Contacts of the helix formed by residues 1232 - 1263 (chain D) 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 D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1266B PRO* 5.2 0.2 - - - -
1356B PHE* 4.1 10.1 - - + -
1359B ARG* 3.8 31.4 - - + +
1360B LEU* 4.3 10.8 - - + -
1231D LEU* 1.3 75.2 - - - +
1233D PRO* 1.3 77.5 - - - +
1234D THR* 3.0 7.9 + - - -
1235D GLU* 2.6 45.7 + - - +
1236D ARG* 2.9 20.6 + - - +
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Residues in contact with PRO1233 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1261B GLU* 4.2 15.3 - - + +
1262B ILE* 4.4 13.9 - - + -
1266B PRO* 3.7 21.5 - - + -
1360B LEU* 3.7 17.5 - - + -
1363B ASP* 6.1 0.7 - - - +
1232D THR* 1.3 88.1 - - - +
1234D THR* 1.3 57.7 + - - +
1236D ARG* 3.5 8.0 + - + +
1237D LYS* 3.0 34.5 + - + +
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Residues in contact with THR1234 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1232D THR* 3.1 7.0 + - - -
1233D PRO* 1.3 79.4 - - - +
1235D GLU* 1.3 69.5 + - + +
1237D LYS* 3.2 5.9 + - - +
1238D ARG* 3.1 17.8 + - - +
1394D GLU 5.1 0.9 - - - +
1395D ASN* 3.6 43.4 + - - +
1397D PRO* 5.4 4.7 - - + -
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Residues in contact with GLU1235 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1359B ARG* 3.4 18.6 + - - -
1230D MET 3.5 5.8 - - - +
1231D LEU* 3.2 24.6 - - + +
1232D THR* 2.6 44.2 + - - +
1234D THR* 1.3 79.4 - - + +
1236D ARG* 1.3 63.1 + - - +
1238D ARG* 3.3 10.9 + - - +
1239D GLN* 3.3 25.5 + - - +
1395D ASN 5.0 1.8 - - - -
1397D PRO* 6.5 1.3 - - + -
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Residues in contact with ARG1236 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1266B PRO* 5.8 1.7 - - - +
1269B GLU* 3.4 45.9 + - - +
31C GLU* 6.5 1.3 - - - +
32C TYR* 5.0 5.0 - - + -
1229D ASP* 3.9 18.2 + - - -
1231D LEU* 3.1 46.6 + - - +
1232D THR 2.9 14.8 + - - +
1233D PRO* 3.7 7.2 - - + +
1235D GLU* 1.3 74.8 - - - +
1237D LYS* 1.3 63.0 + - + +
1239D GLN* 3.4 4.0 + - - +
1240D GLY* 2.9 26.0 + - - -
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Residues in contact with LYS1237 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C GLU 4.5 7.0 - - - +
32C TYR* 3.6 37.0 - - + +
1233D PRO* 3.0 18.3 + - + +
1234D THR* 3.2 9.4 + - - +
1236D ARG* 1.3 75.7 - - + +
1238D ARG* 1.3 66.3 + - - +
1240D GLY* 3.3 0.9 + - - +
1241D TYR* 3.0 38.0 + - + -
1395D ASN* 3.6 27.4 - - - +
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Residues in contact with ARG1238 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1234D THR 3.1 6.7 + - - +
1235D GLU* 3.4 12.6 - - - +
1236D ARG 3.2 0.2 - - - -
1237D LYS* 1.3 78.4 - - - +
1239D GLN* 1.3 75.6 + - - +
1241D TYR* 3.1 5.4 + - - +
1242D ILE* 3.0 41.6 + - + +
1312D VAL 2.8 25.3 + - - -
1313D LYS* 3.1 20.8 + - - +
1314D MET* 4.1 0.6 - - - +
1392D ILE* 4.4 8.7 - - + +
1395D ASN* 3.6 25.7 - - - +
1396D THR* 3.1 27.2 + - - +
1397D PRO* 5.6 0.9 - - - -
1400D HIS* 3.4 24.0 + - - -
1402D ASP* 2.5 36.6 + - - +
1406D LEU* 4.5 0.6 - - - +
