Contacts of the helix formed by residues 113 - 145 (chain 2) in PDB entry 2JD6
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 ASP 113 (chain 2).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12 MET 4.2 10.3 - - - +
22 LEU* 3.9 7.1 - - - +
62 MET* 3.4 16.3 - - + +
602 TYR* 4.4 0.3 + - - -
642 ARG* 4.9 2.3 + - - -
1082 ALA* 3.0 20.5 + - - +
1112 GLU* 3.1 14.2 - - + +
1122 LYS* 1.3 72.7 - - - +
1142 TYR* 1.3 63.1 + - - +
1152 SER* 3.5 9.4 + - - -
1162 THR* 2.5 39.9 + - - -
1172 ARG* 3.0 23.2 + - - +
1023 TYR* 5.2 0.9 + - - -
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Residues in contact with TYR 114 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1122 LYS* 3.1 33.7 + - + +
1132 ASP* 1.3 72.0 + - - +
1152 SER* 1.3 56.7 + - - +
1172 ARG* 3.4 5.7 + - + +
1182 ALA* 2.8 33.3 + - - +
1023 TYR* 3.4 58.8 - + + -
1053 ALA* 3.7 17.5 - - + -
1063 ALA* 3.3 22.9 - - + +
1093 GLU* 3.1 34.2 + - - -
1173 ARG* 3.9 18.1 + - - -
1243 ILE* 3.8 10.9 - - + +
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Residues in contact with SER 115 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
602 TYR* 3.2 13.6 + - - -
642 ARG* 3.6 14.8 + - - -
1132 ASP* 3.3 3.9 + - - -
1142 TYR* 1.3 78.7 - - - +
1162 THR* 1.3 56.8 + - - +
1182 ALA* 3.8 2.1 - - - +
1192 PHE* 3.1 25.1 + - - +
1023 TYR* 2.6 28.5 + - - -
1243 ILE* 3.7 14.7 + - - +
1253 ASN* 5.0 1.2 - - - +
1273 GLN* 5.8 1.0 - - - +
1283 VAL* 3.4 30.0 + - - +
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Residues in contact with THR 116 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22 LEU* 3.8 6.8 - - - +
62 MET* 3.9 21.7 - - - +
102 LEU* 4.2 16.6 - - + -
602 TYR* 2.8 27.7 + - + -
1082 ALA* 4.1 4.5 - - + -
1132 ASP* 2.5 33.0 + - - -
1152 SER* 1.3 72.7 - - - +
1172 ARG* 1.3 67.2 + - - +
1182 ALA 3.1 1.3 - - - -
1192 PHE* 3.1 2.9 + - + +
1202 LEU* 3.0 39.1 + - + +
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Residues in contact with ARG 117 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1052 ALA* 3.7 28.8 - - - +
1082 ALA* 3.4 17.3 - - + +
1092 GLU* 3.0 33.3 + - + +
1132 ASP 3.0 13.3 + - - +
1142 TYR* 3.9 5.8 - - + +
1162 THR* 1.3 78.1 - - - +
1182 ALA* 1.3 63.2 + - - +
1202 LEU* 3.3 9.9 + - - +
1212 GLU* 2.6 34.8 + - - +
1242 ILE* 3.4 17.9 - - - +
1173 ARG* 5.9 4.7 - - - +
1213 GLU* 5.6 0.4 + - - -
114Y TYR* 3.6 23.2 + - - +
117Y ARG* 5.5 8.5 - - - +
118Y ALA* 5.9 1.0 - - - +
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Residues in contact with ALA 118 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1142 TYR 2.8 18.7 + - - +
1152 SER 3.8 3.6 - - - +
1162 THR 3.1 0.2 - - - -
1172 ARG* 1.3 79.5 - - - +
1192 PHE* 1.3 60.4 + - - +
1212 GLU* 3.2 20.2 - - - +
1222 TRP 4.4 0.5 + - - -
1173 ARG* 5.8 1.1 - - - +
1213 GLU* 3.3 31.8 - - - +
1243 ILE* 4.0 13.2 - - + -
1253 ASN* 3.6 23.5 + - - +
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Residues in contact with PHE 119 (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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102 LEU* 4.3 2.7 - - + -
