Contacts of the helix formed by residues 967 - 1001 (chain A) in PDB entry 3KSS
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 GLN 967 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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965A SER 3.0 2.0 + - - -
966A GLU* 1.3 95.6 + - - +
968A LYS* 1.3 63.0 + - - +
969A LEU 3.1 3.1 - - - +
970A ASP* 3.1 20.1 + - + +
971A GLU* 2.7 42.2 + - + +
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Residues in contact with LYS 968 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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955A VAL* 3.2 25.5 - - - +
956A PRO* 3.7 26.1 - - + +
959A ASN* 3.4 58.6 - - + +
960A ASN* 4.7 1.8 - - + -
965A SER 3.6 5.8 + - - +
966A GLU* 5.0 2.0 - - + -
967A GLN* 1.3 85.4 + - - +
969A LEU* 1.3 51.8 + - - +
971A GLU* 3.0 34.1 + - - +
972A ALA* 2.7 32.2 + - - +
975A HIS* 5.8 2.2 - - - -
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Residues in contact with LEU 969 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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533A LEU* 6.3 0.4 - - + -
952A ILE* 6.4 2.5 - - + -
956A PRO* 5.3 2.0 - - - -
960A ASN* 4.5 16.9 - - - +
965A SER* 3.9 37.6 + - - +
967A GLN 3.1 0.4 - - - -
968A LYS* 1.3 78.0 - - - +
970A ASP* 1.3 76.1 + - - +
972A ALA* 3.0 8.9 + - - +
973A LEU* 2.8 61.2 + - + +
1036A LYS* 5.2 17.5 - - + -
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Residues in contact with ASP 970 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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530A LEU* 5.0 9.3 - - + +
533A LEU* 3.9 35.1 - - + +
534A HIS* 5.6 4.7 - - - -
966A GLU 5.0 1.7 - - - +
967A GLN* 3.1 21.5 + - + +
969A LEU* 1.3 100.7 - - - +
971A GLU* 1.3 61.8 + - - +
973A LEU* 3.6 7.0 + - - +
974A TYR* 3.5 21.2 + - - +
1036A LYS* 6.6 0.2 - - - -
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Residues in contact with GLU 971 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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967A GLN* 2.7 20.3 + - + +
968A LYS* 3.0 60.6 - - + +
970A ASP* 1.3 76.9 - - - +
972A ALA* 1.3 59.9 + - - +
974A TYR* 2.8 64.6 + - + +
975A HIS* 4.1 1.7 - - - -
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Residues in contact with ALA 972 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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951A ALA* 4.8 0.7 - - + -
952A ILE* 6.0 0.4 - - + -
956A PRO* 3.1 40.2 - - + -
968A LYS* 2.7 19.6 + - - +
969A LEU* 3.1 12.8 - - - +
971A GLU* 1.3 74.8 - - - +
973A LEU* 1.3 68.3 + - + +
974A TYR 2.9 0.5 + - - -
975A HIS* 2.8 43.4 + - + -
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Residues in contact with LEU 973 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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533A LEU* 4.7 13.5 - - + -
944A MET* 5.4 1.6 - - - +
948A LEU* 4.7 31.9 - - + +
951A ALA* 5.4 1.1 - - + -
952A ILE* 5.3 10.5 - - + -
969A LEU* 2.8 46.3 + - + +
970A ASP* 4.1 6.1 - - - +
971A GLU 3.4 0.2 - - - -
972A ALA* 1.3 80.1 - - + +
974A TYR* 1.3 60.2 + - - +
975A HIS* 3.3 1.3 - - - -
976A GLY* 3.6 3.9 + - - +
