Contacts of the helix formed by residues 113 - 144 (chain 3) 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 3).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13 MET 6.2 0.2 - - - -
23 LEU* 3.7 17.2 - - - +
33 SER 5.6 0.5 + - - -
63 MET* 3.8 10.8 - - + +
643 ARG* 4.3 8.1 + - - -
1083 ALA* 2.7 29.6 + - - +
1113 GLU* 3.2 12.9 - - + +
1123 LYS* 1.3 70.1 - - - +
1143 TYR* 1.3 63.1 + - - +
1153 SER* 3.7 13.2 + - - -
1163 THR* 2.6 28.3 + - - +
1173 ARG* 3.3 16.9 + - - +
102Y TYR* 5.3 1.2 + - - -
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Residues in contact with TYR 114 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1123 LYS* 3.4 29.2 + - + +
1133 ASP* 1.3 72.0 + - - +
1153 SER* 1.3 59.8 + - - +
1173 ARG* 3.3 8.5 + - + +
1183 ALA* 2.8 32.1 + - - +
102Y TYR* 3.5 58.8 - + + -
105Y ALA* 4.4 5.4 - - + -
106Y ALA* 3.4 19.9 - - + +
109Y GLU* 2.9 37.9 + - - -
117Y ARG* 3.9 19.7 + - - -
124Y ILE* 3.7 15.3 - - + +
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Residues in contact with SER 115 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603 TYR* 3.1 17.8 + - - -
643 ARG* 3.3 26.2 + - - -
1133 ASP* 3.3 3.3 + - - -
1143 TYR* 1.3 79.7 - - - +
1163 THR* 1.3 55.7 + - - +
1183 ALA* 3.6 2.4 + - - +
1193 PHE* 3.1 23.7 + - - +
102Y TYR* 2.8 29.4 + - - -
124Y ILE* 3.8 11.9 + - - +
125Y ASN* 5.0 0.9 - - - +
128Y VAL* 3.7 19.2 - - - +
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Residues in contact with THR 116 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23 LEU* 3.7 7.8 - - - +
63 MET* 3.9 16.6 - - + -
103 LEU* 3.9 28.0 - - + -
603 TYR* 2.8 21.5 + - + -
1083 ALA* 4.2 5.2 - - + -
1133 ASP* 2.6 32.5 + - - -
1143 TYR 3.3 0.2 - - - -
1153 SER* 1.3 72.4 - - - +
1173 ARG* 1.3 61.4 + - - +
1193 PHE* 3.2 2.6 + - + +
1203 LEU* 2.9 43.5 + - + +
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Residues in contact with ARG 117 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1142 TYR* 3.7 23.8 + - - +
1172 ARG* 5.3 9.5 - - - +
1182 ALA* 5.9 0.6 - - - +
1053 ALA* 3.8 29.1 - - - +
1083 ALA* 3.9 9.3 - - + +
1093 GLU* 3.1 32.9 + - + +
1133 ASP 3.3 11.8 + - - +
1143 TYR* 3.3 15.1 + - + +
1163 THR* 1.3 78.5 - - - +
1183 ALA* 1.3 60.4 + - - +
1203 LEU* 3.5 4.0 + - - +
1213 GLU* 2.9 39.1 + - - +
1243 ILE* 3.4 21.1 - - - +
117Y ARG* 5.4 9.0 - - - +
121Y GLU* 4.7 0.6 - - - +
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Residues in contact with ALA 118 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1143 TYR 2.8 17.6 + - - +
1153 SER 3.8 4.7 - - - +
1173 ARG* 1.3 73.4 - - - +
1193 PHE* 1.3 64.6 + - - +
1213 GLU* 3.4 15.2 - - - +
1223 TRP* 4.3 1.7 + - - +
117Y ARG* 6.1 0.4 - - - +
121Y GLU* 3.5 26.9 - - - +
124Y ILE* 3.9 15.3 - - + -
125Y ASN* 3.4 30.8 + - - +
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Residues in contact with PHE 119 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103 LEU* 4.3 2.0 - - + -
563 ARG* 3.5 29.4 - - + -