562 ARG* 3.5 18.2 - - + -
572 PHE* 3.7 30.7 - + - -
602 TYR* 3.4 60.8 - + + -
1152 SER 3.1 16.7 + - - +
1162 THR* 3.1 8.5 + - + +
1182 ALA* 1.3 75.2 - - - +
1202 LEU* 1.3 73.8 - - + +
1212 GLU 3.2 1.3 + - - -
1222 TRP* 3.6 18.0 + - + +
1232 PHE* 3.7 27.3 - + - -
1253 ASN* 4.2 6.0 + - - +
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Residues in contact with LEU 120 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102 LEU* 4.7 2.0 - - + -
572 PHE* 4.0 10.3 - - + -
1012 ILE* 4.3 13.9 - - + +
1042 LEU* 3.6 35.7 - - + +
1052 ALA* 3.5 34.8 - - + +
1082 ALA* 4.5 0.2 - - + -
1162 THR* 3.0 33.6 + - + +
1172 ARG* 3.7 9.6 - - - +
1182 ALA 3.2 0.4 - - - -
1192 PHE* 1.3 94.4 - - + +
1212 GLU* 1.3 65.8 + - - +
1222 TRP 3.2 2.2 - - - -
1232 PHE* 3.0 9.4 + - + +
1242 ILE* 2.9 25.1 + - + +
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Residues in contact with GLU 121 (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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1172 ARG* 2.6 44.5 + - - +
1182 ALA 3.2 16.5 + - - +
1192 PHE 3.2 0.4 - - - -
1202 LEU* 1.3 79.3 - - - +
1222 TRP* 1.3 62.6 + - - +
1242 ILE* 3.1 8.9 + - - +
1252 ASN* 2.9 35.8 + - - +
1213 GLU* 4.6 13.6 - - + +
118Y ALA* 3.9 20.1 - - - +
121Y GLU* 3.7 26.3 - - + +
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Residues in contact with TRP 122 (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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532 HIS* 3.8 14.8 - + - -
562 ARG* 3.5 50.3 - - - +
1182 ALA 4.4 0.6 + - - -
1192 PHE* 3.6 13.0 + - + +
1212 GLU* 1.3 79.2 - - - +
1232 PHE* 1.3 94.8 + + + +
1252 ASN* 3.4 6.0 + - + +
1262 GLU* 2.8 62.9 + - + -
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Residues in contact with PHE 123 (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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172 GLU* 4.5 4.7 - - - -
532 HIS* 3.8 23.1 - + + -
562 ARG* 3.7 22.2 - - + -
572 PHE* 3.3 37.9 - + - -
1012 ILE* 3.9 25.8 - - + -
1192 PHE* 3.7 40.4 - + - -
1202 LEU* 3.0 10.2 + - - +
1222 TRP* 1.3 105.2 - + + +
1242 ILE* 1.3 65.2 + - - +
1262 GLU* 3.9 2.9 - - + +
1272 GLN* 2.9 37.2 + - + +
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Residues in contact with ILE 124 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1012 ILE* 4.0 16.4 - - + -
1022 TYR* 4.6 8.9 - - + -
1052 ALA* 4.5 8.3 - - + -
1172 ARG* 3.4 39.0 - - - +
1202 LEU 2.9 17.0 + - - +
1212 GLU* 3.1 11.8 + - - +
1232 PHE* 1.3 78.0 - - - +
1252 ASN* 1.3 64.5 + - - +
1272 GLN* 3.2 10.6 + - - +
1282 VAL* 3.5 13.5 + - - +
114Y TYR* 3.8 22.4 - - + +
115Y SER* 3.7 23.5 + - - +
118Y ALA* 3.7 22.4 - - + -
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Residues in contact with ASN 125 (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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1212 GLU* 2.9 36.6 + - - +
1222 TRP* 3.8 6.3 - - + +
1242 ILE* 1.3 76.6 - - - +
1262 GLU* 1.3 61.5 + - - +
1282 VAL* 3.4 23.0 - - - +
1292 GLU* 3.6 11.9 + - - +
115Y SER 4.7 1.2 - - - +