977A ALA* 3.3 20.4 + - - +
1031A ILE* 5.9 1.3 - - + -
1032A PRO* 4.3 32.8 - - + +
1035A TYR* 5.7 4.5 - - + -
1036A LYS* 5.9 4.0 - - + -
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Residues in contact with TYR 974 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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526A HIS* 3.3 32.0 - + + +
529A LEU* 3.4 29.6 - - + -
530A LEU* 4.4 17.5 - - + -
970A ASP 3.5 8.7 + - - +
971A GLU* 2.8 61.3 + - + +
972A ALA 2.9 2.2 + - - -
973A LEU* 1.3 75.5 - - - +
975A HIS* 1.3 76.0 + + + +
977A ALA* 3.5 2.4 + - - +
978A VAL 3.4 4.9 + - - -
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Residues in contact with HIS 975 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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947A TYR 5.0 1.6 - - - -
950A HIS* 5.4 4.7 - + - -
951A ALA* 3.1 35.5 - - + +
955A VAL* 6.2 0.7 - - + -
956A PRO* 3.6 12.8 - - + +
968A LYS* 5.8 2.9 - - - -
971A GLU 4.1 3.6 - - - -
972A ALA* 2.8 35.3 + - - -
973A LEU* 5.1 0.4 - - - -
974A TYR* 1.3 88.6 - + + +
976A GLY* 1.3 84.8 + - - +
977A ALA 3.1 1.6 - - - -
978A VAL* 2.9 26.7 - - + +
979A LEU* 3.5 14.9 - - - +
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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
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944A MET* 3.0 18.8 - - - +
947A TYR* 4.7 9.9 - - - -
948A LEU* 5.6 3.1 - - - -
973A LEU* 3.6 5.7 + - - -
974A TYR 3.4 0.2 - - - -
975A HIS* 1.3 92.6 + - - +
977A ALA* 1.3 59.3 + - - +
979A LEU* 3.0 38.3 + - - +
980A ARG 3.5 1.2 + - - -
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Residues in contact with ALA 977 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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525A TYR* 3.0 44.5 - - + +
529A LEU* 4.5 3.6 - - + -
944A MET* 3.6 12.3 - - + +
973A LEU 3.3 17.3 + - - +
974A TYR* 3.7 9.4 - - - +
975A HIS 3.1 0.8 - - - -
976A GLY* 1.3 79.7 - - - +
978A VAL* 1.3 56.2 + - - +
980A ARG* 3.1 22.0 - - - +
981A VAL* 3.5 5.2 - - - +
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Residues in contact with VAL 978 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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522A ILE* 3.6 18.2 - - + -
526A HIS* 2.7 36.6 - - + +
974A TYR* 3.4 3.0 + - + +
975A HIS* 2.9 32.3 - - + +
977A ALA* 1.3 75.0 - - - +
979A LEU* 1.3 60.8 + - + +
980A ARG 3.1 5.2 - - - -
981A VAL* 2.9 21.7 + - - +
982A ARG* 3.2 28.1 + - - +
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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
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412A GLU* 3.3 14.6 - - - +
416A LYS* 4.7 17.7 - - - +
947A TYR* 3.3 52.3 - - + -
975A HIS* 3.5 16.8 - - - +
976A GLY* 3.0 33.0 - - - +
978A VAL* 1.3 82.2 - - + +
980A ARG* 1.3 57.0 + - - +
982A ARG* 3.7 12.1 - - - +
983A PRO* 3.0 22.2 - - - +
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Residues in contact with ARG 980 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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943A VAL* 6.3 0.2 - - + -
944A MET* 3.4 56.5 - - + +
947A TYR* 5.0 3.8 - - + -
976A GLY 3.8 1.1 - - - +