573 PHE* 3.5 37.9 - + - -
603 TYR* 3.5 45.5 - + + -
1153 SER 3.1 19.1 + - - +
1163 THR* 3.2 10.3 + - + +
1183 ALA* 1.3 77.4 - - - +
1203 LEU* 1.3 67.7 + - + +
1213 GLU 3.4 0.9 + - - -
1223 TRP* 3.6 18.8 + - + +
1233 PHE* 3.5 31.2 - + - -
125Y ASN* 4.1 5.1 + - - +
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Residues in contact with LEU 120 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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573 PHE* 4.2 22.7 - - + -
1013 ILE* 4.3 15.7 - - + -
1043 LEU* 3.5 59.0 - - + +
1053 ALA* 3.7 11.7 - - + +
1083 ALA* 4.6 0.7 - - + -
1163 THR* 2.9 36.1 + - + +
1173 ARG* 3.5 10.5 + - - +
1183 ALA 3.3 0.4 - - - -
1193 PHE* 1.3 78.6 - - + +
1213 GLU* 1.3 58.9 + - - +
1223 TRP 3.2 2.9 - - - -
1233 PHE* 3.0 23.0 + - + +
1243 ILE* 3.0 19.1 + - + +
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Residues in contact with GLU 121 (chain 3).
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* 4.8 1.7 + - - +
1182 ALA* 3.4 33.6 - - - +
1212 GLU* 4.4 17.1 - - + +
1173 ARG* 2.9 42.7 + - - +
1183 ALA 3.4 15.3 - - - +
1193 PHE 3.2 0.4 - - - -
1203 LEU* 1.3 78.0 - - - +
1223 TRP* 1.3 60.9 + - - +
1243 ILE* 3.4 7.0 + - - +
1253 ASN* 3.3 36.4 + - - +
121Y GLU* 4.3 15.8 - - + +
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Residues in contact with TRP 122 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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533 HIS* 3.7 14.4 - + - -
563 ARG* 3.4 43.7 - - - -
1183 ALA 4.3 2.1 + - - +
1193 PHE* 3.6 13.7 + - + +
1203 LEU 3.2 0.4 - - - -
1213 GLU* 1.3 79.5 - - - +
1233 PHE* 1.3 93.4 + + + +
1253 ASN* 3.5 5.9 + - - +
1263 GLU* 3.0 52.1 + - + +
11733 AG 4.0 4.9 - - - -
170L MET* 4.2 18.6 - - + -
172L GLY* 3.4 37.4 + - - +
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Residues in contact with PHE 123 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173 GLU* 3.9 10.3 - - - -
533 HIS* 3.6 34.5 - - + -
563 ARG* 3.7 18.4 - - + -
573 PHE* 3.5 26.5 - + - -
1013 ILE* 4.1 21.5 - - + -
1193 PHE* 3.5 44.2 - + - -
1203 LEU* 3.0 11.4 + - - +
1223 TRP* 1.3 95.9 - + + +
1243 ILE* 1.3 61.2 + - - +
1263 GLU* 3.6 15.8 - - - +
1273 GLN* 3.0 34.7 + - - +
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Residues in contact with ILE 124 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1142 TYR* 3.5 42.0 - - + +
1152 SER* 3.8 14.4 + - - +
1182 ALA* 3.9 8.3 - - + -
1013 ILE* 3.8 18.6 - - + +
1023 TYR* 4.5 7.6 - - + -
1053 ALA* 4.5 9.9 - - + -
1173 ARG* 3.4 39.9 - - - +
1203 LEU* 3.0 13.3 + - + +
1213 GLU* 3.8 9.6 - - - +
1223 TRP 3.4 0.2 - - - -
1233 PHE* 1.3 78.7 - - - +
1253 ASN* 1.3 60.8 + - - +
1273 GLN* 3.6 4.2 + - - +
1283 VAL* 3.3 21.7 + - - +
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Residues in contact with ASN 125 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1152 SER 4.8 1.2 - - - +
1182 ALA* 3.4 36.5 + - - +
1192 PHE* 4.1 4.5 + - - +
