Contacts of the helix formed by residues 113 - 143 (chain 5) in PDB entry 2X17
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 5).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15 MET 6.2 0.2 - - - -
25 LEU* 3.7 11.3 - - - +
35 SER 5.4 0.7 + - - -
65 MET* 3.6 20.7 - - + +
605 TYR* 4.4 0.3 + - - -
645 ARG* 4.6 6.8 + - - -
1085 ALA* 2.8 25.2 + - - +
1115 GLU* 3.2 9.3 - - + +
1125 LYS* 1.3 70.7 - - - +
1145 TYR* 1.3 60.2 + - - +
1155 SER* 3.3 11.1 + - - -
1165 THR* 2.7 33.1 + - - +
1175 ARG* 3.2 22.5 + - - +
1026 TYR* 5.1 1.6 + - - -
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Residues in contact with TYR 114 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1125 LYS* 3.3 38.8 + - + +
1135 ASP* 1.3 72.4 + - - +
1155 SER* 1.3 56.3 + - - +
1175 ARG* 3.8 8.7 - - + +
1185 ALA* 3.0 30.8 + - - +
1026 TYR* 3.6 48.1 - + + -
1056 ALA* 3.8 14.4 - - + -
1066 ALA* 3.4 25.4 - - + +
1096 GLU* 3.0 38.9 + - - -
1176 ARG* 3.6 19.9 + - - -
1246 ILE* 3.4 14.1 - - + +
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Residues in contact with SER 115 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605 TYR* 3.0 16.6 + - - -
645 ARG* 3.3 26.3 + - - -
1135 ASP* 3.2 4.4 + - - -
1145 TYR* 1.3 79.8 - - - +
1165 THR* 1.3 57.9 + - - +
1185 ALA* 3.6 2.3 + - - +
1195 PHE* 3.1 24.1 + - - +
1026 TYR* 2.5 29.9 + - - -
1246 ILE* 3.7 12.0 + - - +
1256 ASN* 5.0 1.0 - - - +
1286 VAL* 4.0 15.1 - - - +
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Residues in contact with THR 116 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25 LEU* 3.7 8.8 - - - +
65 MET* 3.8 21.7 - - - +
105 LEU* 3.9 20.6 - - + -
605 TYR* 2.8 19.8 + - + -
1085 ALA* 4.2 4.7 - - + -
1135 ASP* 2.7 32.7 + - - -
1155 SER* 1.3 74.3 - - - +
1175 ARG* 1.3 60.8 + - - +
1195 PHE* 3.2 2.1 + - + +
1205 LEU* 2.9 46.3 + - + +
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Residues in contact with ARG 117 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1141 TYR* 3.6 24.2 + - - +
1171 ARG* 5.2 10.9 - - - +
1181 ALA 6.1 0.2 - - - +
1055 ALA* 3.7 28.8 - - - +
1085 ALA* 3.8 10.6 - - + +
1095 GLU* 3.1 30.7 + - + -
1135 ASP 3.2 16.5 + - - +
1145 TYR* 3.8 10.5 - - + +
1155 SER 3.4 0.2 - - - -
1165 THR* 1.3 77.0 - - - +
1185 ALA* 1.3 61.6 + - - +
1205 LEU* 3.5 3.9 + - - +
1215 GLU* 2.9 38.8 + - - +
1245 ILE* 3.5 18.8 - - - +
1176 ARG* 5.1 11.7 - - - +
1216 GLU* 5.6 0.8 + - - -
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Residues in contact with ALA 118 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1145 TYR 3.0 19.0 + - - +
1155 SER 3.9 2.0 - - - +
1175 ARG* 1.3 74.0 - - - +
1195 PHE* 1.3 63.4 + - - +
1215 GLU* 3.4 15.1 - - - +
1225 TRP* 4.4 1.4 + - - +
1176 ARG* 5.8 0.6 - - - +
1216 GLU* 3.4 32.3 - - - +
1246 ILE* 3.8 16.6 - - + -
1256 ASN* 3.5 27.2 + - - +
