Contacts of the helix formed by residues 966 - 996 (chain A) in PDB entry 2KNC
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 966 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
963A ALA 5.6 0.2 - - - +
964A ILE* 2.9 12.3 + - + +
965A PRO* 1.3 69.2 - - - +
967A TRP* 1.3 55.2 + - - +
969A VAL* 2.7 18.7 + - + -
970A LEU* 2.3 56.1 + - + +
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Residues in contact with TRP 967 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
965A PRO* 3.1 6.3 - - + -
966A ILE* 1.3 77.3 - - - +
968A TRP* 1.3 77.0 + + + +
970A LEU* 3.0 18.8 + - + +
971A VAL* 2.5 61.3 + - + +
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Residues in contact with TRP 968 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
965A PRO* 3.3 22.3 + - + +
967A TRP* 1.3 105.0 - + + +
969A VAL* 1.3 63.4 + - + +
971A VAL* 3.4 11.0 + - + +
972A GLY 3.0 18.0 + - - -
687B GLY* 4.6 19.3 - - - -
693B ILE* 3.5 39.1 - - + +
696B VAL* 4.4 11.4 - - + -
697B LEU* 4.1 24.2 - - + +
700B VAL* 3.8 15.1 - - + +
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Residues in contact with VAL 969 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
964A ILE* 5.0 12.6 - - + -
965A PRO 3.6 15.0 - - - +
966A ILE* 2.7 23.5 + - + +
968A TRP* 1.3 73.5 - - + +
970A LEU* 1.3 51.7 + - - +
972A GLY* 3.0 1.6 + - - -
973A VAL* 2.5 55.8 + - + +
700B VAL* 4.0 27.3 - - + +
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Residues in contact with LEU 970 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
966A ILE* 2.3 46.3 + - + +
967A TRP* 3.2 22.2 - - + +
969A VAL* 1.3 67.9 - - - +
971A VAL* 1.3 54.2 + - + +
973A VAL* 3.6 9.7 - - + +
974A LEU* 2.5 46.0 + - + +
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Residues in contact with VAL 971 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
967A TRP* 2.5 53.9 + - + +
968A TRP* 3.7 14.4 - - + +
970A LEU* 1.3 73.5 - - + +
972A GLY* 1.3 61.9 + - - +
974A LEU* 3.5 8.2 + - + +
975A GLY* 3.2 16.5 + - - -
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Residues in contact with GLY 972 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
968A TRP 3.0 10.3 + - - -
969A VAL 3.4 2.5 - - - -
971A VAL* 1.3 77.7 - - - +
973A VAL* 1.3 65.0 + - - +
975A GLY* 3.0 3.7 + - - -
976A GLY 2.9 6.1 + - - -
700B VAL* 3.6 13.2 - - - -
701B MET* 5.1 6.5 - - - -
704B ILE* 2.7 40.2 - - - +
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Residues in contact with VAL 973 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
969A VAL* 2.5 42.2 + - + +
970A LEU* 3.6 10.3 - - + +
972A GLY* 1.3 71.6 - - - -
974A LEU* 1.3 62.7 + - - +
976A GLY* 3.0 10.0 + - - +
977A LEU* 3.3 21.8 + - + +
700B VAL* 5.9 0.2 - - + -
703B ALA* 4.4 11.2 - - + -
704B ILE* 3.7 3.8 - - - +
707B ILE* 3.8 26.9 - - + -
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Residues in contact with LEU 974 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
970A LEU* 2.5 28.3 + - + +
971A VAL* 3.5 11.2 - - - +
973A VAL* 1.3 74.9 - - - +
975A GLY* 1.3 64.2 + - - +
977A LEU* 3.0 27.1 + - + +
978A LEU* 3.3 5.8 + - + +
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Residues in contact with GLY 975 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
971A VAL 3.2 7.9 + - - -
972A GLY 3.0 8.2 + - - -
974A LEU* 1.3 78.1 - - - +
976A GLY* 1.3 54.6 + - - +
978A LEU* 2.9 14.4 + - - +
979A LEU* 2.5 35.0 + - - +
704B ILE* 4.1 5.1 - - - +
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Residues in contact with GLY 976 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
972A GLY 2.9 8.9 + - - -
973A VAL* 3.0 6.9 + - - -
974A LEU 3.0 0.8 - - - -