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Residues in contact with GLN1239 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1231D LEU* 4.1 16.8 - - + -
1235D GLU 3.3 12.6 + - - +
1236D ARG 3.4 6.9 + - - +
1238D ARG* 1.3 95.2 - - - +
1240D GLY* 1.3 60.7 + - - +
1242D ILE* 3.2 4.8 + - - +
1243D HIS* 2.9 30.8 + - - +
1311D PRO* 3.4 28.1 - - + +
1312D VAL* 2.9 50.6 + - - +
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Residues in contact with GLY1240 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C TYR* 2.1 42.4 + - - -
1236D ARG 2.9 13.8 + - - -
1237D LYS 3.3 0.4 + - - -
1239D GLN* 1.3 77.6 - - - +
1241D TYR* 1.3 54.0 + - - +
1243D HIS* 3.1 8.9 + - - +
1244D GLU 2.9 20.4 + - - -
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Residues in contact with TYR1241 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C TYR* 2.9 47.0 + + + +
33C VAL* 3.1 25.3 + - - +
35C THR* 4.4 1.3 - - - -
1237D LYS* 3.0 35.0 + - + +
1238D ARG 3.7 1.8 - - - +
1240D GLY* 1.3 76.0 - - - +
1242D ILE* 1.3 57.9 + - - +
1244D GLU* 3.8 17.2 - - - +
1245D LEU* 3.0 25.3 + - - +
1388D ILE* 4.0 6.1 - - + +
1391D ASN* 3.5 50.6 + - + -
1392D ILE* 3.5 25.6 - - + +
1395D ASN* 3.7 17.9 - - - -
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Residues in contact with ILE1242 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1238D ARG* 3.0 56.7 + - + +
1239D GLN* 3.2 7.8 + - - +
1241D TYR* 1.3 75.0 - - - +
1243D HIS* 1.3 65.9 + - - +
1245D LEU* 3.3 4.1 + - - +
1246D ILE* 3.2 35.5 + - + +
1312D VAL* 3.2 38.1 - - + +
1315D ILE* 4.1 24.2 - - + -
1392D ILE* 4.0 23.3 - - + -
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Residues in contact with HIS1243 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C TYR* 5.2 1.6 + - - -
1239D GLN 2.9 13.0 + - - +
1240D GLY* 3.3 13.1 + - - +
1242D ILE* 1.3 79.1 - - - +
1244D GLU* 1.3 59.1 + - - +
1246D ILE* 3.3 9.8 + - + +
1247D VAL* 3.0 52.9 + - + +
1303D LYS* 6.1 5.2 - - - -
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Residues in contact with GLU1244 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C TYR* 3.6 17.0 - - - +
34C PRO* 3.0 31.9 - - - +
35C THR* 3.0 31.6 + - - -
36C VAL* 3.6 16.6 + - + +
1240D GLY 2.9 6.7 + - - +
1241D TYR* 3.8 16.4 - - - +
1242D ILE 3.3 0.2 - - - -
1243D HIS* 1.3 78.9 + - - +
1245D LEU* 1.3 56.7 + - - +
1247D VAL* 4.6 4.3 - - - +
1248D THR* 2.7 49.8 + - + +
1388D ILE* 5.1 4.5 - - + +
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Residues in contact with LEU1245 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1241D TYR 3.0 14.6 + - - +
1242D ILE* 3.4 11.7 - - - +
1244D GLU* 1.3 77.3 - - - +
1246D ILE* 1.3 57.7 + - + +
1248D THR* 3.1 6.6 + - - -
1249D GLU* 3.0 25.4 + - - +
1295D LEU* 5.7 0.4 - - + -
1299D LEU* 4.2 20.2 - - + -
1315D ILE* 4.1 22.2 - - + -
1319D LEU* 4.0 33.4 - - + -
1381D ARG* 3.5 13.9 + - - +
1385D TYR* 4.4 15.3 - - + -
1388D ILE* 3.9 24.9 - - + -
1389D ILE* 6.0 0.4 - - + -
1392D ILE* 4.5 6.7 - - + -
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Residues in contact with ILE1246 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1242D ILE* 3.2 27.7 + - + +
