Contacts of the helix formed by residues 74 - 102 (chain 3) in PDB entry 3KMB
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 ILE 74 (chain 3).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
741 ILE* 3.6 27.6 - - + -
751 GLU* 3.9 21.5 - - + +
781 LEU* 3.9 26.6 - - + +
742 ILE* 4.3 26.9 - - + -
733 ALA* 1.3 77.9 - - + +
753 GLU* 1.3 68.3 + - - +
773 LYS* 3.4 5.4 + - - +
783 LEU* 2.9 28.7 + - + +
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Residues in contact with GLU 75 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
742 ILE* 3.8 26.9 - - + +
733 ALA 3.0 5.0 + - - -
743 ILE* 1.3 82.5 + - - +
763 VAL* 1.3 63.3 + - + +
783 LEU* 3.4 6.4 + - - +
793 ALA* 2.9 31.4 + - - +
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Residues in contact with VAL 76 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
733 ALA* 2.7 26.9 + - - +
753 GLU* 1.3 71.4 - - + +
773 LYS* 1.3 66.1 + - + +
793 ALA* 3.3 5.9 + - - +
803 ASN* 3.0 24.7 + - + +
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Residues in contact with LYS 77 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
781 LEU* 4.6 23.6 - - + -
821 GLU* 5.0 12.0 - - + +
733 ALA* 2.7 43.6 + - - +
743 ILE* 3.7 7.4 - - - +
763 VAL* 1.3 74.6 - - + +
783 LEU* 1.3 57.8 + - - +
803 ASN* 3.4 7.3 + - - +
813 MET* 3.0 35.5 + - + +
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Residues in contact with LEU 78 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
781 LEU* 3.6 25.1 - - + +
742 ILE* 3.9 49.6 - - + +
772 LYS* 4.2 20.2 - - + -
782 LEU* 3.8 17.0 - - + +
812 MET* 3.5 33.5 - - - +
743 ILE* 2.9 18.0 + - + +
753 GLU* 3.7 6.1 - - - +
763 VAL 3.2 0.2 - - - -
773 LYS* 1.3 75.1 - - - +
793 ALA* 1.3 64.9 + - - +
813 MET* 3.3 7.5 + - + +
823 GLU* 3.1 19.6 + - - +
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Residues in contact with ALA 79 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
772 LYS* 5.3 4.4 - - - +
753 GLU 2.9 18.6 + - - +
763 VAL* 3.8 5.8 - - - +
783 LEU* 1.3 75.9 - - - +
803 ASN* 1.3 62.2 + - - +
823 GLU* 3.2 21.4 + - - +
833 ALA* 3.3 12.5 + - - +
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Residues in contact with ASN 80 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
821 GLU* 4.6 12.1 + - - -
763 VAL* 3.0 19.2 + - + +
773 LYS* 3.6 7.2 + - - +
793 ALA* 1.3 78.5 - - - +
813 MET* 1.3 57.8 + - - +
833 ALA* 3.0 11.8 + - - +
843 GLU* 2.8 56.3 + - - +
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Residues in contact with MET 81 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
781 LEU* 3.8 25.8 - - + +
811 MET* 3.2 49.1 - - + -
821 GLU* 3.2 29.4 - - - +
851 ILE* 3.6 12.5 - - + +
782 LEU* 4.5 1.1 - - + -
812 MET* 3.4 22.9 - - + -
773 LYS* 3.0 17.6 + - + +
783 LEU* 3.3 12.3 + - + +
803 ASN* 1.3 75.7 - - - +
823 GLU* 1.3 57.8 + - - +
843 GLU* 3.1 10.2 + - - +
853 ILE* 2.8 33.6 + - + +
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Residues in contact with GLU 82 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
772 LYS* 2.9 35.1 + - - +
812 MET* 3.2 19.0 - - + +
783 LEU 3.1 10.7 + - - +
793 ALA* 3.4 14.5 - - - +
803 ASN 3.1 0.2 - - - -
813 MET* 1.3 77.1 - - - +
833 ALA* 1.3 57.3 + - - +
853 ILE* 3.2 6.2 + - + +
863 ASN* 2.9 45.5 + - - +
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Residues in contact with ALA 83 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
793 ALA 3.3 8.0 + - - +
803 ASN* 3.0 15.1 + - - +
823 GLU* 1.3 78.6 - - - +
843 GLU* 1.3 58.1 + - - +
863 ASN* 3.7 9.1 - - - +
873 THR* 2.8 36.0 + - - +
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Residues in contact with GLU 84 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