977A ALA 3.1 19.5 - - - +
979A LEU* 1.3 81.8 - - + +
981A VAL* 1.3 67.6 + - - +
983A PRO* 2.9 11.5 - - - +
984A LYS* 2.8 79.4 + - + +
1024A PRO 4.1 4.8 + - - -
1027A SER* 3.4 25.5 + - - -
1028A LEU* 3.0 47.2 - - - +
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Residues in contact with VAL 981 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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521A LEU* 4.9 10.6 - - + +
522A ILE* 3.5 26.9 - - + -
525A TYR* 4.0 28.3 - - + -
526A HIS* 4.8 2.5 - - - +
977A ALA 3.5 11.2 - - - +
978A VAL* 2.9 29.8 - - - +
980A ARG* 1.3 90.8 - - - +
982A ARG* 1.3 66.4 + - - +
984A LYS* 4.6 0.9 - - - +
985A ALA* 3.1 34.4 + - + +
1028A LEU* 4.7 3.4 - - + -
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Residues in contact with ARG 982 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356A PHE* 3.0 31.2 - - + -
357A LEU* 5.8 1.5 - - + +
412A GLU* 3.9 21.9 + - - +
416A LYS* 5.7 3.2 - - - +
518A ASN* 3.1 50.6 - - + +
521A LEU* 6.0 1.1 - - - -
522A ILE* 4.6 8.1 - - + +
978A VAL* 3.2 45.7 + - - +
979A LEU* 3.7 14.1 - - - +
981A VAL* 1.3 82.1 - - - +
983A PRO* 1.3 68.3 - - + +
986A MET* 3.7 5.4 - - - +
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Residues in contact with PRO 983 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408A ILE* 4.0 18.8 - - + +
409A VAL* 5.3 4.9 - - + -
412A GLU* 3.1 36.8 - - + -
947A TYR* 5.9 3.6 - - + +
979A LEU 3.0 20.2 - - - +
980A ARG* 2.9 18.8 - - - +
982A ARG* 1.3 88.2 - - + +
984A LYS* 1.3 67.8 + - + +
986A MET* 2.8 29.9 + - + +
987A THR* 3.1 10.2 + - - -
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Residues in contact with LYS 984 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409A VAL* 4.0 12.1 - - - +
939A GLU* 3.8 4.4 + - - -
940A PHE* 3.2 39.4 - - + -
943A VAL* 2.9 39.3 - - - +
947A TYR* 5.8 1.0 - - - -
980A ARG* 2.8 65.8 + - + +
981A VAL* 4.6 1.3 - - - +
983A PRO* 1.3 78.7 - - + +
985A ALA* 1.3 65.2 + - - +
986A MET 3.0 0.3 + - - -
987A THR* 3.1 8.6 - - - +
988A VAL* 2.8 31.4 + - + +
1024A PRO* 5.3 9.4 - - + -
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Residues in contact with ALA 985 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356A PHE* 3.5 21.4 - - + -
521A LEU* 3.8 16.4 - - + -
981A VAL* 3.1 21.6 + - + +
984A LYS* 1.3 78.0 - - - +
986A MET* 1.3 60.4 + - - +
988A VAL* 4.0 5.1 - - - +
989A ALA* 3.2 21.1 + - - +
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Residues in contact with MET 986 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352A VAL* 3.7 16.7 - - + +
353A CYS* 4.0 18.4 - - - +
356A PHE* 3.2 41.6 - - + -
357A LEU* 3.8 25.4 - - + -
408A ILE* 3.9 38.4 - - + +
411A ILE* 5.9 2.2 - - + -
412A GLU* 5.7 3.6 - - + +
982A ARG 3.8 13.7 - - - +
983A PRO* 2.8 14.8 + - + +
985A ALA* 1.3 68.3 - - - +
987A THR* 1.3 65.4 + - - +
988A VAL 3.1 1.8 - - - -
989A ALA* 3.0 16.2 + - - +
990A VAL* 3.1 13.2 + - + +
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Residues in contact with THR 987 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404A VAL* 4.2 0.9 - - - +
405A ASP* 4.0 22.8 + - - +
408A ILE* 4.0 23.9 - - - +
