Contacts of the helix formed by residues 86 - 124 (chain 2) in PDB entry 6NRB
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 VAL 86 (chain 2).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
702 CYS* 3.4 33.2 - - + -
712 TYR 4.6 1.8 - - - +
812 ARG* 3.3 44.2 - - + +
822 THR 3.7 2.2 + - - +
832 VAL 4.6 3.6 - - - +
842 LYS 3.2 1.2 - - - -
852 GLU* 1.3 78.1 - - - +
872 LEU* 1.3 66.1 + - + +
892 ALA* 2.9 13.7 + - - +
902 LEU* 3.2 34.2 + - + +
1303 ASN 4.3 2.7 - - - +
1313 VAL* 3.6 21.1 - - + -
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Residues in contact with LEU 87 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
622 LYS* 3.6 35.7 - - - +
662 GLU* 4.2 12.6 - - - +
832 VAL 4.1 11.4 - - - +
842 LYS* 3.3 16.6 + - + +
862 VAL* 1.3 78.1 - - + +
882 PRO* 1.3 67.3 - - + +
892 ALA 3.2 1.0 + - - -
902 LEU* 3.3 19.3 + - + +
912 GLU* 3.7 19.8 + - + +
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Residues in contact with PRO 88 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
812 ARG* 4.9 0.9 - - - +
842 LYS 3.4 10.8 - - - +
852 GLU* 3.2 21.5 - - - +
872 LEU* 1.3 91.4 - - + +
892 ALA* 1.3 58.1 + - - +
922 ASN* 3.4 25.8 + - + +
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Residues in contact with ALA 89 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
722 ARG* 3.3 33.4 - - - +
812 ARG* 3.8 10.8 - - - +
862 VAL 2.9 10.3 + - - +
882 PRO* 1.3 81.1 - - - +
902 LEU* 1.3 67.6 + - + +
922 ASN* 4.5 0.7 - - - +
932 ASN* 2.8 35.7 + - - +
1303 ASN* 5.6 2.7 - - + +
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Residues in contact with LEU 90 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542 HIS* 3.7 10.8 + - - -
572 VAL* 5.3 3.4 - - + -
582 ILE* 5.9 5.6 - - + -
612 LEU* 4.7 7.2 - - + -
622 LYS* 4.9 5.8 - - - -
662 GLU* 5.6 0.4 - - - +
862 VAL* 3.2 27.3 + - + +
872 LEU* 3.3 18.3 + - + +
892 ALA* 1.3 83.3 - - + +
912 GLU* 1.3 70.0 + - + +
932 ASN* 3.3 12.7 + - - +
942 LYS* 3.3 8.0 + - - +
1293 ALA* 3.0 30.1 - - + +
1303 ASN* 3.4 21.5 - - + +
1313 VAL* 3.5 29.4 - - + -
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Residues in contact with GLU 91 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542 HIS* 6.1 0.2 - - - -
582 ILE* 4.0 23.6 - - + +
622 LYS* 3.1 26.9 + - - +
872 LEU* 3.7 13.6 + - - +
902 LEU* 1.3 78.2 - - + +
922 ASN* 1.3 61.2 + - - +
932 ASN 3.2 1.3 - - - -
942 LYS* 3.1 18.9 + - - +
952 GLU* 2.8 29.2 + - - +
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Residues in contact with ASN 92 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
872 LEU 5.0 0.2 + - - -
882 PRO* 3.4 22.5 + - + +
892 ALA 4.5 0.9 - - - +
902 LEU 3.4 0.2 - - - -
912 GLU* 1.3 78.4 - - - +
932 ASN* 1.3 54.3 + - - +
952 GLU* 3.6 9.0 - - - +
962 GLN* 2.7 38.6 + - - +
992 LYS* 5.6 2.8 + - - -
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Residues in contact with ASN 93 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542 HIS* 3.5 14.0 - - + -
892 ALA* 2.8 26.7 + - - +
902 LEU* 3.3 9.4 + - - +
912 GLU 3.2 0.4 - - - -
922 ASN* 1.3 80.8 + - - +
942 LYS* 1.3 51.8 + - - +
962 GLN* 3.1 9.6 + - - +
972 ILE* 2.5 43.0 + - + +
1303 ASN* 3.1 31.3 - - - +
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Residues in contact with LYS 94 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512 LEU* 3.5 17.0 - - + -
542 HIS* 3.3 41.5 + - + +
552 SER* 3.6 23.4 + - - +
582 ILE* 3.8 25.8 - - - +
902 LEU 3.3 3.7 + - - +
912 GLU* 3.1 17.9 + - - +
932 ASN* 1.3 78.2 - - - +
952 GLU* 1.3 60.3 + - - +
972 ILE* 3.2 6.9 - - - +
982 GLN* 2.8 49.6 + - - +
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Residues in contact with GLU 95 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
912 GLU 2.8 15.6 + - - +
922 ASN* 3.7 10.8 - - - +
