Contacts of the helix formed by residues 1232 - 1263 (chain B) in PDB entry 1KI1
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 THR1232 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1230B MET 5.2 1.6 - - - +
1231B LEU* 1.3 75.0 - - - +
1233B PRO* 1.3 77.9 - - - +
1234B THR* 3.0 7.9 + - - -
1235B GLU* 2.6 47.4 + - - +
1236B ARG* 2.9 20.6 + - - +
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Residues in contact with PRO1233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1231B LEU 4.7 0.4 - - - +
1232B THR* 1.3 88.0 - - + +
1234B THR* 1.3 57.7 + - - +
1236B ARG* 3.5 8.0 + - + +
1237B LYS* 3.0 34.7 + - + +
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Residues in contact with THR1234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1232B THR* 3.1 7.0 + - - -
1233B PRO* 1.3 79.2 - - - +
1235B GLU* 1.3 69.0 + - + +
1237B LYS* 3.2 6.1 + - - +
1238B ARG* 3.1 17.8 + - - +
1394B GLU 5.1 0.9 - - - +
1395B ASN* 3.6 44.0 + - - +
1397B PRO* 5.4 4.7 - - + -
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Residues in contact with GLU1235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1230B MET 3.5 5.6 - - - +
1231B LEU* 3.2 24.6 - - + +
1232B THR* 2.6 48.7 + - - +
1234B THR* 1.3 79.9 - - + +
1236B ARG* 1.3 63.1 + - - +
1238B ARG* 3.3 10.9 + - - +
1239B GLN* 3.3 25.5 + - - +
1395B ASN 5.0 1.8 - - - -
1397B PRO* 6.5 1.3 - - + -
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Residues in contact with ARG1236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A GLU* 6.5 1.3 - - - +
32A TYR* 5.0 5.2 - - + -
1229B ASP* 3.9 21.8 + - - +
1231B LEU* 3.1 46.6 + - - +
1232B THR 2.9 14.8 + - - +
1233B PRO* 3.7 7.2 - - + +
1235B GLU* 1.3 74.6 - - - +
1237B LYS* 1.3 63.5 + - + +
1239B GLN* 3.4 4.0 + - - +
1240B GLY* 2.9 25.6 + - - -
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Residues in contact with LYS1237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A GLU 4.5 7.0 - - - +
32A TYR* 3.6 37.0 - - + +
1233B PRO* 3.0 18.1 + - + +
1234B THR* 3.2 9.4 + - - +
1236B ARG* 1.3 75.1 - - + +
1238B ARG* 1.3 66.2 + - - +
1240B GLY* 3.3 1.1 + - - +
1241B TYR* 3.0 38.2 + - + -
1395B ASN* 3.6 27.4 - - - +
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Residues in contact with ARG1238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1234B THR 3.1 6.7 + - - +
1235B GLU* 3.4 12.6 - - - +
1236B ARG 3.2 0.2 - - - -
1237B LYS* 1.3 78.6 - - - +
1239B GLN* 1.3 75.6 + - - +
1241B TYR* 3.1 5.4 + - - +
1242B ILE* 3.0 41.8 + - + +
1312B VAL 2.8 25.3 + - - -
1313B LYS* 3.1 20.6 + - - +
1314B MET* 4.1 0.6 - - - +
1392B ILE* 4.4 8.2 - - + +
1395B ASN* 3.6 25.9 - - - +
1396B THR* 3.1 27.2 + - - +
1397B PRO* 5.6 0.9 - - - -
1400B HIS* 3.4 24.0 + - - -
1402B ASP* 2.5 36.8 + - - +
1406B LEU* 4.5 0.6 - - - +
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Residues in contact with GLN1239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1231B LEU* 4.1 16.8 - - + -
1235B GLU 3.3 12.6 + - - +
1236B ARG 3.4 6.9 + - - +
1238B ARG* 1.3 95.4 - - - +
1240B GLY* 1.3 60.9 + - - +
1242B ILE* 3.2 4.7 + - - +
1243B HIS* 2.9 30.2 + - - +
1311B PRO* 3.4 27.4 - - + +
1312B VAL* 2.9 50.6 + - - +
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Residues in contact with GLY1240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A TYR* 2.1 42.4 + - - -
1236B ARG 2.9 13.8 + - - -
1237B LYS 3.3 0.4 + - - -
1239B GLN* 1.3 77.2 - - - +
1241B TYR* 1.3 54.2 + - - +
1243B HIS* 3.1 9.1 + - - +