118Y ALA* 3.4 31.0 + - - +
119Y PHE* 4.2 3.5 + - - -
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Residues in contact with GLU 126 (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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492 GLU* 3.1 11.1 - - - +
532 HIS* 3.6 24.2 - - + +
1222 TRP* 2.8 53.8 + - + +
1232 PHE* 3.9 5.4 - - + +
1242 ILE 3.4 0.2 - - - -
1252 ASN* 1.3 72.0 - - - +
1272 GLN* 1.3 66.7 + - - +
1292 GLU* 2.9 33.9 + - - +
1302 GLU* 2.7 36.6 + - + +
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Residues in contact with GLN 127 (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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172 GLU* 5.2 1.0 + - - -
532 HIS* 4.5 3.4 - - - -
942 GLU* 3.2 32.0 + - - +
972 ILE* 3.6 22.6 - - - +
982 SER* 3.3 34.2 + - - +
1012 ILE* 4.5 9.8 - - + +
1022 TYR* 5.9 2.7 - - + +
1232 PHE* 2.9 30.4 + - - +
1242 ILE* 3.2 5.1 + - - +
1262 GLU* 1.3 71.1 - - - +
1282 VAL* 1.3 67.9 + - - +
1302 GLU* 2.9 10.3 + - - +
1312 GLU* 2.8 31.0 + - - +
2012 FE 3.6 17.0 - - - -
64Y ARG* 5.6 0.2 - - - -
115Y SER* 6.2 0.2 - - - +
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Residues in contact with VAL 128 (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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1242 ILE 3.5 13.4 + - - +
1252 ASN* 3.4 13.5 - - - +
1272 GLN* 1.3 78.0 - - + +
1292 GLU* 1.3 65.8 + - + +
1312 GLU* 4.0 1.2 - - - +
1322 ALA* 3.1 22.9 + - - +
60Y TYR* 4.2 20.0 - - + -
63Y ASP* 4.1 27.6 - - + +
64Y ARG* 4.2 18.3 + - - +
115Y SER* 3.7 33.2 - - - +
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Residues in contact with GLU 129 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1252 ASN* 3.6 10.7 + - - +
1262 GLU* 2.9 29.9 + - - +
1282 VAL* 1.3 80.0 - - + +
1302 GLU* 1.3 65.9 + - - +
1322 ALA* 3.1 6.9 + - - +
1332 SER* 2.9 25.7 + - - -
63Y ASP* 6.1 2.7 - - - +
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Residues in contact with GLU 130 (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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462 GLN* 2.7 31.0 + - - +
492 GLU* 2.7 31.9 - - - +
502 GLU* 4.3 0.7 - - - -
532 HIS* 3.4 12.7 - - - -
942 GLU* 3.0 26.3 - - - +
1262 GLU* 2.7 28.3 + - + +
1272 GLN* 2.9 20.0 + - - +
1292 GLU* 1.3 76.1 - - - +
1312 GLU* 1.3 64.0 + - - +
1332 SER* 3.1 8.7 + - - -
1342 VAL* 2.9 29.1 + - - +
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Residues in contact with GLU 131 (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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912 TYR* 3.9 11.3 - - + -
942 GLU* 4.0 26.0 + - + -
952 LYS* 4.1 17.9 - - - +
982 SER* 2.6 32.6 + - - +
1022 TYR* 4.6 2.8 + - - -
1272 GLN* 2.8 18.8 + - - +
1282 VAL 4.0 2.7 - - - +
1302 GLU* 1.3 73.1 - - - +
1322 ALA* 1.3 53.4 + - - +
1342 VAL* 3.2 3.3 + - - +
1352 LYS* 2.6 38.4 + - - +
1Y MET* 3.2 39.8 - - + +
64Y ARG* 3.3 13.5 + - - +
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Residues in contact with ALA 132 (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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1282 VAL 3.1 18.0 + - - +