942 LYS* 1.3 77.1 + - - +
962 GLN* 1.3 60.3 + - - +
972 ILE 3.0 1.1 - - - -
982 GLN* 2.9 27.3 + - - +
992 LYS* 2.8 68.3 + - - +
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Residues in contact with GLN 96 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472 LEU* 6.0 0.4 - - + -
922 ASN* 2.7 26.4 + - - +
932 ASN* 3.4 11.4 - - - +
952 GLU* 1.3 71.5 - - - +
972 ILE* 1.3 61.8 + - + +
992 LYS* 4.6 11.2 - - - +
1002 ILE* 3.2 51.7 + - + +
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Residues in contact with ILE 97 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472 LEU* 3.1 55.3 - - + +
482 GLU* 4.2 1.1 - - - +
502 GLU* 3.4 21.8 - - + +
512 LEU* 3.6 20.2 - - + +
542 HIS* 3.3 34.1 - - + +
932 ASN* 2.5 25.0 + - + +
942 LYS* 3.2 7.4 - - - +
962 GLN* 1.3 73.3 - - + +
982 GLN* 1.3 68.2 + - - +
992 LYS 3.1 1.0 + - - -
1012 ILE* 3.1 30.8 + - + +
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Residues in contact with GLN 98 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512 LEU* 3.3 37.5 - - + +
552 SER* 5.3 0.4 + - - -
942 LYS* 2.8 37.4 + - - +
952 GLU* 2.9 29.1 + - - +
972 ILE* 1.3 72.7 - - - +
992 LYS* 1.3 62.1 + - - +
1012 ILE* 3.3 22.5 - - + +
1022 GLU* 4.1 10.6 - - - +
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Residues in contact with LYS 99 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
922 ASN* 5.6 3.0 + - - -
952 GLU* 2.8 51.8 + - + +
962 GLN* 4.1 12.6 - - - +
972 ILE 3.1 0.6 - - - -
982 GLN* 1.3 78.9 - - - +
1002 ILE* 1.3 67.7 + - + +
1022 GLU* 3.2 31.6 - - - +
1032 THR* 3.8 6.9 + - - -
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Residues in contact with ILE 100 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472 LEU* 3.6 23.8 - - + -
962 GLN* 3.2 42.4 - - + +
972 ILE 3.5 0.2 + - - -
992 LYS* 1.3 80.6 - - + +
1012 ILE* 1.3 62.8 + - - +
1022 GLU 3.3 1.1 - - - -
1032 THR* 4.1 9.6 - - - +
1042 LEU* 3.2 40.9 + - + +
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Residues in contact with ILE 101 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432 LYS 5.3 0.4 - - - +
442 ALA* 3.3 28.5 - - - +
472 LEU* 3.7 24.2 - - + -
482 GLU* 3.6 33.2 - - + +
512 LEU* 4.8 10.5 - - + -
972 ILE* 3.1 26.7 + - + +
982 GLN* 3.3 21.8 - - + +
1002 ILE* 1.3 80.1 - - - +
1022 GLU* 1.3 61.4 + - + +
1042 LEU* 4.4 1.3 - - - +
1052 THR* 2.7 32.4 + - - -
623 PHE* 4.4 15.2 - - + -
663 ASN* 5.1 0.2 - - - +
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Residues in contact with GLU 102 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
982 GLN 4.1 9.7 - - - +
992 LYS* 3.2 20.2 - - - +
1012 ILE* 1.3 84.2 - - + +
1032 THR* 1.3 66.5 + - - +
1052 THR* 3.4 6.1 + - - -
1062 GLN* 3.0 39.8 + - - +
623 PHE* 5.5 10.5 - - + -
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Residues in contact with THR 103 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
992 LYS 3.8 12.3 + - - -
1002 ILE* 3.9 9.0 + - - -
1022 GLU* 1.3 80.9 + - - +
1042 LEU* 1.3 69.0 + - + +
1062 GLN* 3.2 20.9 + - - +
1072 GLN* 3.1 38.4 + - + +
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Residues in contact with LEU 104 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402 LEU* 5.2 22.0 - - + +
432 LYS* 3.8 38.8 - - + +
442 ALA* 5.4 8.3 - - - +
472 LEU* 5.9 2.2 - - + -
1002 ILE* 3.2 35.7 + - + +
1012 ILE* 4.5 2.2 - - - +
1022 GLU 3.4 0.2 - - - -
1032 THR* 1.3 80.4 - - + +
1052 THR* 1.3 57.0 + - - +
1072 GLN* 3.1 27.8 + - + +
1082 LEU* 3.0 25.0 + - - +
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Residues in contact with THR 105 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442 ALA* 3.5 21.8 - - + +
482 GLU* 5.4 1.9 + - - -
1012 ILE 2.7 23.5 + - - -
1022 GLU* 3.7 6.7 - - - -
1032 THR 3.2 0.4 - - - -
1042 LEU* 1.3 77.0 - - - +
