU 987 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
982J PHE 3.2 17.5 - - - +
983J LEU* 3.3 19.0 - - + +
984J THR* 3.0 48.5 + - - +
986J ARG* 1.3 78.7 - - + +
988J ARG* 1.3 60.2 + - - +
990J ASP* 3.4 11.4 + - - +
991J GLN* 2.9 31.4 + - - +
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Residues in contact with ARG 988 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
971J LEU* 5.8 3.0 - - - +
974J ILE* 3.6 25.8 - - + +
975J GLU* 4.9 7.4 - - - +
978J TYR* 3.5 42.8 - - + -
983J LEU* 4.1 7.4 - - + -
984J THR 3.2 20.5 + - - +
985J ASP* 3.4 24.4 + - - +
986J ARG 3.3 0.2 - - - -
987J GLU* 1.3 78.7 - - - +
989J TYR* 1.3 72.5 + - - +
991J GLN* 3.2 3.1 + - - +
992J VAL* 2.9 46.9 + - + +
1054J GLU* 3.7 25.7 + - - -
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Residues in contact with TYR 989 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
985J ASP* 2.9 16.3 + - - +
986J ARG* 3.2 13.0 - - - +
988J ARG* 1.3 89.6 - - - +
990J ASP* 1.3 70.0 + - - +
992J VAL* 3.2 5.2 + - - +
993J ILE* 2.9 58.5 + - + +
1051J GLU* 4.3 14.9 + - + +
1052J THR* 2.5 43.4 + - + +
1053J PHE 4.4 4.0 - - - -
1054J GLU* 3.5 26.0 - - + -
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Residues in contact with ASP 990 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
986J ARG* 2.9 27.7 + - - +
987J GLU* 3.7 9.3 - - - +
989J TYR* 1.3 87.6 - - - +
991J GLN* 1.3 57.7 + - - +
993J ILE* 3.2 9.1 + - - +
994J GLN* 2.9 32.3 + - - +
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Residues in contact with GLN 991 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
831D GLY* 5.5 5.9 + - - -
970J LYS* 5.5 3.6 - - + +
973J GLN* 5.6 2.8 - - - +
974J ILE* 3.3 39.6 - - + +
977J ALA* 5.1 2.0 - - - +
983J LEU* 3.3 27.7 - - - +
987J GLU 2.9 17.1 + - - +
988J ARG 3.5 4.7 - - - +
990J ASP* 1.3 78.4 - - - +
992J VAL* 1.3 56.8 + - - +
994J GLN* 3.2 23.7 + - - +
995J LEU* 2.9 28.2 + - - +
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Residues in contact with VAL 992 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
971J LEU* 3.7 19.3 - - + -
974J ILE* 3.8 27.6 - - + -
988J ARG* 2.9 36.3 + - + +
989J TYR 3.5 7.0 - - - +
991J GLN* 1.3 75.4 - - - +
993J ILE* 1.3 60.2 + - + +
995J LEU* 3.1 3.3 + - - +
996J TRP* 2.9 53.7 + - + +
1054J GLU* 3.4 22.2 - - + +
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Residues in contact with ILE 993 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
989J TYR* 2.9 56.9 + - + +
990J ASP* 3.2 11.4 + - - +
992J VAL* 1.3 78.8 - - + +
994J GLN* 1.3 56.3 + - + +
996J TRP* 3.3 3.1 + - - +
997J THR* 2.5 42.5 + - - +
1044J LEU* 4.5 11.3 - - + +
1052J THR* 3.8 28.5 - - + +
1053J PHE 3.9 11.9 - - - +
1054J GLU* 4.3 7.4 - - - +
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Residues in contact with GLN 994 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
990J ASP 2.9 14.9 + - - +
991J GLN* 3.2 32.3 + - + +
993J ILE* 1.3 80.9 - - + +
995J LEU* 1.3 57.2 + - - +
997J THR* 3.6 7.9 - - - -
998J GLU* 2.9 39.4 + - - +
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Residues in contact with LEU 995 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
967J ALA* 3.9 18.8 - - + +
970J LYS* 3.5 38.1 - - + +
971J LEU* 3.7 31.9 - - + +
974J ILE* 3.7 9.9 - - + -
991J GLN 2.9 15.6 + - - +
992J VAL 3.2 7.9 - - - +
993J ILE 3.1 0.2 - - - -
994J GLN* 1.3 75.3 - - - +
996J TRP* 1.3 67.5 + - + +
998J GLU* 3.0 23.6 - - + +
999J THR* 2.8 42.9 + - - +
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Residues in contact with TRP 996 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
964J LEU* 5.0 3.8 - - + -
967J ALA* 3.8 33.9 - - + -
968J ASP* 4.7 2.0 - - - -
971J LEU* 3.6 26.2 - - + +