1244B GLU 2.9 20.3 + - - -
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Residues in contact with TYR1241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A TYR* 2.9 45.4 + + + +
33A VAL* 3.1 25.7 + - - +
35A THR* 4.4 1.3 - - - -
1237B LYS* 3.0 36.1 + - + +
1238B ARG 3.7 2.0 - - - +
1240B GLY* 1.3 75.5 - - - +
1242B ILE* 1.3 57.6 + - - +
1244B GLU* 3.4 17.2 + - - +
1245B LEU* 3.0 25.1 + - - +
1388B ILE* 4.0 6.3 - - + +
1391B ASN* 3.5 50.4 + - + -
1392B ILE* 3.5 25.1 - - + +
1395B ASN* 3.7 17.9 - - - -
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Residues in contact with ILE1242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1238B ARG* 3.0 56.7 + - + +
1239B GLN* 3.2 7.8 + - - +
1241B TYR* 1.3 75.4 - - - +
1243B HIS* 1.3 65.7 + - - +
1245B LEU* 3.3 4.1 + - - +
1246B ILE* 3.2 35.8 + - + +
1312B VAL* 3.2 37.5 - - + +
1315B ILE* 4.1 24.0 - - + -
1392B ILE* 4.0 23.3 - - + -
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Residues in contact with HIS1243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A TYR* 5.2 1.6 + - - -
1239B GLN 2.9 12.8 + - - +
1240B GLY* 3.3 13.1 + - - +
1242B ILE* 1.3 79.3 - - - +
1244B GLU* 1.3 59.9 + - - +
1246B ILE* 3.3 9.6 + - + +
1247B VAL* 3.0 52.9 + - + +
1303B LYS* 6.1 5.2 - - - -
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Residues in contact with GLU1244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A TYR* 3.6 17.0 - - - +
34A PRO* 3.0 31.9 - - - +
35A THR* 3.0 31.8 + - - -
36A VAL* 3.6 16.6 + - + +
1240B GLY 2.9 6.7 + - - +
1241B TYR* 3.8 16.4 - - - +
1242B ILE 3.3 0.2 - - - -
1243B HIS* 1.3 78.7 + - - +
1245B LEU* 1.3 56.9 + - - +
1247B VAL* 4.6 4.3 - - - +
1248B THR* 2.7 49.4 + - + +
1388B ILE* 5.1 4.5 - - + +
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Residues in contact with LEU1245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1241B TYR 3.0 14.9 + - - +
1242B ILE* 3.4 11.4 - - - +
1244B GLU* 1.3 76.9 - - - +
1246B ILE* 1.3 57.5 + - + +
1248B THR* 3.1 6.8 + - - -
1249B GLU* 3.0 25.6 + - - +
1295B LEU* 5.7 0.4 - - + -
1299B LEU* 4.2 20.2 - - + -
1315B ILE* 4.1 22.0 - - + -
1319B LEU* 4.0 33.4 - - + -
1381B ARG* 3.5 14.1 + - - +
1385B TYR* 4.4 15.3 - - + -
1388B ILE* 3.9 24.9 - - + -
1389B ILE* 6.0 0.4 - - + -
1392B ILE* 4.5 6.7 - - + -
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Residues in contact with ILE1246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1242B ILE* 3.2 27.7 + - + +
1243B HIS* 3.7 10.5 - - + +
1245B LEU* 1.3 77.2 - - + +
1247B VAL* 1.3 66.6 + - + +
1249B GLU* 3.2 7.6 + - - +
1250B GLU* 3.0 35.4 + - + +
1296B LEU* 4.5 2.6 - - + +
1299B LEU* 4.5 34.1 - - + +
1300B ARG* 5.6 3.6 - - + -
1303B LYS* 4.3 35.9 - - + -
1312B VAL* 6.0 1.1 - - + -
1315B ILE* 5.1 5.4 - - + -
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Residues in contact with VAL1247 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1243B HIS* 3.0 52.3 + - + +
1244B GLU* 4.3 4.3 - - - +
1246B ILE* 1.3 78.2 - - + +
1248B THR* 1.3 61.3 + - + +
1250B GLU* 3.3 9.5 + - + +
1251B ASN* 3.0 43.7 + - - +
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Residues in contact with THR1248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A VAL* 3.9 24.9 - - + -
38A ASP* 5.2 6.5 - - - +
1244B GLU* 2.7 41.6 + - + +
1245B LEU* 3.1 3.8 + - - -
1247B VAL* 1.3 76.9 - - + +
1249B GLU* 1.3 60.3 + - - +
1251B ASN* 3.9 10.2 - - - +
1252B TYR* 3.0 28.9 + - - +
1381B ARG* 3.1 31.6 + - - -
1388B ILE* 4.0 4.2 - - - +