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Residues in contact with PHE 119 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105 LEU* 4.2 4.3 - - + -
565 ARG* 3.6 28.7 - - + -
575 PHE* 3.5 36.6 - + - -
605 TYR* 3.6 46.4 - + + -
1155 SER 3.1 18.4 + - - +
1165 THR 3.2 6.7 + - - +
1185 ALA* 1.3 76.9 - - - +
1205 LEU* 1.3 69.1 + - + +
1215 GLU 3.2 1.0 + - - -
1225 TRP* 3.5 18.6 + - + +
1235 PHE* 3.5 31.7 - + - -
1256 ASN* 4.1 6.9 + - - +
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Residues in contact with LEU 120 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105 LEU* 5.2 0.7 - - + -
575 PHE* 4.1 22.2 - - + -
1015 ILE* 4.4 14.3 - - + +
1045 LEU* 3.6 60.8 - - + +
1055 ALA* 3.7 8.7 - - + +
1085 ALA* 4.5 0.2 - - + -
1165 THR* 2.9 36.0 + - + +
1175 ARG* 3.5 7.6 + - - +
1185 ALA 3.4 0.2 - - - -
1195 PHE* 1.3 79.4 - - + +
1215 GLU* 1.3 59.9 + - - +
1225 TRP 3.2 1.1 - - - -
1235 PHE* 2.9 23.1 + - + +
1245 ILE* 3.0 24.1 + - + +
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Residues in contact with GLU 121 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1171 ARG* 4.9 1.6 + - - +
1181 ALA* 3.7 28.5 - - - +
1211 GLU* 4.3 23.0 - - + +
1175 ARG* 2.9 39.7 + - - +
1185 ALA 3.4 15.3 - - - +
1195 PHE 3.2 0.4 - - - -
1205 LEU* 1.3 78.0 - - - +
1225 TRP* 1.3 61.5 + - - +
1245 ILE* 3.4 11.3 + - - +
1255 ASN* 3.0 38.5 + - - +
1216 GLU* 4.1 15.3 - - + +
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Residues in contact with TRP 122 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535 HIS* 3.3 39.7 - + - -
565 ARG* 3.4 53.9 - - - +
1185 ALA 4.4 1.4 + - - +
1195 PHE* 3.5 13.1 + - + +
1205 LEU 3.2 0.6 - - - -
1215 GLU* 1.3 78.2 - - - +
1235 PHE* 1.3 78.6 + + + +
1255 ASN* 3.5 6.9 + - + +
1265 GLU* 2.9 39.2 + - + +
11735 AG 4.0 4.0 - - - -
170N MET* 4.2 21.8 - - + -
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Residues in contact with PHE 123 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175 GLU* 4.2 8.3 - - - -
535 HIS* 3.4 42.2 - - + -
565 ARG* 3.7 18.8 - - + -
575 PHE* 3.4 33.4 - + - -
1015 ILE* 4.1 20.6 - - + -
1195 PHE* 3.5 42.0 - + - -
1205 LEU* 2.9 11.0 + - - +
1225 TRP* 1.3 87.3 - + + +
1245 ILE* 1.3 58.8 + - - +
1265 GLU* 3.4 17.6 - - - +
1275 GLN* 3.0 35.3 + - - +
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Residues in contact with ILE 124 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1141 TYR* 3.5 44.2 - - + +
1151 SER* 3.8 12.7 + - - +
1181 ALA* 3.8 7.6 - - + -
1015 ILE* 3.8 18.6 - - + -
1025 TYR* 4.4 6.7 - - + -
1055 ALA* 4.4 11.0 - - + -
1175 ARG* 3.5 36.1 - - - +
1205 LEU 3.0 14.8 + - - +
1215 GLU* 3.4 12.8 + - - +
1235 PHE* 1.3 75.9 - - - +
1255 ASN* 1.3 61.5 + - - +
1275 GLN* 3.7 4.2 + - - +
1285 VAL* 3.3 22.6 + - - +