1292 GLU* 3.5 5.8 - - - +
1312 GLU* 1.3 78.4 - - - +
1332 SER* 1.3 58.0 + - - +
1352 LYS* 3.3 6.4 + - - +
1362 LYS* 2.8 30.9 + - - +
1Y MET* 5.6 0.2 - - - -
63Y ASP* 3.7 40.7 + - + +
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Residues in contact with SER 133 (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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422 TRP* 4.9 14.1 - - - -
462 GLN* 5.4 2.1 + - - -
1292 GLU 2.9 16.0 + - - -
1302 GLU* 3.1 16.3 + - - -
1322 ALA* 1.3 69.2 - - - +
1342 VAL* 1.3 66.9 + - - +
1362 LYS* 3.9 8.7 - - - +
1372 ILE* 3.3 29.3 + - - +
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Residues in contact with VAL 134 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242 TYR* 5.2 3.8 - - + +
422 TRP* 4.1 22.7 - - + -
462 GLN* 5.4 4.7 - - - +
872 PHE* 3.8 14.3 - - + +
902 ALA* 4.0 15.5 - - + +
912 TYR* 3.5 44.0 - - + +
942 GLU* 4.2 16.8 - - + -
1302 GLU* 2.9 20.1 + - - +
1312 GLU 3.7 2.7 - - - +
1332 SER* 1.3 79.7 + - - +
1352 LYS* 1.3 62.8 + - - +
1372 ILE 3.4 0.2 + - - -
1382 LEU* 3.1 20.8 + - + +
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Residues in contact with LYS 135 (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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912 TYR* 3.6 45.1 - - + +
1312 GLU 2.6 21.7 + - - +
1322 ALA* 3.6 6.5 - - - +
1342 VAL* 1.3 71.7 - - - +
1362 LYS* 1.3 66.6 + - - +
1382 LEU* 3.3 13.9 + - + +
1392 ASP* 2.4 67.3 + - - +
1422 LYS* 5.5 3.4 - - - +
1Y MET* 5.3 2.2 - - + -
65Y ASN* 4.2 28.8 + - + +
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Residues in contact with LYS 136 (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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1322 ALA 2.8 21.9 + - - +
1332 SER* 3.3 8.9 + - - +
1352 LYS* 1.3 73.4 - - - +
1372 ILE* 1.3 62.2 + - + +
1392 ASP* 3.8 6.5 + - - +
1402 LYS* 3.0 52.3 + - + +
37G GLU* 3.0 43.0 + - - +
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Residues in contact with ILE 137 (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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392 PHE* 4.5 7.2 - - + -
422 TRP* 3.6 41.5 - - + +
872 PHE* 3.4 36.6 - - + -
1332 SER* 3.3 11.5 + - - +
1342 VAL 4.0 1.6 - - - +
1352 LYS 3.1 0.6 - - - -
1362 LYS* 1.3 79.1 - - + +
1382 LEU* 1.3 66.0 + - - +
1402 LYS* 2.9 24.7 + - - +
1412 LEU* 3.1 13.6 + - + +
1542 LEU* 4.9 6.7 - - + -
1582 LEU* 3.9 28.9 - - + -
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Residues in contact with LEU 138 (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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842 LEU* 3.7 9.2 - - + +
872 PHE* 3.9 18.5 - - + +
882 GLU* 4.0 26.9 - - + +
912 TYR* 3.9 40.6 - - + -
1342 VAL 3.1 16.6 + - - +
1352 LYS* 3.6 12.1 - - + +
1372 ILE* 1.3 74.9 - - - +
1392 ASP* 1.3 72.1 + - - +
1412 LEU* 3.2 9.4 + - - +
1422 LYS* 3.1 47.5 + - + +