1062 GLN* 1.3 64.9 + - - +
1082 LEU* 3.1 20.3 + - + +
1092 GLN* 3.3 21.8 + - + +
613 LYS* 5.4 10.5 - - - +
623 PHE* 5.7 10.4 - - + -
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Residues in contact with GLN 106 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1022 GLU* 3.0 28.1 + - + +
1032 THR* 3.2 24.2 + - - +
1052 THR* 1.3 76.2 - - - +
1072 GLN* 1.3 62.9 + - + +
1082 LEU 3.5 0.2 + - - -
1092 GLN* 3.7 6.4 + - - +
1102 ALA* 3.5 18.9 + - - +
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Residues in contact with GLN 107 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402 LEU* 5.2 3.4 - - + +
1032 THR* 3.1 27.0 + - + +
1042 LEU* 3.1 33.4 + - + +
1062 GLN* 1.3 76.3 - - + +
1082 LEU* 1.3 62.9 + - - +
1102 ALA* 3.8 7.2 + - - +
1112 LYS* 3.2 43.2 + - - +
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Residues in contact with LEU 108 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372 GLN* 3.6 27.0 + - + +
402 LEU* 3.4 30.7 - - + +
412 ALA* 3.7 20.4 - - + +
442 ALA* 5.4 7.0 - - + -
1042 LEU 3.0 11.8 + - - +
1052 THR* 3.1 14.5 + - + +
1072 GLN* 1.3 76.1 - - - +
1092 GLN* 1.3 79.7 + - + +
1112 LYS* 3.0 11.4 + - - +
1122 GLY 2.8 24.9 + - - -
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Residues in contact with GLN 109 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1052 THR* 3.3 18.9 + - + +
1062 GLN* 4.2 6.3 - - - +
1072 GLN 3.5 0.2 - - - -
1082 LEU* 1.3 95.6 - - - +
1102 ALA* 1.3 60.3 + - - +
1122 GLY* 3.3 2.8 + - - +
1132 LYS* 2.8 36.7 + - - +
573 TYR* 5.6 1.8 + - - -
583 GLN* 4.0 15.8 - - - +
613 LYS* 3.1 30.9 + - - +
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Residues in contact with ALA 110 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1062 GLN 3.5 11.6 + - - +
1072 GLN* 3.9 10.1 - - - +
1082 LEU 3.2 0.4 - - - -
1092 GLN* 1.3 76.7 - - - +
1112 LYS* 1.3 64.8 + - + +
1132 LYS* 3.3 20.9 + - - +
1142 GLU* 3.4 24.4 + - - +
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Residues in contact with LYS 111 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332 LEU* 4.2 25.7 - - + +
362 GLU* 3.6 23.8 + - - -
372 GLN* 3.1 37.2 - - + +
402 LEU* 3.3 31.5 - - + +
1072 GLN* 3.2 30.1 + - - +
1082 LEU* 3.0 10.1 + - - +
1102 ALA* 1.3 76.0 - - + +
1122 GLY* 1.3 54.4 + - - +
1132 LYS 3.2 0.2 + - - -
1142 GLU* 3.3 1.1 + - - -
1152 LEU* 2.6 38.3 + - - +
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Residues in contact with GLY 112 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372 GLN* 3.1 23.2 + - - -
1082 LEU 2.8 15.4 + - - -
1092 GLN* 3.3 4.7 + - - -
1102 ALA 3.3 0.4 - - - -
1112 LYS* 1.3 72.6 - - - +
1132 LYS* 1.3 57.0 + - - +
1152 LEU* 3.9 2.8 - - - +
1162 ASN* 3.0 30.0 + - - +
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Residues in contact with LYS 113 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1092 GLN* 2.8 40.5 + - - +
1102 ALA* 3.3 16.2 - - - +
1112 LYS 3.1 1.0 - - - -
1122 GLY* 1.3 78.5 - - - +
1142 GLU* 1.3 55.1 + - + +
1162 ASN* 3.6 3.7 - - - +
1172 GLU* 2.7 34.4 + - - +
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Residues in contact with GLU 114 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332 LEU* 3.5 22.9 - - + +
1102 ALA 3.4 12.5 + - - +
1112 LYS* 3.3 1.9 + - - -
1132 LYS* 1.3 78.9 - - + +
1152 LEU* 1.3 57.4 + - - +
1172 GLU* 3.3 23.0 - - - +
1182 PHE* 2.6 54.3 + - + -
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Residues in contact with LEU 115 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302 PHE* 3.5 31.4 - - + +
332 LEU* 3.4 18.3 - - + +
342 ARG* 3.4 28.5 - - - +
372 GLN* 3.2 26.0 - - + +
1112 LYS 2.6 23.8 + - - +
1122 GLY* 3.9 3.6 - - - +
1142 GLU* 1.3 72.4 - - - +
1162 ASN* 1.3 51.6 + - - +
1182 PHE* 3.0 3.0 + - - -
1192 ARG* 2.5 66.8 + - - +
