Contacts of the helix formed by residues 74 - 102 (chain 2) 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 2).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
741 ILE* 3.6 28.7 - - + -
732 ALA* 1.3 78.4 - - + +
752 GLU* 1.3 65.3 + - - +
772 LYS* 3.3 9.4 + - + +
782 LEU* 2.8 30.1 + - - +
743 ILE* 4.3 13.0 - - + -
753 GLU* 3.8 32.1 - - + +
783 LEU* 3.9 25.0 - - + +
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Residues in contact with GLU 75 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
741 ILE* 3.7 26.5 - - + +
771 LYS* 6.3 1.1 - - - +
732 ALA 3.3 6.3 + - - -
742 ILE* 1.3 85.6 + - - +
762 VAL* 1.3 59.3 + - + +
782 LEU* 3.7 2.7 - - - +
792 ALA* 3.0 28.9 + - - +
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Residues in contact with VAL 76 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
732 ALA* 2.9 21.6 + - - +
752 GLU* 1.3 75.7 - - + +
772 LYS* 1.3 61.7 + - - +
792 ALA* 3.3 4.9 + - - +
802 ASN* 2.9 52.9 + - - +
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Residues in contact with LYS 77 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
732 ALA* 2.7 21.6 + - + +
742 ILE* 3.6 9.2 - - + +
762 VAL* 1.3 74.0 - - - +
782 LEU* 1.3 61.0 + - - +
802 ASN* 3.5 7.9 + - + +
812 MET* 3.1 38.4 + - + +
783 LEU* 4.2 26.2 - - + -
793 ALA* 5.3 5.6 - - - +
823 GLU* 2.9 35.9 + - - +
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Residues in contact with LEU 78 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
741 ILE* 3.4 34.5 - - + +
771 LYS* 3.6 30.3 - - + +
781 LEU* 4.0 10.1 - - + +
811 MET* 3.8 27.1 - - + -
742 ILE* 2.8 17.5 + - + +
752 GLU* 3.7 5.2 - - - +
772 LYS* 1.3 74.1 - - - +
792 ALA* 1.3 65.2 + - - +
812 MET* 3.1 4.8 + - - +
822 GLU* 2.9 36.2 + - - +
783 LEU* 3.8 27.3 - - + +
813 MET* 4.5 1.3 - - + -
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Residues in contact with ALA 79 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
752 GLU 3.0 17.9 + - - +
762 VAL* 3.3 6.9 + - - +
782 LEU* 1.3 74.5 - - - +
802 ASN* 1.3 66.6 + - - +
822 GLU* 3.3 18.5 + - - +
832 ALA* 3.1 22.0 + - - +
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Residues in contact with ASN 80 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
762 VAL* 2.9 36.2 + - - +
772 LYS* 3.7 8.8 - - - +
782 LEU 3.2 0.2 - - - -
792 ALA* 1.3 78.5 - - - +
812 MET* 1.3 58.4 + - + +
832 ALA* 3.2 10.5 + - - +
842 GLU* 3.1 32.0 + - + +
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Residues in contact with MET 81 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
811 MET* 4.2 2.5 - - - -
772 LYS* 3.1 24.9 + - + +
782 LEU* 3.1 5.8 + - - +
802 ASN* 1.3 76.3 - - + +
822 GLU* 1.3 63.5 + - - +
842 GLU* 3.2 12.7 + - + +
852 ILE* 3.0 26.3 + - - +
783 LEU* 3.5 31.2 - - - +
813 MET* 3.4 34.3 - - + -
823 GLU* 3.2 44.9 - - + +
853 ILE* 3.6 11.3 - - + +
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Residues in contact with GLU 82 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
771 LYS* 4.0 36.6 + - - +
801 ASN* 5.2 3.8 + - - -
811 MET* 3.4 37.7 - - + +
782 LEU* 2.9 24.0 + - - +
792 ALA* 3.3 20.0 + - - +
812 MET* 1.3 75.8 - - - +
832 ALA* 1.3 63.3 + - - +
852 ILE* 3.4 2.8 + - - +
862 ASN* 3.1 33.7 + - - +
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Residues in contact with ALA 83 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
792 ALA 3.1 13.0 + - - +
802 ASN* 3.3 13.2 - - - +
812 MET 3.2 0.2 - - - -
822 GLU* 1.3 78.1 - - - +
842 GLU* 1.3 61.7 + - + +
862 ASN* 3.3 8.6 + - - +
872 THR* 3.0 28.2 + - - +
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Residues in contact with GLU 84 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
802 ASN* 3.1 22.3 + - + +
812 MET* 3.2 14.8 + - + +
832 ALA* 1.3 77.9 - - + +