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Residues in contact with ASN 125 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1151 SER 5.2 0.5 - - - +
1181 ALA* 3.6 32.2 + - - +
1191 PHE* 4.2 3.5 + - - -
1215 GLU* 3.0 39.1 + - - +
1225 TRP* 3.8 7.4 - - + +
1245 ILE* 1.3 75.9 - - - +
1265 GLU* 1.3 62.5 + - - +
1285 VAL* 3.6 18.8 + - - +
1295 GLU* 3.8 9.7 + - - +
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Residues in contact with GLU 126 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535 HIS* 3.4 31.4 + - + +
1225 TRP* 2.9 27.8 + - + +
1235 PHE* 3.4 31.8 - - - +
1245 ILE 3.4 0.2 - - - -
1255 ASN* 1.3 77.0 - - - +
1275 GLN* 1.3 85.1 + - - +
1295 GLU* 3.1 8.7 + - - +
1305 GLU* 3.0 44.9 + - - +
170N MET* 3.8 23.2 - - + +
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Residues in contact with GLN 127 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
641 ARG* 5.2 0.7 - - - -
175 GLU* 4.8 6.7 + - - -
505 GLU* 5.1 2.6 + - - -
945 GLU* 3.0 32.3 + - - +
975 ILE* 3.5 28.9 - - + +
985 SER* 3.0 31.2 + - - +
1015 ILE* 4.6 8.7 - - + -
1025 TYR* 6.1 0.4 - - - +
1235 PHE* 3.0 21.1 + - + +
1245 ILE* 4.1 5.6 - - - +
1255 ASN 3.4 0.2 - - - -
1265 GLU* 1.3 100.2 + - - +
1285 VAL* 1.3 60.4 + - - +
1295 GLU 3.3 0.2 - - - -
1305 GLU* 3.8 5.1 + - - +
1315 GLU* 3.0 35.1 + - - +
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Residues in contact with VAL 128 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601 TYR* 4.1 17.0 - - + -
631 ASP* 4.2 15.1 - - + +
641 ARG* 3.9 29.1 + - - +
1151 SER* 3.7 35.0 - - - +
1245 ILE 3.3 18.6 + - - +
1255 ASN* 3.6 11.9 - - - +
1265 GLU 3.2 0.6 - - - -
1275 GLN* 1.3 77.8 - - - +
1295 GLU* 1.3 62.6 + - + +
1315 GLU* 4.1 1.9 - - - +
1325 ALA* 3.2 23.2 + - - +
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Residues in contact with GLU 129 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
631 ASP* 5.5 7.0 - - - +
1255 ASN 3.8 7.5 + - - +
1265 GLU* 3.1 9.9 + - - +
1285 VAL* 1.3 79.8 - - + +
1305 GLU* 1.3 55.2 + - + +
1325 ALA* 3.4 5.7 + - - +
1335 SER* 2.8 36.0 + - - -
170N MET* 3.4 25.4 - - + +
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Residues in contact with GLU 130 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465 GLN* 3.2 23.3 + - - +
495 GLU* 4.6 0.7 - - - +
505 GLU* 2.9 21.4 - - - +
535 HIS* 3.0 28.4 + - - -
945 GLU* 2.9 31.1 - - - +
1265 GLU* 3.0 30.4 + - + +
1275 GLN* 3.6 4.6 + - - +
1285 VAL 3.4 0.2 - - - -
1295 GLU* 1.3 74.3 - - + +
1315 GLU* 1.3 59.2 + - - +
1335 SER* 3.4 5.5 + - - -
1345 VAL* 3.1 35.7 + - + +
11735 AG 4.0 1.7 - - - -
170N MET* 5.3 6.1 - - + -
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Residues in contact with GLU 131 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11 MET 5.2 5.5 + - - -
631 ASP 5.0 2.5 - - - +
641 ARG* 3.7 25.6 + - - +
915 TYR* 3.6 23.0 + - + -