975A GLY* 1.3 79.4 - - - +
977A LEU* 1.3 56.2 + - - +
979A LEU* 3.7 1.4 - - - +
980A LEU* 2.5 35.3 + - - +
704B ILE* 3.5 32.3 - - - +
707B ILE* 4.3 10.3 - - - +
708B GLY 5.2 0.2 + - - -
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Residues in contact with LEU 977 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
973A VAL* 3.3 25.4 - - + +
974A LEU* 3.0 20.2 + - + +
976A GLY* 1.3 77.5 - - - +
978A LEU* 1.3 59.4 + - - +
980A LEU* 3.4 22.3 - - + +
981A THR* 2.6 35.2 + - - +
707B ILE* 4.8 10.3 - - + -
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Residues in contact with LEU 978 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
974A LEU* 3.3 6.5 + - + +
975A GLY* 3.1 21.3 - - - +
977A LEU* 1.3 83.4 - - - +
979A LEU* 1.3 59.7 + - - +
981A THR* 3.4 6.9 + - - +
982A ILE* 3.3 43.8 + - + +
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Residues in contact with LEU 979 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
975A GLY 2.5 19.3 + - - +
976A GLY 3.7 1.1 - - - +
978A LEU* 1.3 74.0 - - - +
980A LEU* 1.3 65.9 + - - +
981A THR 3.0 0.3 + - - -
982A ILE* 3.0 7.7 + - + +
983A LEU* 2.7 50.7 + - + +
704B ILE* 3.5 44.4 - - + +
705B LEU* 4.3 8.5 - - + -
708B GLY* 4.0 16.6 - - - -
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Residues in contact with LEU 980 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
976A GLY 2.5 22.5 + - - +
977A LEU* 3.4 24.5 - - + +
979A LEU* 1.3 73.7 - - - +
981A THR* 1.3 63.3 + - + +
983A LEU* 3.9 4.6 - - - +
984A VAL* 2.9 48.4 + - + +
707B ILE* 4.0 20.4 - - + +
708B GLY* 4.5 8.1 - - - -
711B ALA* 3.3 31.9 - - + -
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Residues in contact with THR 981 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
977A LEU 2.6 18.4 + - - -
978A LEU* 3.7 9.2 + - - +
979A LEU 3.0 0.2 - - - -
980A LEU* 1.3 81.5 - - + +
982A ILE* 1.3 62.3 + - - +
984A VAL* 3.4 8.9 + - + +
985A LEU* 2.9 27.8 + - + +
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Residues in contact with ILE 982 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
978A LEU* 3.3 36.3 + - + +
979A LEU* 3.0 7.9 + - + +
981A THR* 1.3 75.8 - - - +
983A LEU* 1.3 63.7 + - + +
985A LEU* 3.7 7.3 - - + +
986A ALA* 2.8 30.4 + - + +
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Residues in contact with LEU 983 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
979A LEU* 2.7 37.2 + - + +
980A LEU* 3.9 4.7 - - - +
982A ILE* 1.3 78.6 - - + +
984A VAL* 1.3 66.0 + - - +
986A ALA* 2.9 7.7 + - + +
987A MET* 2.8 42.8 + - + +
705B LEU* 5.4 3.8 - - + +
708B GLY* 3.4 36.3 - - - +
709B LEU* 4.2 4.9 - - + +
712B LEU* 4.3 11.2 - - + -
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Residues in contact with VAL 984 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
980A LEU* 2.9 42.6 + - + +
981A THR* 3.6 10.8 - - + +
983A LEU* 1.3 76.2 - - - +
985A LEU* 1.3 62.8 + - + +
987A MET* 2.8 29.2 - - + +
988A TRP* 3.0 13.6 + - + +
711B ALA* 4.6 9.0 - - + -
715B TRP* 3.4 45.0 - - + +
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Residues in contact with LEU 985 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
981A THR* 2.9 17.4 + - + +
982A ILE* 3.7 7.6 - - + +
984A VAL* 1.3 79.5 - - + +
986A ALA* 1.3 55.3 + - - +
988A TRP* 3.2 19.8 - - + +
989A LYS* 2.5 72.5 + - + +
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Residues in contact with ALA 986 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
982A ILE* 2.8 22.7 + - + +
983A LEU* 3.6 9.4 - - + +
985A LEU* 1.3 77.8 - - - +
987A MET* 1.3 58.8 + - - +
989A LYS* 3.2 9.1 + - - +
990A VAL* 2.9 31.8 + - + +