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Residues in contact with GLU1249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1245B LEU* 3.0 18.4 + - + +
1246B ILE 3.2 5.1 + - - +
1248B THR* 1.3 75.3 + - - +
1250B GLU* 1.3 60.6 + - - +
1252B TYR* 3.6 6.9 - - - +
1253B VAL* 2.9 38.1 + - - +
1292B ASN* 2.7 35.0 - - - +
1295B LEU* 3.8 9.8 - - + +
1296B LEU* 4.1 17.7 - - + -
1299B LEU* 4.0 23.6 - - + -
1381B ARG* 2.7 29.5 + - - +
1385B TYR* 2.8 21.7 + - - -
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Residues in contact with GLU1250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1246B ILE* 3.0 27.4 + - + +
1247B VAL* 3.4 11.7 - - + +
1249B GLU* 1.3 76.4 - - - +
1251B ASN* 1.3 62.6 + - - +
1253B VAL* 3.5 1.4 + - - +
1254B ASN* 2.9 30.3 + - - +
1296B LEU* 3.1 19.5 - - + +
1300B ARG* 2.7 51.7 + - - +
121C ASP 4.6 0.7 - - - +
123C PRO* 3.4 31.2 - - + +
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Residues in contact with ASN1251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ASP* 4.6 15.6 + - - +
1247B VAL* 3.0 32.8 + - - +
1248B THR* 4.0 9.5 - - - +
1250B GLU* 1.3 80.6 - - - +
1252B TYR* 1.3 58.4 + - - +
1254B ASN* 3.5 6.8 + - - +
1255B ASP* 3.0 38.7 + - - +
123C PRO* 6.1 0.7 - - - +
----------------------------------------------------------
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Residues in contact with TYR1252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1248B THR 3.0 19.1 + - - +
1249B GLU* 3.6 21.3 - - - +
1250B GLU 3.2 0.2 - - - -
1251B ASN* 1.3 73.9 - - - +
1253B VAL* 1.3 60.3 + - + +
1255B ASP* 3.0 9.2 + - - +
1256B LEU* 2.9 57.8 + - + +
1288B LEU* 4.8 1.0 - - - +
1292B ASN* 3.3 15.0 - - - -
1329B TYR* 2.7 31.4 + - - -
1377B LYS* 3.6 36.6 - - + -
1378B PRO* 3.4 18.0 - - - +
1381B ARG* 3.6 30.3 - - + +
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Residues in contact with VAL1253 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1249B GLU* 2.9 27.3 + - - +
1250B GLU 4.0 2.2 - - - +
1252B TYR* 1.3 75.5 - - + +
1254B ASN* 1.3 63.8 + - - +
1256B LEU* 3.2 10.8 + - + +
1257B GLN* 3.1 39.8 + - + +
1289B ILE* 5.6 1.6 - - + +
1292B ASN* 3.7 39.0 - - + +
1293B ILE* 3.9 22.2 - - + -
1296B LEU* 4.3 19.3 - - + -
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Residues in contact with ASN1254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1250B GLU 2.9 19.4 + - - +
1251B ASN* 3.7 8.5 - - - +
1253B VAL* 1.3 78.5 - - - +
1255B ASP* 1.3 59.7 + - - +
1257B GLN* 3.3 9.5 + - - +
1258B LEU* 3.0 53.6 + - - +
122C ASP* 5.1 7.9 + - - -
124C SER* 6.1 3.0 - - - -
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Residues in contact with ASP1255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ASP* 5.2 4.0 - - - +
1251B ASN* 3.0 23.9 + - - +
1252B TYR* 3.5 8.2 - - - +
1254B ASN* 1.3 77.3 - - - +
1256B LEU* 1.3 65.1 + - + +
1258B LEU* 3.4 19.9 + - - +
1259B VAL* 3.2 28.2 + - - +
1285B TRP* 5.1 0.4 - - - -
1365B ARG 5.4 0.9 - - - +
1374B PHE* 4.3 10.0 - - + -
1377B LYS* 3.3 45.7 + - + +
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Residues in contact with LEU1256 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1252B TYR* 2.9 64.4 + - + +
1253B VAL* 3.2 13.2 + - + +
1255B ASP* 1.3 77.4 - - + +
1257B GLN* 1.3 61.7 + - - +
1258B LEU 3.5 0.2 + - - -
1259B VAL 3.5 0.2 + - - -
1260B THR* 3.5 10.6 + - - -
1285B TRP* 2.8 52.5 + - + +
1288B LEU* 4.0 27.4 - - + +
1289B ILE* 3.8 21.5 - - + -
1292B ASN* 4.4 4.7 - - + -
1377B LYS* 5.5 2.0 - - + -