945 GLU* 3.6 25.5 - - + +
955 LYS* 4.0 22.3 - - - +
985 SER* 2.7 32.3 + - - +
1025 TYR* 5.0 0.9 + - - -
1275 GLN 3.0 18.1 + - - +
1285 VAL 4.1 3.1 - - - +
1305 GLU* 1.3 74.8 - - - +
1325 ALA* 1.3 58.4 + - - +
1345 VAL* 3.5 0.5 + - - -
1355 LYS* 2.9 32.0 + - - +
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Residues in contact with ALA 132 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621 TYR 5.3 0.4 - - - +
631 ASP* 3.4 47.9 + - + +
1285 VAL 3.2 13.6 + - - +
1295 GLU* 3.7 4.9 - - - +
1315 GLU* 1.3 78.3 - - - +
1335 SER* 1.3 58.3 + - - +
1355 LYS* 4.1 5.1 - - - +
1365 LYS* 3.1 30.5 + - - +
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Residues in contact with SER 133 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425 TRP* 3.5 21.7 - - - -
465 GLN* 5.2 3.0 + - - -
1295 GLU 2.8 19.1 + - - -
1305 GLU* 3.6 9.2 - - - -
1325 ALA* 1.3 78.6 - - - +
1345 VAL* 1.3 62.2 + - - +
1365 LYS* 3.7 7.2 + - - +
1375 ILE* 3.6 25.6 + - - +
1615 ARG* 4.9 2.1 + - - -
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Residues in contact with VAL 134 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245 TYR* 4.9 7.4 - - + +
425 TRP* 4.3 19.7 - - + -
465 GLN* 5.6 4.0 - - - +
875 PHE* 3.7 28.3 - - + +
905 ALA* 4.1 6.3 - - + -
915 TYR* 3.8 37.7 - - + +
945 GLU* 4.2 17.5 - - + -
1305 GLU* 3.1 17.0 + - + +
1315 GLU 4.1 2.2 - - - +
1335 SER* 1.3 74.8 - - - +
1355 LYS* 1.3 60.0 + - - +
1375 ILE 3.3 1.9 + - - -
1385 LEU* 2.9 25.5 + - - +
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Residues in contact with LYS 135 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11 MET* 5.4 1.8 - - - -
651 ASN* 3.4 41.1 + - + +
915 TYR* 3.5 41.7 - - + +
1315 GLU 2.9 19.8 + - - +
1325 ALA* 4.1 5.8 - - - +
1345 VAL* 1.3 75.0 - - - +
1365 LYS* 1.3 60.1 + - - +
1385 LEU* 3.5 11.9 - - + +
1395 ASP* 2.7 73.8 + - - +
1425 LYS* 5.4 4.4 - - - +
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Residues in contact with LYS 136 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1325 ALA 3.1 19.1 + - - +
1335 SER* 3.8 9.2 - - - +
1345 VAL 3.3 0.4 - - - -
1355 LYS* 1.3 78.0 - - - +
1375 ILE* 1.3 63.2 + - + +
1395 ASP* 3.8 6.3 + - - +
1405 LYS* 3.4 49.1 + - - +
35J GLY* 6.1 1.1 - - - +
37J GLU* 3.0 42.7 + - + +
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Residues in contact with ILE 137 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395 PHE* 4.3 7.9 - - + -
425 TRP* 3.6 38.4 - - + +
875 PHE* 3.7 36.1 - - + -
1335 SER* 3.6 11.9 - - - +
1345 VAL 3.3 2.1 + - - +
1355 LYS 3.3 0.2 - - - -
1365 LYS* 1.3 80.0 - - + +
1385 LEU* 1.3 65.2 + - - +
1405 LYS* 3.2 9.6 + - + +
1415 LEU* 3.0 25.6 + - + +
1545 LEU* 4.8 9.4 - - + -
1585 LEU* 3.8 32.5 - - + -
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Residues in contact with LEU 138 (chain 5).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