821 GLU* 5.2 3.1 - - - +
851 ILE* 4.2 19.7 - - + -
891 LYS* 2.9 36.2 + - - -
803 ASN* 2.8 45.6 + - - +
813 MET* 3.1 12.1 + - - +
833 ALA* 1.3 76.4 - - - +
853 ILE* 1.3 57.3 + - - +
873 THR* 3.3 9.9 + - - +
883 LEU* 2.9 34.6 + - - +
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Residues in contact with ILE 85 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
851 ILE* 4.3 9.9 - - + -
812 MET* 3.6 43.3 - - + +
842 GLU* 4.1 13.2 - - + -
852 ILE* 3.6 37.7 - - + -
882 LEU* 3.9 17.7 - - + -
813 MET 2.8 11.6 + - - +
823 GLU* 3.6 5.8 - - + +
843 GLU* 1.3 73.0 - - - +
863 ASN* 1.3 63.9 + - - +
883 LEU* 3.1 9.8 + - + +
893 LYS* 2.9 44.4 + - - +
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Residues in contact with ASN 86 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
823 GLU* 2.9 38.2 + - - +
833 ALA* 3.7 9.3 - - - +
853 ILE* 1.3 77.7 - - - +
873 THR* 1.3 62.2 + - - +
893 LYS* 3.3 24.9 + - - +
903 SER* 3.2 25.9 + - - -
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Residues in contact with THR 87 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
891 LYS* 6.4 1.6 - - - -
833 ALA* 2.8 24.4 + - - +
843 GLU* 3.5 11.2 - - - +
863 ASN* 1.3 78.0 - - - +
883 LEU* 1.3 63.7 + - + +
903 SER* 3.2 8.1 + - - -
913 LYS* 3.0 46.6 + - + +
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Residues in contact with LEU 88 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
851 ILE* 4.2 19.1 - - + +
881 LEU* 4.0 29.2 - - + -
891 LYS* 3.9 41.3 - - + +
921 LEU* 4.0 24.2 - - + +
882 LEU* 4.1 12.1 - - + -
843 GLU 2.9 18.3 + - - +
853 ILE* 3.1 11.2 + - + +
873 THR* 1.3 78.0 - - + +
893 LYS* 1.3 57.0 + - - +
913 LYS* 3.2 12.2 + - + +
923 LEU* 2.9 31.0 + - - +
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Residues in contact with LYS 89 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
842 GLU* 2.9 36.6 + - - -
882 LEU* 3.7 30.7 - - + +
853 ILE* 2.9 33.9 + - - +
863 ASN* 3.5 23.9 + - - +
873 THR 3.3 0.2 - - - -
883 LEU* 1.3 76.4 - - - +
903 SER* 1.3 62.9 + - - +
923 LEU* 3.4 2.3 + - - +
933 GLU* 3.0 37.0 + - - +
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Residues in contact with SER 90 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
863 ASN 3.2 13.2 + - - -
873 THR* 3.5 9.8 - - - -
893 LYS* 1.3 78.4 - - - +
913 LYS* 1.3 59.7 + - - +
933 GLU* 3.1 16.4 + - - +
943 LEU* 2.9 28.6 + - - +
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Residues in contact with LYS 91 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
891 LYS* 6.1 4.4 - - - +
921 LEU* 3.6 20.4 - - + -
873 THR* 3.0 36.7 + - + +
883 LEU* 3.6 16.7 - - + +
903 SER* 1.3 77.2 - - - +
923 LEU* 1.3 56.7 - - - +
943 LEU* 3.2 14.8 + - + +
953 THR* 2.9 31.4 + - - -
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Residues in contact with LEU 92 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
921 LEU* 4.1 13.2 - - + +
882 LEU* 3.9 19.1 - - + +
912 LYS* 3.6 33.4 - - + -
922 LEU* 3.7 32.8 - - + +
952 THR* 3.5 22.9 - - + +
883 LEU 2.9 16.9 + - - +
893 LYS* 3.9 5.6 - - - +
913 LYS* 1.3 73.8 - - - +
933 GLU* 1.3 66.4 + - - +
953 THR* 3.3 8.1 + - - -
963 ASN* 2.9 29.4 + - - +
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Residues in contact with GLU 93 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
893 LYS* 3.0 32.2 + - - +
903 SER* 3.3 16.0 - - - +
923 LEU* 1.3 77.2 - - - +
943 LEU* 1.3 55.4 + - - +
963 ASN* 3.2 9.3 + - - +
973 LYS* 2.9 50.4 + - - +
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Residues in contact with LEU 94 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1301 GLU 3.1 27.4 - - - +