1213 GLU* 3.3 27.7 + - - +
1223 TRP* 3.9 5.5 - - - +
1243 ILE* 1.3 74.6 - - - +
1263 GLU* 1.3 65.3 + - - +
1283 VAL* 3.5 20.7 + - - +
1293 GLU* 3.7 11.1 + - - +
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Residues in contact with GLU 126 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173 GLU* 5.2 0.2 - - - +
533 HIS* 3.2 14.3 + - - -
1223 TRP* 3.0 42.2 + - + +
1233 PHE* 3.6 16.8 - - - +
1243 ILE 3.3 0.2 - - - -
1253 ASN* 1.3 77.9 - - - +
1273 GLN* 1.3 82.1 + - - +
1293 GLU* 3.3 7.4 + - - +
1303 GLU* 3.0 57.9 + - - +
11733 AG 3.7 12.3 - - - -
170L MET* 3.8 17.4 - - + +
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Residues in contact with GLN 127 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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642 ARG* 5.4 0.4 - - - -
173 GLU* 5.0 5.3 + - - -
503 GLU* 5.3 2.0 + - - -
533 HIS* 5.2 2.0 - - - -
943 GLU* 3.0 31.5 + - - +
973 ILE* 3.6 25.6 - - + +
983 SER* 3.1 34.1 + - - +
1013 ILE* 4.6 8.3 - - + -
1023 TYR* 6.5 0.2 - - + -
1233 PHE* 3.0 22.4 + - + +
1243 ILE* 4.0 6.1 - - - +
1253 ASN 3.4 0.2 - - - -
1263 GLU* 1.3 102.3 + - - +
1283 VAL* 1.3 59.5 + - - +
1303 GLU* 4.0 4.9 + - - +
1313 GLU* 2.9 35.9 + - - +
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Residues in contact with VAL 128 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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602 TYR* 4.2 15.5 - - + -
632 ASP* 4.2 21.1 - - + +
642 ARG* 3.9 28.4 + - - +
1152 SER* 3.9 29.2 - - - +
1243 ILE 3.3 18.4 - - - +
1253 ASN* 3.6 13.9 - - - +
1263 GLU 3.3 0.4 - - - -
1273 GLN* 1.3 77.3 - - + +
1293 GLU* 1.3 63.9 + - + +
1313 GLU* 4.1 1.8 - - - +
1323 ALA* 3.2 23.7 + - - +
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Residues in contact with GLU 129 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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632 ASP* 5.9 3.8 - - - +
1253 ASN 3.7 8.7 + - - +
1263 GLU* 3.3 10.8 + - - +
1283 VAL* 1.3 81.8 - - + +
1303 GLU* 1.3 57.7 + - + +
1323 ALA* 3.5 5.1 + - - +
1333 SER* 2.8 31.0 + - - -
170L MET* 3.3 25.9 - - + +
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Residues in contact with GLU 130 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243 TYR* 4.7 0.2 + - - -
463 GLN* 2.8 32.4 + - - +
493 GLU* 4.6 0.9 - - - +
503 GLU* 3.0 13.9 - - - +
533 HIS* 3.1 11.5 - - - -
943 GLU* 3.0 36.4 - - - +
1263 GLU* 3.0 36.1 + - + +
1273 GLN* 4.0 6.5 + - - +
1283 VAL 3.4 0.2 - - - -
1293 GLU* 1.3 79.1 - - + +
1313 GLU* 1.3 65.2 + - - +
1333 SER* 3.4 6.4 + - - -
1343 VAL* 3.1 30.9 + - + +
170L MET* 5.6 5.4 - - + +
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Residues in contact with GLU 131 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12 MET 5.7 3.1 + - - -
632 ASP 5.6 2.0 - - - +
642 ARG* 4.0 23.6 + - - +
913 TYR* 3.6 25.2 + - + -
943 GLU* 4.0 20.9 + - + +
953 LYS* 4.1 20.7 - - - +
983 SER* 2.7 34.6 + - - +
1023 TYR* 4.6 2.6 + - - -