992J VAL* 2.9 41.1 + - + +
993J ILE 4.1 2.7 - - - +
995J LEU* 1.3 79.1 - - + +
997J THR* 1.3 53.5 + - - +
999J THR* 3.7 19.5 - - + -
1000J THR* 2.6 37.4 + - - +
1041J MET* 4.6 5.9 - - + +
1044J LEU* 4.5 20.9 - - + +
1054J GLU 3.5 19.1 + - - -
1056J PRO* 3.4 41.3 - - + +
1058J ARG* 3.8 27.4 - - - -
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Residues in contact with THR 997 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
993J ILE* 2.5 31.6 + - - +
994J GLN* 3.6 9.2 - - - -
996J TRP* 1.3 77.5 - - - +
998J GLU* 1.3 56.6 + - - +
1000J THR* 3.1 10.7 + - - -
1001J GLU* 2.9 31.6 + - + +
1044J LEU* 6.1 0.2 - - - +
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Residues in contact with GLU 998 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
970J LYS* 4.0 13.7 + - - -
994J GLN* 2.9 22.1 + - - +
995J LEU* 3.0 40.5 - - + +
997J THR* 1.3 76.7 - - - +
999J THR* 1.3 59.9 + - - +
1001J GLU* 3.3 11.4 + - - +
1002J LYS* 2.9 32.0 + - + +
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Residues in contact with THR 999 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
963J TYR 3.9 21.5 - - - +
964J LEU* 4.8 4.7 - - + -
967J ALA* 3.4 24.1 - - + +
995J LEU* 2.8 24.4 + - - +
996J TRP* 3.7 19.9 - - + -
998J GLU* 1.3 75.6 - - - +
1000J THR* 1.3 60.6 + - - +
1002J LYS* 3.1 9.6 + - + +
1003J VAL* 2.9 39.6 + - + +
1041J MET* 4.6 7.9 - - - -
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Residues in contact with THR1000 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
996J TRP 2.6 21.9 + - - -
997J THR* 3.1 12.1 + - - -
999J THR* 1.3 77.2 - - - +
1001J GLU* 1.3 55.3 + - - +
1003J VAL* 3.1 9.0 - - - +
1004J THR* 2.5 38.7 + - - +
1036J ARG* 3.8 37.2 - - - +
1041J MET* 3.5 21.5 - - + +
1043J GLY* 4.3 11.8 - - - -
1044J LEU* 4.7 2.6 + - - +
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Residues in contact with GLU1001 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
997J THR* 2.9 18.9 + - + +
998J GLU* 3.4 13.2 - - - +
999J THR 3.2 0.2 - - - -
1000J THR* 1.3 76.2 - - - +
1002J LYS* 1.3 65.4 + - - +
1004J THR* 3.2 9.6 + - - +
1005J GLN* 2.9 50.9 + - + +
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Residues in contact with LYS1002 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
963J TYR* 3.3 69.2 + - + +
966J GLU* 5.8 1.5 + - - -
998J GLU* 2.9 18.8 + - + +
999J THR* 3.3 13.7 - - - +
1001J GLU* 1.3 75.4 - - - +
1003J VAL* 1.3 57.6 + - - +
1005J GLN* 3.8 5.2 - - - +
1006J ALA* 2.9 28.5 + - - +
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Residues in contact with VAL1003 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
957J PRO* 4.5 1.6 - - + +
960J LYS* 3.9 32.3 - - + +
963J TYR* 4.6 13.9 - - + -
964J LEU* 5.6 1.8 - - + +
999J THR* 2.9 28.7 + - + +
1000J THR* 3.1 15.3 - - + +
1002J LYS* 1.3 75.1 - - - +
1004J THR* 1.3 62.5 + - - +
1006J ALA* 3.3 8.8 - - - +
1007J VAL* 2.9 33.0 + - - +
1036J ARG* 5.2 0.7 - - + -
1040J GLY* 4.7 1.8 - - - -
1041J MET* 3.6 41.3 - - + +
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Residues in contact with THR1004 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1000J THR* 2.5 26.3 + - - +
1001J GLU* 3.8 12.7 + - - +
1003J VAL* 1.3 75.1 - - - +
1005J GLN* 1.3 69.4 + - - +
1007J VAL* 2.9 18.8 + - + +
1008J PHE* 3.0 26.2 + - + -
1032J PRO* 4.6 10.1 - - + +
1036J ARG* 3.2 40.9 - - + +
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Residues in contact with GLN1005 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1001J GLU* 2.9 39.7 + - + +
1002J LYS* 3.8 5.2 - - - +
1004J THR* 1.3 77.9 - - - +
1006J ALA* 1.3 58.0 + - - +
1008J PHE* 3.5 5.5 + - - +
1009J LYS* 2.9 61.4 + - - +