1378B PRO* 4.3 5.6 - - + -
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Residues in contact with GLN1257 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1253B VAL* 3.1 28.4 + - + +
1254B ASN* 3.8 8.0 + - - +
1256B LEU* 1.3 74.3 - - - +
1258B LEU* 1.3 65.8 + - - +
1260B THR* 3.4 4.8 + - - +
1261B GLU* 3.1 23.9 + - - +
1289B ILE* 4.1 26.8 - - + +
1293B ILE* 3.6 28.0 - - - +
----------------------------------------------------------
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Residues in contact with LEU1258 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1254B ASN* 3.0 41.3 + - - +
1255B ASP* 3.6 19.5 - - - +
1256B LEU 3.3 0.2 - - - -
1257B GLN* 1.3 77.0 - - - +
1259B VAL* 1.3 54.6 + - + +
1261B GLU* 3.2 4.4 + - - +
1262B ILE* 2.8 48.6 + - + +
1365B ARG* 3.2 71.8 - - + +
1374B PHE* 5.3 6.5 - - + -
----------------------------------------------------------
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Residues in contact with VAL1259 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1255B ASP 3.2 13.6 + - - +
1256B LEU 3.7 1.8 - - - +
1258B LEU* 1.3 77.8 - - + +
1260B THR* 1.3 57.3 + - - +
1263B PHE* 2.9 40.0 + - + -
1264B GLN 2.9 9.7 + - - -
1282B PHE* 3.7 28.3 - - + -
1285B TRP* 3.6 34.8 - - + +
1371B LEU* 4.5 4.3 - - + -
1374B PHE* 3.5 37.7 - - + -
----------------------------------------------------------
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Residues in contact with THR1260 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1256B LEU 3.5 1.2 + - - -
1257B GLN* 3.4 8.8 + - - -
1258B LEU 3.3 0.6 - - - -
1259B VAL* 1.3 78.0 - - - +
1261B GLU* 1.3 63.1 + - - +
1264B GLN* 3.3 30.6 + - - +
1265B LYS* 3.1 48.8 + - + +
1285B TRP* 3.4 17.3 - - - -
1286B LYS* 5.9 0.3 - - - -
1289B ILE* 3.5 15.7 - - + +
----------------------------------------------------------
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Residues in contact with GLU1261 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1257B GLN 3.1 15.0 + - - +
1258B LEU* 3.2 5.1 + - - +
1260B THR* 1.3 83.6 - - - +
1262B ILE* 1.3 60.5 + - + +
1265B LYS* 4.3 11.6 - - + +
1266B PRO* 3.4 16.3 - - - +
1365B ARG* 2.6 44.8 + - - -
1233D PRO* 4.2 9.6 - - + +
----------------------------------------------------------
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Residues in contact with ILE1262 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1258B LEU* 2.8 34.5 + - + +
1261B GLU* 1.3 80.7 - - + +
1263B PHE* 1.3 73.0 + - + +
1266B PRO* 3.4 5.4 - - - +
1360B LEU* 3.4 38.3 - - - +
1363B ASP* 3.7 18.8 - - + +
1365B ARG* 3.7 28.7 - - - +
1366B CYS* 3.1 37.7 - - - +
1374B PHE* 6.1 0.2 - - + -
1233D PRO* 4.4 11.0 - - + -
----------------------------------------------------------
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Residues in contact with PHE1263 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1259B VAL* 2.9 23.1 + - + +
1261B GLU 3.6 0.6 - - - -
1262B ILE* 1.3 95.8 - - + +
1264B GLN* 1.3 65.2 + - - +
1265B LYS 3.6 0.9 - - - -
1266B PRO* 3.5 0.9 - - - +
1267B LEU* 3.0 30.9 + - + +
1282B PHE* 4.0 7.9 - - + -
1357B VAL* 4.2 7.0 - - + -
1360B LEU* 3.8 15.5 - - + -
1361B GLU* 3.8 28.5 - - + -
1366B CYS* 3.8 31.2 - - - -
1369B MET 4.7 0.2 - - - -
1370B PRO 4.5 1.3 - - - -
1371B LEU* 3.8 62.6 - - + -
1374B PHE* 4.2 12.1 - + - -
----------------------------------------------------------
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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