1273 GLN 2.9 18.9 + - - +
1283 VAL* 4.1 3.8 - - - +
1303 GLU* 1.3 75.5 - - - +
1323 ALA* 1.3 59.0 + - - +
1343 VAL* 3.4 1.2 + - - -
1353 LYS* 2.9 31.1 + - - +
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Residues in contact with ALA 132 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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622 TYR 5.4 0.4 - - - +
632 ASP* 3.5 41.9 + - + +
1283 VAL 3.2 17.0 + - - +
1293 GLU* 3.8 4.3 - - - +
1313 GLU* 1.3 78.5 - - - +
1333 SER* 1.3 58.5 + - - +
1353 LYS* 4.1 5.8 - - - +
1363 LYS* 3.0 30.7 + - - +
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Residues in contact with SER 133 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423 TRP* 3.7 19.8 - - - -
463 GLN* 5.2 3.0 + - - -
1293 GLU 2.8 19.3 + - - -
1303 GLU* 3.7 10.1 - - - -
1313 GLU 3.3 0.2 - - - -
1323 ALA* 1.3 79.1 - - - +
1343 VAL* 1.3 60.3 - - - +
1363 LYS* 3.9 5.8 - - - +
1373 ILE* 3.4 26.9 + - - +
1613 ARG* 5.2 0.9 + - - -
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Residues in contact with VAL 134 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243 TYR* 4.8 7.9 - - + +
423 TRP* 4.3 19.3 - - + -
463 GLN* 5.9 2.7 - - - +
873 PHE* 3.8 25.8 - - + +
903 ALA* 4.1 5.4 - - + -
913 TYR* 3.8 37.5 - - + +
943 GLU* 4.1 16.6 - - + -
1303 GLU* 3.1 17.9 + - + +
1313 GLU 3.9 2.9 - - - +
1333 SER* 1.3 77.3 - - - +
1353 LYS* 1.3 59.3 + - - +
1363 LYS 3.3 0.2 - - - -
1373 ILE* 3.2 4.9 + - - +
1383 LEU* 2.9 25.8 + - - +
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Residues in contact with LYS 135 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12 MET* 5.4 1.6 - - - -
652 ASN* 3.3 41.7 + - + +
913 TYR* 3.6 41.2 - - + +
1313 GLU 2.9 19.8 + - - +
1323 ALA* 4.1 5.8 - - - +
1343 VAL* 1.3 74.8 - - - +
1363 LYS* 1.3 63.4 + - - +
1383 LEU* 3.5 11.1 - - + +
1393 ASP* 2.8 68.1 + - - +
1423 LYS* 5.2 6.1 - - - +
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Residues in contact with LYS 136 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1323 ALA 3.0 20.5 + - - +
1333 SER* 3.9 9.4 - - - +
1343 VAL 3.3 0.2 - - - -
1353 LYS* 1.3 77.5 - - - +
1373 ILE* 1.3 66.2 + - + +
1393 ASP* 3.8 5.6 + - - +
1403 LYS* 3.4 49.8 + - - +
37K GLU* 3.2 41.9 + - - +
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Residues in contact with ILE 137 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393 PHE* 4.6 2.5 - - + -
423 TRP* 3.6 33.7 - - + +
873 PHE* 3.7 34.5 - - + -
1333 SER* 3.4 18.2 - - - +
1343 VAL 3.2 2.5 + - - +
1363 LYS* 1.3 81.3 - - + +
1383 LEU* 1.3 65.6 - - - +
1403 LYS* 3.2 10.2 + - + +
1413 LEU* 3.1 27.5 + - + +
1543 LEU* 4.8 8.7 - - + -
1583 LEU* 3.8 31.0 - - + -
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Residues in contact with LEU 138 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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843 LEU* 4.0 3.7 - - + +
873 PHE* 3.4 41.0 - - + +
883 GLU* 3.8 25.1 - - + -