852 ILE* 1.3 56.4 + - - +
872 THR* 3.3 11.1 + - - +
882 LEU* 2.9 33.7 + - - +
853 ILE* 4.1 18.6 - - + -
893 LYS* 2.9 31.3 + - - -
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Residues in contact with ILE 85 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
811 MET* 3.1 39.9 - - + +
841 GLU* 4.0 18.6 - - + +
851 ILE* 3.8 22.7 - - + -
881 LEU* 4.5 10.3 - - + -
812 MET 3.0 9.9 + - - +
822 GLU 3.7 7.2 - - - +
842 GLU* 1.3 76.8 - - - +
862 ASN* 1.3 60.7 + - - +
882 LEU* 3.1 9.0 + - + +
892 LYS* 2.9 51.9 + - + +
853 ILE* 3.6 29.8 - - + -
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Residues in contact with ASN 86 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
841 GLU* 5.3 2.8 + - - -
822 GLU* 3.1 20.5 + - - +
832 ALA* 3.6 9.8 - - - +
852 ILE* 1.3 79.6 - - - +
872 THR* 1.3 63.2 + - - +
892 LYS* 3.3 30.1 + - - +
902 SER* 3.1 25.9 + - - -
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Residues in contact with THR 87 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
832 ALA* 3.0 14.1 + - - +
842 GLU* 3.5 15.9 - - - +
862 ASN* 1.3 79.2 - - - +
882 LEU* 1.3 57.3 + - + +
902 SER* 3.2 9.2 + - - -
912 LYS* 3.0 55.0 + - + +
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Residues in contact with LEU 88 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
881 LEU* 4.0 18.6 - - + +
842 GLU 2.9 13.8 + - - +
852 ILE* 3.5 9.6 - - - +
872 THR* 1.3 73.8 - - + +
892 LYS* 1.3 59.1 + - - +
912 LYS* 3.2 14.2 + - + +
922 LEU* 3.0 29.1 + - - +
853 ILE* 3.9 27.4 - - + +
883 LEU* 4.1 15.3 - - + -
893 LYS* 3.7 45.3 - - + +
923 LEU* 3.9 24.4 - - + +
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Residues in contact with LYS 89 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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841 GLU* 3.0 30.3 + - - +
871 THR* 6.4 1.1 - - - -
881 LEU* 3.8 29.2 - - + -
911 LYS* 6.2 1.8 - - - +
852 ILE* 2.9 35.4 + - + +
862 ASN* 3.5 23.8 - - - +
882 LEU* 1.3 76.0 - - - +
902 SER* 1.3 62.4 + - - +
922 LEU* 3.5 2.8 + - - +
932 GLU* 3.1 24.1 + - - +
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Residues in contact with SER 90 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
862 ASN 3.1 14.6 + - - -
872 THR* 3.4 11.1 - - - -
882 LEU 3.2 0.2 - - - -
892 LYS* 1.3 77.6 - - - +
912 LYS* 1.3 61.6 + - - +
932 GLU* 3.2 8.8 + - - +
942 LEU* 3.0 22.2 + - - +
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Residues in contact with LYS 91 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
872 THR* 3.0 40.7 + - + +
882 LEU* 3.5 19.7 - - + +
902 SER* 1.3 77.9 - - - +
922 LEU* 1.3 57.0 + - - +
942 LEU* 3.1 14.2 + - + +
952 THR* 2.9 28.6 + - - -
923 LEU* 3.6 18.2 - - + -
963 ASN* 5.4 2.1 - - - +
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Residues in contact with LEU 92 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
881 LEU* 4.0 18.6 - - + -
911 LYS* 3.7 33.7 - - + +
921 LEU* 3.7 39.3 - - + +
951 THR* 3.7 22.9 - - + +
882 LEU 3.0 15.6 + - - +
892 LYS 3.8 4.7 - - - +
912 LYS* 1.3 73.4 - - - +
932 GLU* 1.3 65.9 + - - +
952 THR* 3.0 8.8 + - - -
962 ASN* 2.9 27.7 + - - +
923 LEU* 3.7 16.3 - - + +
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Residues in contact with GLU 93 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41 CA 2.4 30.0 - - - -
892 LYS 3.1 14.6 + - - +
902 SER* 3.2 11.6 + - - +
922 LEU* 1.3 76.6 - - - +
942 LEU* 1.3 57.6 + - - +
962 ASN* 3.2 19.1 + - - +
972 LYS* 3.0 50.1 + - - +
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Residues in contact with LEU 94 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
902 SER 3.0 12.2 + - - +
912 LYS* 3.3 15.7 - - + +
922 LEU 3.1 0.2 - - - -
932 GLU* 1.3 74.9 - - - +
952 THR* 1.3 65.4 + - - +
972 LYS* 3.2 9.3 + - + +