409A VAL* 6.4 0.2 - - - -
940A PHE* 3.2 38.5 - - + -
983A PRO 3.1 1.6 + - - -
984A LYS* 3.1 20.3 + - + +
986A MET* 1.3 79.3 - - - +
988A VAL* 1.3 63.7 + - + +
990A VAL* 2.9 14.6 - - - +
991A ILE* 2.9 37.3 - - - +
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Residues in contact with VAL 988 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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940A PHE* 4.6 4.3 - - + -
984A LYS* 2.8 23.5 + - + +
985A ALA* 4.0 5.8 - - - +
987A THR* 1.3 82.8 - - + +
989A ALA* 1.3 66.9 + - - +
991A ILE* 3.5 1.0 + - - +
992A ILE* 3.0 39.0 + - + +
1020A MET* 3.3 37.2 - - + +
1021A ILE* 5.4 5.4 - - + -
1024A PRO* 3.3 32.1 - - + -
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Residues in contact with ALA 989 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352A VAL* 3.9 22.4 - - + -
356A PHE* 5.5 3.6 - - + -
985A ALA 3.2 15.0 + - - +
986A MET* 3.0 10.9 + - - +
988A VAL* 1.3 77.4 - - - +
990A VAL* 1.3 51.9 + - - +
992A ILE* 3.3 5.2 + - - +
993A ALA* 2.7 37.8 + - - +
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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
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345A GLU* 3.7 5.7 - - - +
348A VAL* 4.9 2.2 - - + +
349A VAL* 3.5 42.6 - - + +
352A VAL* 4.0 17.9 - - + -
404A VAL* 3.5 28.9 - - + -
408A ILE* 5.1 2.2 - - + -
986A MET* 3.1 10.1 + - + +
987A THR* 2.9 31.2 - - - +
989A ALA* 1.3 78.3 - - - +
991A ILE* 1.3 57.4 + - + +
993A ALA* 3.1 7.8 + - - +
994A GLY* 2.7 33.1 + - - -
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Residues in contact with ILE 991 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401A GLY* 3.3 31.0 - - - +
402A ALA* 5.7 0.4 - - - -
404A VAL* 4.0 5.4 - - + -
936A VAL* 5.5 4.3 - - + -
987A THR* 2.9 33.8 + - - +
988A VAL 3.8 0.4 - - - +
989A ALA 3.3 0.2 - - - -
990A VAL* 1.3 85.2 - - + +
992A ILE* 1.3 63.5 + - - +
994A GLY* 3.0 7.3 + - - -
995A LEU* 2.9 41.2 - - + +
1016A MET* 4.3 11.2 - - + -
1020A MET* 3.2 50.5 - - + -
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Residues in contact with ILE 992 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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988A VAL* 3.0 27.5 + - + +
989A ALA* 3.7 5.2 - - - +
991A ILE* 1.3 74.8 - - - +
993A ALA* 1.3 60.7 + - - +
995A LEU 3.7 0.2 + - - -
996A LEU* 3.3 24.8 + - + +
1017A ILE* 3.6 41.5 - - + +
1020A MET* 3.6 33.0 - - + +
1021A ILE* 4.7 12.3 - - + +
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Residues in contact with ALA 993 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344A GLU* 4.6 0.7 - - - +
345A GLU* 4.0 4.6 - - - +
348A VAL* 3.5 31.6 - - + +
352A VAL* 5.3 3.8 - - + -
989A ALA 2.7 19.1 + - - +
990A VAL* 3.3 4.9 - - - +
991A ILE 3.1 0.2 - - - -
992A ILE* 1.3 75.8 - - - +
994A GLY* 1.3 58.0 + - - +
995A LEU 3.5 0.2 - - - -
996A LEU* 4.7 4.8 - - - +
997A PRO* 3.1 22.0 - - - +
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Residues in contact with GLY 994 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341A LYS* 3.6 24.3 + - - -
345A GLU* 3.0 27.6 - - - -
401A GLY* 6.2 2.2 - - - -
990A VAL 2.7 13.2 + - - -