----------------------------------------------------------
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Residues in contact with ASN 116 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1122 GLY 3.0 19.6 + - - +
1132 LYS* 3.8 3.4 - - - +
1152 LEU* 1.3 76.9 - - - +
1172 GLU* 1.3 63.3 + - - +
1192 ARG* 4.0 19.5 + - - +
1202 GLU* 3.1 48.8 + - - +
----------------------------------------------------------
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Residues in contact with GLU 117 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1132 LYS 2.7 22.0 + - - +
1142 GLU* 3.3 29.9 - - - +
1152 LEU 3.2 0.2 - - - -
1162 ASN* 1.3 75.0 - - - +
1182 PHE* 1.3 81.3 + - + +
1192 ARG 3.7 0.2 + - - -
1202 GLU* 3.9 11.8 + - - +
1212 LYS* 4.0 25.6 + - - +
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Residues in contact with PHE 118 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252 GLN* 5.1 12.6 - - + -
262 VAL* 4.1 7.0 - - - +
292 GLY* 3.4 29.8 - - - -
302 PHE* 3.2 31.6 - - - +
322 ARG* 4.2 10.8 - - - -
332 LEU* 3.6 19.1 - - + -
1142 GLU* 2.6 39.9 + - + +
1152 LEU 3.3 0.9 - - - +
1172 GLU* 1.3 102.6 - - + +
1192 ARG* 1.3 63.0 + - - +
1212 LYS* 4.2 21.3 + - + +
1222 HIS* 3.7 16.6 + - - -
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Residues in contact with ARG 119 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302 PHE* 3.1 44.6 - - + -
342 ARG* 4.6 7.7 - - - +
1152 LEU* 2.5 57.8 + - - +
1162 ASN* 3.3 24.1 + - - +
1182 PHE* 1.3 73.6 - - - +
1202 GLU* 1.3 65.2 + - + +
1212 LYS 3.2 0.4 - - - -
1222 HIS* 3.0 15.6 + - + +
1232 ASN* 3.1 31.8 + - - +
----------------------------------------------------------
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Residues in contact with GLU 120 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1162 ASN* 3.1 43.8 + - - +
1172 GLU* 3.9 7.2 + - - +
1182 PHE 3.5 0.2 - - - -
1192 ARG* 1.3 77.2 - - + +
1212 LYS* 1.3 58.9 + - + +
1232 ASN* 3.6 5.5 - - - +
1242 ILE* 2.9 32.1 + - - +
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Residues in contact with LYS 121 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262 VAL* 3.7 39.4 - - + +
1172 GLU* 4.0 24.1 + - - +
1182 PHE* 4.5 23.1 - - + +
1192 ARG 3.2 0.8 - - - -
1202 GLU* 1.3 77.5 - - + +
1222 HIS* 1.3 59.8 + - - +
1242 ILE* 3.2 23.7 - - - +
135 PRO* 4.7 2.8 - - - +
165 GLU* 3.6 8.0 - - - +
----------------------------------------------------------
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Residues in contact with HIS 122 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262 VAL* 2.5 41.2 + - + -
272 ILE* 3.2 15.3 - - + +
302 PHE* 3.2 30.7 - + + +
1182 PHE 3.7 4.5 - - - -
1192 ARG* 3.0 8.4 + - + +
1212 LYS* 1.3 80.0 - - - +
1232 ASN* 1.3 63.3 + - - +
1242 ILE 3.2 5.5 + - - +
135 PRO* 4.2 12.6 - - - +
165 GLU* 2.9 33.2 - - + -
175 MET* 3.6 30.2 - - + +
205 ASN* 2.8 27.8 + - - +
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Residues in contact with ASN 123 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1192 ARG* 3.1 38.5 + - - +
1202 GLU* 3.3 5.6 + - - +
1222 HIS* 1.3 75.7 - - - +
1242 ILE* 1.3 66.9 + - - +
175 MET* 3.3 34.7 - - - +
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Residues in contact with ILE 124 (chain 2).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1202 GLU 2.9 13.3 + - - +
1212 LYS* 3.2 23.8 - - - +
1222 HIS 4.2 5.7 - - - +
1232 ASN* 1.3 84.4 - - - +
135 PRO* 4.8 15.7 - - + +
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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
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Atomic class I II III IV V VI VII VIII
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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