1311 LEU* 3.7 21.3 - - + +
1321 ARG* 3.6 30.5 - - + +
903 SER 2.9 12.0 + - - +
913 LYS* 3.2 16.1 + - + +
933 GLU* 1.3 73.8 - - - +
953 THR* 1.3 60.4 + - - +
973 LYS* 3.1 15.2 + - + +
983 LEU* 2.9 32.5 + - + +
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Residues in contact with THR 95 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
921 LEU* 3.6 12.6 - - + +
951 THR* 4.4 5.4 - - + -
961 ASN* 3.1 28.7 + - - +
952 THR* 4.0 13.7 - - + -
913 LYS 2.9 16.0 + - - -
923 LEU* 3.4 12.6 - - - -
943 LEU* 1.3 76.6 - - - +
963 ASN* 1.3 58.2 + - - +
983 LEU* 3.4 4.8 + - - -
993 HIS* 2.8 65.7 + - + +
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Residues in contact with ASN 96 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
912 LYS* 5.4 1.7 - - - +
952 THR* 2.8 41.9 + - - +
982 LEU* 6.2 1.8 - - - +
923 LEU* 2.9 23.3 + - - +
933 GLU* 3.2 11.0 + - - +
953 THR* 1.3 79.1 - - - +
973 LYS* 1.3 61.6 + - + +
993 HIS* 3.3 5.0 + - - +
1003 ALA* 3.0 24.9 + - - +
1033 MET* 5.3 0.7 - - - +
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Residues in contact with LYS 97 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1301 GLU* 3.8 33.4 + - + +
1311 LEU* 3.9 13.1 - - + +
933 GLU* 2.9 39.2 + - - +
943 LEU* 3.1 17.4 + - + +
963 ASN* 1.3 76.5 - - - +
983 LEU* 1.3 57.1 + - - +
1003 ALA* 3.3 6.1 + - - +
1013 PHE* 3.0 28.4 + - - +
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Residues in contact with LEU 98 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
961 ASN* 5.8 5.2 - - - +
991 HIS* 3.7 22.9 - - + +
1111 PHE* 5.1 7.9 - - + -
1131 VAL* 4.9 3.4 - - + -
1311 LEU* 3.8 24.2 - - + +
2191 PHE* 3.6 43.7 - - + -
943 LEU* 2.9 17.7 + - + +
953 THR* 3.8 7.2 - - - +
973 LYS* 1.3 76.7 - - - +
993 HIS* 1.3 55.3 + - + +
1013 PHE* 3.4 7.3 + - + +
1023 SER* 2.6 43.7 + - - +
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Residues in contact with HIS 99 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
951 THR* 4.0 11.2 - - + -
961 ASN* 4.5 4.4 + - - -
991 HIS* 3.2 54.1 + + + +
952 THR* 3.9 19.0 + - + +
992 HIS* 4.3 17.5 - - + +
953 THR* 2.8 52.0 + - + +
963 ASN* 3.8 7.2 - - - +
973 LYS 3.3 0.2 - - - -
983 LEU* 1.3 77.9 - - + +
1003 ALA* 1.3 59.0 + - - +
1023 SER* 3.2 3.3 + - - -
1033 MET* 2.9 49.7 + - + +
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Residues in contact with ALA 100 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
963 ASN 3.0 16.6 + - - +
973 LYS* 3.7 6.5 - - - +
993 HIS* 1.3 76.5 - - - +
1013 PHE* 1.3 61.2 + - - +
1033 MET* 3.1 22.1 + - + +
1043 GLY 3.1 0.5 + - - -
1053 LYS* 2.9 50.4 + - + +
1113 PHE* 4.0 13.2 - - + -
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Residues in contact with PHE 101 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1131 VAL* 3.4 38.1 - - + -
1141 THR* 3.7 8.1 - - - +
1151 ASN* 3.2 66.5 - - + +
1271 LEU* 3.7 27.8 - - + -
1311 LEU* 3.7 21.1 - - + -
2151 ALA* 3.9 9.4 - - + -
2171 CYS* 4.0 21.5 - - + -
2191 PHE* 5.4 0.2 - + - -
973 LYS 3.0 17.1 + - - +
983 LEU* 3.5 9.2 - - + +
1003 ALA* 1.3 75.8 - - - +
1023 SER* 1.3 58.7 + - - +
1043 GLY 3.0 14.6 + - - -
1053 LYS* 4.4 5.4 - - - +
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Residues in contact with SER 102 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
991 HIS* 2.9 33.6 + - - -
1031 MET* 3.7 25.3 - - - +
1131 VAL* 3.5 21.6 - - - +
1141 THR 4.4 6.4 - - - +
983 LEU* 2.6 20.4 + - - +
993 HIS 3.2 5.6 + - - -
1013 PHE* 1.3 76.5 - - - +
1033 MET* 1.3 61.1 + - - +
1043 GLY* 3.1 1.3 + - - -
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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