913 TYR* 3.6 30.3 - - + -
1343 VAL 2.9 15.9 + - - +
1353 LYS* 3.3 12.3 + - + +
1373 ILE* 1.3 76.3 - - - +
1393 ASP* 1.3 61.1 + - - +
1413 LEU* 3.0 7.8 + - - +
1423 LYS* 2.9 51.2 + - + +
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Residues in contact with ASP 139 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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652 ASN* 4.4 2.6 - - - +
1353 LYS* 2.8 56.5 + - - +
1363 LYS* 4.0 6.7 - - - +
1383 LEU* 1.3 75.8 - - - +
1403 LYS* 1.3 58.0 + - + +
1423 LYS* 3.3 25.2 + - - +
1433 PHE* 3.0 26.7 + - - +
35K GLY* 6.2 4.0 - - - -
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Residues in contact with LYS 140 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1363 LYS* 3.4 42.6 + - + +
1373 ILE* 3.2 13.6 + - + +
1393 ASP* 1.3 78.6 - - + +
1413 LEU* 1.3 57.3 + - - +
1433 PHE* 3.5 10.6 - - + +
1443 ALA* 3.4 19.4 + - - +
1503 ILE* 4.9 2.3 - - - +
1543 LEU* 3.7 38.8 - - + +
1573 GLU* 3.7 19.8 + - - -
35K GLY* 4.5 16.8 - - - +
37K GLU* 6.0 0.6 - - - -
152K PHE* 4.6 17.0 - - + -
155K ASP* 5.4 6.0 + - - -
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Residues in contact with LEU 141 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393 PHE* 4.1 14.8 - - + -
833 PRO* 3.4 32.5 - - + +
843 LEU* 3.8 22.9 - - + +
873 PHE* 3.6 31.2 - - + -
1373 ILE* 3.1 20.0 + - + +
1383 LEU* 3.0 8.1 + - - +
1403 LYS* 1.3 75.6 - - - +
1423 LYS* 1.3 64.2 + - - +
1433 PHE 3.1 1.1 - - - -
1443 ALA* 3.4 22.6 + - + +
1453 LYS* 4.0 2.4 + - - -
1513 LEU* 3.8 28.3 - - + -
1543 LEU* 4.3 9.4 - - + -
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Residues in contact with LYS 142 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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843 LEU* 3.6 20.8 - - + +
883 GLU* 4.8 8.5 - - - +
1353 LYS* 5.2 5.1 - - - +
1383 LEU* 2.9 28.7 + - + +
1393 ASP* 3.4 27.7 + - - +
1413 LEU* 1.3 76.3 - - - +
1433 PHE* 1.3 57.1 + - - +
1453 LYS* 2.8 43.6 - - - +
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Residues in contact with PHE 143 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1393 ASP 3.0 16.5 + - - +
1403 LYS* 3.5 12.8 - - + +
1413 LEU 3.1 0.4 - - - -
1423 LYS* 1.3 78.5 - - - +
1443 ALA* 1.3 57.1 + - - +
1453 LYS* 3.4 4.6 + - - +
1503 ILE* 4.5 15.2 - - + +
34K LEU 5.7 5.4 - - - -
36K LEU* 5.8 6.3 - - + -
148K PRO* 3.8 41.0 - - + +
151K LEU* 3.9 25.6 - - + -
152K PHE* 5.3 9.6 - + + -
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Residues in contact with ALA 144 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1403 LYS 3.4 10.4 + - - +
1413 LEU* 3.4 14.6 + - + +
1423 LYS 3.3 0.6 - - - -
1433 PHE* 1.3 75.6 - - - +
1453 LYS* 1.3 64.5 + - - +
1463 ASP 3.6 1.3 - - - -
1473 SER* 3.9 19.3 + - - +
1503 ILE* 3.6 41.5 - - + -
1513 LEU* 4.5 7.2 - - + +
1543 LEU* 5.2 2.2 - - + -
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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