991A ILE* 3.0 3.3 + - - -
993A ALA* 1.3 76.5 - - - +
995A LEU* 1.3 66.5 + - - +
997A PRO* 3.4 10.4 - - - +
998A ILE* 4.1 4.2 - - - +
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Residues in contact with LEU 995 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341A LYS* 6.1 0.9 - - - +
398A ILE* 6.0 9.6 - - + -
401A GLY* 5.8 7.9 - - - -
991A ILE* 2.9 22.6 + - + +
992A ILE 3.7 0.2 + - - -
994A GLY* 1.3 83.2 - - - +
996A LEU* 1.3 64.9 + - - +
997A PRO* 3.2 2.7 - - - -
998A ILE* 3.3 16.2 - - - +
999A LEU* 3.0 20.5 - - + +
1013A ALA* 3.3 21.8 - - + +
1016A MET* 3.1 45.8 - - + -
1017A ILE* 3.2 33.9 - - + +
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Residues in contact with LEU 996 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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992A ILE* 3.3 17.9 + - + +
993A ALA* 4.7 3.4 - - - +
995A LEU* 1.3 78.1 - - - +
997A PRO* 1.3 77.4 - - + +
999A LEU* 2.9 30.3 + - + +
1000A TRP* 3.6 13.2 + - + +
1017A ILE* 4.2 3.5 - - + +
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Residues in contact with PRO 997 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341A LYS* 4.8 6.1 - - + -
344A GLU* 2.9 33.0 - - - +
345A GLU* 4.5 0.7 - - - +
348A VAL* 6.0 0.2 - - + -
993A ALA 3.1 25.8 - - - +
994A GLY* 3.4 11.4 - - - +
995A LEU 3.2 4.9 - - - -
996A LEU* 1.3 104.3 - - + +
998A ILE* 1.3 61.5 + - + +
999A LEU 2.9 5.7 + - - -
1000A TRP* 3.4 11.0 + - + +
1001A GLY 4.1 7.6 + - - +
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Residues in contact with ILE 998 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341A LYS* 4.2 24.7 - - + -
994A GLY 4.1 15.5 - - - +
995A LEU* 3.3 14.1 - - - +
997A PRO* 1.3 73.7 - - - +
999A LEU* 1.3 66.2 + - + +
1001A GLY 3.6 16.2 + - - +
1002A THR* 4.6 1.9 - - - +
1006A SER* 4.4 12.4 - - - -
1009A MET* 3.8 31.6 - - + +
1010A SER* 3.3 45.4 - - - +
1013A ALA* 4.1 10.8 - - + -
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Residues in contact with LEU 999 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
914A LEU* 6.2 0.7 - - + -
918A MET* 5.5 15.7 - - + -
995A LEU* 3.0 27.6 - - + +
996A LEU* 2.9 26.1 + - + +
998A ILE* 1.3 90.9 - - + +
1000A TRP* 1.3 63.3 + - - +
1001A GLY 3.5 0.4 + - - -
1002A THR* 5.9 1.1 - - - +
1010A SER* 3.5 28.3 - - - +
1013A ALA* 4.7 5.6 - - + -
1014A ALA* 5.2 9.0 - - + +
1017A ILE* 4.0 17.0 - - + -
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Residues in contact with TRP1000 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
996A LEU* 3.6 14.5 + - + +
997A PRO* 3.4 8.8 + - + +
999A LEU* 1.3 80.1 - - - +
1001A GLY* 1.3 58.1 + - - +
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Residues in contact with GLY1001 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A ASN* 5.2 1.6 - - - +
997A PRO 4.1 6.0 + - - +
998A ILE* 3.6 14.1 - - - +
999A LEU 3.5 1.4 - - - -
1000A TRP* 1.3 83.3 - - - +
1002A THR* 1.3 68.9 + - - -
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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) + - + + + + + -
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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