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Residues in contact with ALA1006 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
957J PRO* 3.6 11.5 - - + +
959J GLU* 3.6 33.1 - - + +
960J LYS 5.5 0.2 - - - +
963J TYR* 4.7 4.7 - - + -
1002J LYS 2.9 21.2 + - - +
1003J VAL* 3.3 11.9 - - + +
1004J THR 3.1 0.2 - - - -
1005J GLN* 1.3 77.6 - - - +
1007J VAL* 1.3 55.7 + - - +
1009J LYS* 3.9 5.6 - - - +
1010J ASN* 2.9 31.2 + - - +
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Residues in contact with VAL1007 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
957J PRO* 3.6 12.8 - - + -
1003J VAL 2.9 20.5 + - - +
1004J THR* 2.9 10.5 + - + +
1006J ALA* 1.3 73.6 - - - +
1008J PHE* 1.3 77.5 + - + +
1010J ASN* 3.1 4.0 + - - +
1011J PHE* 2.9 52.2 + - + -
1035J ILE* 4.3 10.3 - - + +
1036J ARG* 5.0 4.0 - - - -
1039J CYS* 3.6 17.9 - - + -
1040J GLY* 3.4 30.5 - - - +
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Residues in contact with PHE1008 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1004J THR* 3.0 27.3 + - + +
1005J GLN* 4.0 7.0 - - - +
1007J VAL* 1.3 88.3 - - + +
1009J LYS* 1.3 58.0 + - + +
1011J PHE* 3.2 8.8 + + - +
1012J GLU* 2.9 47.8 + - - +
1021J TYR* 5.3 6.1 - + - -
1024J ALA* 5.7 5.8 - - + -
1025J GLN* 4.1 22.9 - - - -
1032J PRO* 3.5 51.8 - - + -
1035J ILE* 5.0 9.0 - - + -
1036J ARG 5.7 0.2 - - - -
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Residues in contact with LYS1009 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
959J GLU* 6.4 0.9 - - - -
1005J GLN* 2.9 55.3 + - - +
1006J ALA* 4.0 5.2 - - - +
1008J PHE* 1.3 76.9 - - + +
1010J ASN* 1.3 58.1 + - - +
1012J GLU* 4.5 5.2 - - - +
1013J GLU* 2.9 44.3 + - + +
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Residues in contact with ASN1010 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
955J VAL* 4.5 9.6 + - - +
956J ILE 4.4 4.2 + - - -
957J PRO* 3.8 27.2 - - + +
958J GLU* 4.0 7.8 + - - +
959J GLU* 3.1 17.6 + - - +
1006J ALA 2.9 20.7 + - - +
1007J VAL 3.1 4.5 + - - +
1009J LYS* 1.3 75.3 - - - +
1011J PHE* 1.3 60.0 + - + +
1013J GLU* 4.9 0.7 - - - -
1014J ASN* 3.2 57.1 + - - +
1015J TYR* 3.7 17.9 + - - -
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Residues in contact with PHE1011 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
953J ASP 4.0 10.5 - - - -
954J ALA 4.8 0.7 - - - -
955J VAL* 4.6 13.5 - - + -
1007J VAL* 2.9 46.4 + - + -
1008J PHE* 3.6 6.7 - + - +
1010J ASN* 1.3 78.7 - - + +
1012J GLU* 1.3 62.9 + - - +
1015J TYR* 3.0 42.0 + + + +
1016J PRO* 3.2 3.4 - - - +
1018J ASN* 3.1 34.8 - - + -
1020J LEU* 4.1 13.2 - - + -
1021J TYR* 3.5 39.0 - + + -
1035J ILE* 4.1 12.1 - - + -
1039J CYS* 4.1 15.5 - - - -
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Residues in contact with GLU1012 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1008J PHE* 2.9 36.2 + - - +
1009J LYS* 4.2 5.2 - - - +
1011J PHE* 1.3 75.6 - - - +
1013J GLU* 1.3 63.2 + - + +
1016J PRO* 3.7 17.2 - - - +
1021J TYR* 3.2 33.9 + - + +
1025J GLN* 5.4 2.3 + - - -
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Residues in contact with GLU1013 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
799J LYS* 5.7 5.0 - - - +
1009J LYS* 2.9 27.3 + - + +
1010J ASN* 4.9 0.2 - - - -
1012J GLU* 1.3 78.6 - - + +
1014J ASN* 1.3 73.4 + - - +
1016J PRO* 5.0 2.4 - - - +
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Residues in contact with ASN1014 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
950I LEU 4.8 5.2 - - - +
1010J ASN* 3.2 46.7 + - - +
1013J GLU* 1.3 90.8 - - - +
1015J TYR* 1.3 86.0 + - + +
1016J PRO* 3.1 12.9 - - - +
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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