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Residues in contact with MET 987 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
983A LEU* 2.8 37.5 + - + +
984A VAL* 2.8 29.2 - - + +
986A ALA* 1.3 74.9 - - - +
988A TRP* 1.3 70.7 + - - +
990A VAL* 2.9 25.2 + - - +
991A GLY 3.4 3.5 + - - -
712B LEU* 3.4 64.4 - - + +
715B TRP* 3.8 15.9 - - + -
716B LYS* 3.4 23.2 + - - +
719B ILE* 4.0 10.2 - - + +
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Residues in contact with TRP 988 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
984A VAL 3.2 13.0 - - - +
985A LEU* 3.2 24.0 - - + +
987A MET* 1.3 82.9 - - - +
989A LYS* 1.3 55.3 + - + +
991A GLY* 3.1 2.1 + - - -
992A PHE* 2.5 95.0 + + + +
715B TRP* 2.9 39.1 - + - +
718B LEU* 5.7 2.8 - - - +
719B ILE* 3.0 38.5 - - + +
722B HIS* 5.8 3.9 - + - -
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Residues in contact with LYS 989 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
985A LEU* 2.5 56.4 + - + +
986A ALA* 3.3 10.1 - - - +
988A TRP* 1.3 74.0 - - + +
990A VAL* 1.3 53.7 + - - +
991A GLY 2.5 17.6 + - - -
992A PHE* 4.0 18.2 - - + +
993A PHE* 2.9 62.4 + - + +
994A LYS 4.1 0.2 + - - -
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Residues in contact with VAL 990 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
986A ALA* 2.9 20.1 + - + +
987A MET* 2.9 16.6 + - - +
989A LYS* 1.3 74.4 - - + +
991A GLY* 1.3 55.6 + - - +
994A LYS* 3.4 32.4 + - - +
716B LYS* 5.1 8.3 - - - +
719B ILE* 6.2 0.2 - - - -
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Residues in contact with GLY 991 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
987A MET 3.4 3.1 + - - -
988A TRP 3.1 4.6 + - - -
989A LYS 2.5 6.1 + - - -
990A VAL* 1.3 77.4 - - - +
992A PHE* 1.3 60.5 + - - +
993A PHE 3.2 2.0 + - - -
994A LYS* 3.5 21.3 + - - +
995A ARG* 3.8 18.4 + - - +
719B ILE* 5.6 9.2 - - - -
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Residues in contact with PHE 992 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
988A TRP* 2.5 72.7 + + + +
989A LYS* 4.2 18.8 - - + -
991A GLY* 1.3 73.8 - - - +
993A PHE* 1.3 68.6 + + - +
994A LYS 3.3 1.6 - - - -
995A ARG* 4.4 6.7 - - - +
996A ASN* 4.1 17.9 + - + +
719B ILE* 5.7 2.0 - - + +
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Residues in contact with PHE 993 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
989A LYS* 2.9 52.0 + - + +
992A PHE* 1.3 87.1 - + - +
994A LYS* 1.3 62.6 + - - +
995A ARG 3.5 0.9 - - - -
996A ASN* 3.9 25.5 + - + +
998A PRO* 5.3 3.8 - - - +
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Residues in contact with LYS 994 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
989A LYS 4.1 1.0 + - - -
990A VAL* 3.4 32.8 + - - +
991A GLY* 3.5 15.9 - - - +
993A PHE* 1.3 81.4 - - - +
995A ARG* 1.3 64.6 + - + +
996A ASN 3.5 0.2 + - - -
997A ARG* 3.5 24.4 + - - +
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Residues in contact with ARG 995 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
991A GLY 3.8 16.5 + - - +
992A PHE* 4.3 6.0 + - - +
993A PHE 3.5 0.2 - - - -
994A LYS* 1.3 76.2 - - + +
996A ASN* 1.3 53.3 + - - +
997A ARG* 2.5 28.6 + - - +
1001A GLU* 5.6 0.3 - - - -
722B HIS* 5.6 5.5 - - - +
723B ASP* 4.2 21.2 + - - -
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Residues in contact with ASN 996 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
992A PHE* 4.1 18.6 + - + +
993A PHE* 3.9 26.2 + - + +
994A LYS 3.2 1.8 - - - -
995A ARG* 1.3 75.8 - - - +
997A ARG* 1.3 67.0 + - - +
998A PRO* 2.6 21.7 - - + +
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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