845 LEU* 3.9 3.9 - - + +
875 PHE* 3.4 37.6 - - + +
885 GLU* 3.8 24.0 - - + -
915 TYR* 3.6 30.1 - - + -
1345 VAL 2.9 16.3 + - - +
1355 LYS* 3.3 13.0 + - + +
1375 ILE* 1.3 75.9 - - - +
1395 ASP* 1.3 62.6 + - - +
1415 LEU* 3.0 8.2 + - - +
1425 LYS* 3.0 54.7 + - + +
----------------------------------------------------------
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Residues in contact with ASP 139 (chain 5).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
651 ASN* 4.3 4.3 - - - +
1355 LYS* 2.7 55.9 + - - +
1365 LYS* 4.0 6.9 - - - +
1385 LEU* 1.3 82.1 - - - +
1405 LYS* 1.3 56.8 + - + +
1425 LYS* 3.4 16.8 + - - +
1435 PHE* 3.0 27.0 + - - +
34J LEU 6.0 1.3 - - - +
35J GLY* 6.0 5.2 - - - -
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Residues in contact with LYS 140 (chain 5).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1365 LYS* 3.4 38.7 + - + +
1375 ILE* 3.2 13.6 + - + +
1385 LEU 3.2 0.2 - - - -
1395 ASP* 1.3 77.3 - - + +
1415 LEU* 1.3 59.0 + - - +
1435 PHE* 3.3 13.2 + - + +
1445 ALA* 3.2 25.3 + - - +
1505 ILE* 5.1 1.0 - - - +
1545 LEU* 3.7 36.2 - - + +
1575 GLU* 3.4 23.4 + - - -
35J GLY* 4.5 17.5 - - - +
37J GLU* 6.4 0.2 - - - -
152J PHE* 4.8 15.1 - - + -
155J ASP* 5.5 6.3 + - - -
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Residues in contact with LEU 141 (chain 5).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395 PHE* 4.1 13.2 - - + -
835 PRO* 3.4 33.7 - - + +
845 LEU* 3.8 22.9 - - + +
875 PHE* 3.6 31.0 - - + -
1375 ILE* 3.0 24.2 + - + +
1385 LEU* 3.0 7.1 + - - +
1405 LYS* 1.3 75.2 - - - +
1425 LYS* 1.3 61.9 + - - +
1435 PHE 3.2 0.2 - - - -
1445 ALA* 3.3 23.3 + - + +
1455 LYS* 3.8 3.3 + - - -
1515 LEU* 3.8 29.6 - - + -
1545 LEU* 4.4 7.0 - - + -
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Residues in contact with LYS 142 (chain 5).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
845 LEU* 3.7 20.4 - - + -
885 GLU* 4.3 12.3 - - - -
1355 LYS* 5.4 4.0 - - - +
1385 LEU* 3.0 30.7 + - + +
1395 ASP* 3.5 19.6 + - - +
1415 LEU* 1.3 75.0 - - - +
1435 PHE* 1.3 62.2 + - - +
1455 LYS* 3.3 36.4 - - - +
----------------------------------------------------------
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Residues in contact with PHE 143 (chain 5).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1395 ASP 3.0 14.1 + - - +
1405 LYS* 3.4 18.4 - - + +
1415 LEU 3.2 0.2 - - - -
1425 LYS* 1.3 76.2 - - - +
1445 ALA* 1.3 57.4 + - - +
1455 LYS 3.7 1.2 + - - -
1505 ILE* 4.5 16.1 - - + +
34J LEU* 5.1 15.0 - - + -
36J LEU* 5.0 12.1 - - + -
148J PRO* 4.0 34.9 - - + +
151J LEU* 3.7 30.1 - - + -
152J PHE* 5.0 14.4 - + + -
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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