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Residues in contact with ASP 139 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1352 LYS* 2.4 54.5 + - - +
1362 LYS* 3.9 8.3 - - - +
1382 LEU* 1.3 81.6 - - - +
1402 LYS* 1.3 58.3 + - + +
1422 LYS* 3.1 13.4 + - - +
1432 PHE* 2.9 28.2 + - - +
35G GLY* 5.9 6.2 - - - -
65Y ASN* 5.0 2.3 - - - +
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Residues in contact with LYS 140 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1362 LYS* 3.0 48.3 - - + +
1372 ILE* 2.9 15.0 + - - +
1392 ASP* 1.3 73.2 - - + +
1412 LEU* 1.3 53.2 + - - +
1432 PHE* 3.1 18.9 + - + +
1442 ALA* 2.7 35.8 + - - +
1502 ILE* 4.8 0.9 - - + +
1542 LEU* 4.0 26.9 - - + -
1572 GLU* 3.4 27.7 + - - -
1582 LEU* 6.1 0.4 - - - -
35G GLY 5.1 10.4 + - - +
152G PHE* 4.8 13.8 - - + -
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Residues in contact with LEU 141 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392 PHE* 4.1 8.5 - - + -
832 PRO* 3.4 37.0 - - + +
842 LEU* 3.7 20.3 - - + +
872 PHE* 3.9 25.6 - - + -
1372 ILE* 3.1 11.0 + - + +
1382 LEU 3.2 8.5 + - - +
1402 LYS* 1.3 77.7 - - - +
1422 LYS* 1.3 56.7 + - - +
1442 ALA* 3.3 8.6 + - + +
1452 LYS* 3.0 22.3 + - - -
1512 LEU* 3.6 31.9 - - + -
1542 LEU* 3.6 18.8 - - + -
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Residues in contact with LYS 142 (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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842 LEU* 3.6 24.8 - - + +
882 GLU* 4.3 13.7 - - - -
1352 LYS* 5.5 2.6 - - - +
1382 LEU* 3.1 30.4 + - + +
1392 ASP* 3.1 17.8 + - - +
1412 LEU* 1.3 70.2 - - - +
1432 PHE* 1.3 58.3 + - - +
1442 ALA 2.9 4.3 - - - -
1452 LYS* 2.8 34.8 + - - +
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Residues in contact with PHE 143 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1392 ASP 2.9 14.3 + - - +
1402 LYS* 3.4 18.4 - - + +
1422 LYS* 1.3 75.6 - - - +
1442 ALA* 1.3 57.1 + - - +
1452 LYS* 5.0 0.9 - - - +
1502 ILE* 4.4 10.1 - - + +
34G LEU 5.8 3.8 - - - -
36G LEU* 5.1 9.0 - - + -
148G PRO* 3.7 48.6 - - + +
151G LEU* 4.1 23.1 - - + -
152G PHE* 4.0 34.5 - + + -
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Residues in contact with ALA 144 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1402 LYS 2.7 15.1 + - - +
1412 LEU* 3.4 13.9 - - + +
1422 LYS 2.9 0.4 - - - -
1432 PHE* 1.3 80.4 - - - +
1452 LYS* 1.3 52.4 + - - +
1462 ASP 2.6 20.0 + - - -
1472 SER* 2.8 24.3 + - - +
1502 ILE* 3.5 36.3 - - + -
1512 LEU* 4.5 6.1 - - + +
1542 LEU* 5.4 0.2 - - + -
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Residues in contact with LYS 145 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
842 LEU* 6.5 0.9 - - - -
1412 LEU 3.0 10.3 + - - -
1422 LYS* 2.8 23.2 + - - +
1432 PHE 4.9 1.1 - - - -
1442 ALA* 1.3 66.7 - - - +
1462 ASP* 1.3 82.2 + - + +
1472 SER 3.6 2.3 + - - -
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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) + - + + + + + -
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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