982 LEU* 2.9 27.3 + - + +
1303 GLU 3.3 26.0 - - - +
1313 LEU* 3.6 24.2 - - + +
1323 ARG* 3.4 30.7 - - + +
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Residues in contact with THR 95 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
951 THR* 4.1 9.0 - - + -
912 LYS 2.9 13.9 + - - -
922 LEU* 3.2 12.6 - - - -
942 LEU* 1.3 77.0 - - - +
962 ASN* 1.3 56.8 + - - +
982 LEU* 3.4 5.8 + - - +
992 HIS* 2.9 28.8 + - - +
923 LEU* 3.5 11.0 - - + +
953 THR* 4.0 10.8 - - + -
963 ASN* 2.8 34.4 + - - +
993 HIS* 3.9 27.8 + - + +
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Residues in contact with ASN 96 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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911 LYS* 6.0 0.5 - - - +
951 THR* 2.7 42.7 + - - +
981 LEU* 6.0 4.2 - - - +
922 LEU* 2.9 22.9 + - - +
932 GLU* 3.4 26.5 - - - +
952 THR* 1.3 74.3 - - - +
972 LYS* 1.3 64.6 + - + +
992 HIS* 3.4 6.0 + - - +
1002 ALA* 3.1 24.9 + - - +
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Residues in contact with LYS 97 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
932 GLU* 3.0 40.7 + - + +
942 LEU* 3.7 10.3 - - + +
962 ASN* 1.3 76.5 - - + +
982 LEU* 1.3 59.0 + - - +
1002 ALA* 3.3 6.0 + - - +
1012 PHE* 3.0 29.3 + - - +
1303 GLU* 3.6 42.2 - - + +
1313 LEU* 3.9 13.3 - - + +
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Residues in contact with LEU 98 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
942 LEU* 2.9 19.3 + - + +
952 THR* 3.9 5.4 - - - +
972 LYS* 1.3 74.8 - - - +
992 HIS* 1.3 66.9 + - - +
1012 PHE* 3.5 9.1 + - + -
1022 SER* 2.9 22.9 + - - -
963 ASN* 6.2 1.6 - - - +
1033 MET* 4.0 29.6 - - + -
1113 PHE* 5.1 3.4 - - + -
1133 VAL* 4.7 1.6 - - + -
1313 LEU* 3.8 25.7 - - + +
2193 PHE* 3.6 46.9 - - + -
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Residues in contact with HIS 99 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
951 THR* 5.7 1.7 + - + +
981 LEU* 3.9 31.6 - - + +
991 HIS* 3.7 30.0 + + - -
1021 SER* 2.6 37.9 + - - -
1031 MET* 5.5 1.1 - - + -
952 THR 2.9 18.6 + - - +
962 ASN* 3.8 7.8 + - - +
972 LYS 3.3 0.2 - - - -
982 LEU* 1.3 76.6 - - - +
1002 ALA* 1.3 63.7 + - - +
1022 SER* 2.7 25.0 + - - -
1032 MET* 3.0 25.4 + - + +
1112 PHE* 4.5 6.7 - + - -
993 HIS* 4.3 16.6 - + + +
1033 MET* 5.7 3.6 - - - +
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Residues in contact with ALA 100 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
962 ASN 3.1 17.2 + - - +
972 LYS* 3.7 5.8 - - - +
982 LEU 3.3 0.2 - - - -
992 HIS* 1.3 76.9 + - - +
1012 PHE* 1.3 61.0 + - - +
1032 MET* 3.0 11.3 + - - +
1042 GLY 3.2 0.5 + - - -
1052 LYS* 2.9 52.0 + - + +
1112 PHE* 3.9 25.1 - - + -
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Residues in contact with PHE 101 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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972 LYS 3.0 17.9 + - - +
982 LEU* 3.6 7.0 - - + +
992 HIS 3.3 0.2 - - - -
1002 ALA* 1.3 75.6 - - - +
1022 SER* 1.3 59.9 + - - +
1042 GLY 2.9 17.3 + - - -
1052 LYS* 4.3 6.5 - - - +
1133 VAL* 3.5 39.7 - - + -
1143 THR* 3.7 6.5 - - - -
1153 ASN* 3.1 65.3 - - + +
1273 LEU* 3.7 26.0 - - + -
1313 LEU* 3.7 25.4 - - + -
2153 ALA* 4.0 8.3 - - + -
2173 CYS* 3.9 17.9 - - + -
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Residues in contact with SER 102 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
982 LEU 2.9 15.5 + - - -
992 HIS* 2.7 26.7 + - - -
1012 PHE* 1.3 76.8 - - - +
1032 MET* 1.3 65.6 + - - +
1042 GLY 3.3 1.0 + - - -
1033 MET* 3.7 24.4 - - - +
1133 VAL* 3.6 28.2 - - - +
1143 THR 4.2 7.2 - - - +
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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).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il