1243D HIS* 3.7 10.5 - - + +
1245D LEU* 1.3 77.0 - - + +
1247D VAL* 1.3 66.2 + - + +
1249D GLU* 3.2 7.6 + - - +
1250D GLU* 3.0 35.4 + - + +
1296D LEU* 4.5 2.6 - - + +
1299D LEU* 4.5 34.1 - - + +
1300D ARG* 5.6 3.6 - - + -
1303D LYS* 4.3 36.1 - - + -
1312D VAL* 6.0 1.1 - - + -
1315D ILE* 5.1 5.4 - - + -
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Residues in contact with VAL1247 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1243D HIS* 3.0 55.7 + - + +
1244D GLU* 4.3 4.3 - - - +
1246D ILE* 1.3 75.2 - - + +
1248D THR* 1.3 61.1 + - + +
1250D GLU* 3.3 9.7 + - + +
1251D ASN* 3.0 43.5 + - - +
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Residues in contact with THR1248 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C VAL* 3.9 24.9 - - + -
38C ASP* 5.2 6.5 - - - +
1244D GLU* 2.7 41.7 + - + +
1245D LEU* 3.1 3.8 + - - -
1247D VAL* 1.3 77.3 - - + +
1249D GLU* 1.3 60.5 + - - +
1251D ASN* 3.9 10.0 - - - +
1252D TYR* 3.0 28.8 + - - +
1381D ARG* 3.1 31.4 + - - -
1388D ILE* 4.0 4.2 - - - +
----------------------------------------------------------
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Residues in contact with GLU1249 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1245D LEU* 3.0 18.4 + - + +
1246D ILE 3.2 5.4 + - - +
1248D THR* 1.3 74.9 + - - +
1250D GLU* 1.3 60.9 + - - +
1252D TYR* 3.6 6.9 - - - +
1253D VAL* 2.9 37.9 + - - +
1292D ASN* 2.7 34.8 - - - +
1295D LEU* 3.8 9.8 - - + +
1296D LEU* 4.1 17.7 - - + -
1299D LEU* 4.0 23.8 - - + -
1381D ARG* 2.7 29.5 + - - +
1385D TYR* 2.8 21.4 + - - -
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Residues in contact with GLU1250 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1246D ILE* 3.0 27.4 + - + +
1247D VAL* 3.4 11.7 - - + +
1249D GLU* 1.3 75.9 - - - +
1251D ASN* 1.3 62.0 + - - +
1253D VAL* 3.5 1.4 + - - +
1254D ASN* 2.9 30.3 + - - +
1296D LEU* 3.2 19.5 - - + +
1300D ARG* 2.6 51.9 + - - +
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Residues in contact with ASN1251 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C ASP* 4.6 15.6 + - - +
1247D VAL* 3.0 32.8 + - - +
1248D THR* 4.0 9.5 - - - +
1250D GLU* 1.3 80.8 - - - +
1252D TYR* 1.3 58.4 + - - +
1254D ASN* 3.5 6.8 + - - +
1255D ASP* 3.0 38.1 + - - +
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Residues in contact with TYR1252 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1248D THR 3.0 18.9 + - - +
1249D GLU* 3.6 21.5 - - - +
1250D GLU 3.2 0.2 - - - -
1251D ASN* 1.3 74.1 - - - +
1253D VAL* 1.3 60.7 + - + +
1255D ASP* 3.0 9.2 + - - +
1256D LEU* 2.9 57.2 + - + +
1288D LEU* 4.8 1.0 - - - +
1292D ASN* 3.3 15.0 - - - -
1329D TYR* 2.7 31.4 + - - -
1377D LYS* 3.6 36.8 - - + -
1378D PRO* 3.4 17.5 - - - +
1381D ARG* 3.6 30.1 - - + +
----------------------------------------------------------
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Residues in contact with VAL1253 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1249D GLU* 2.9 27.1 + - - +
1250D GLU 4.0 2.2 - - - +
1252D TYR* 1.3 75.0 - - + +
1254D ASN* 1.3 64.2 + - - +
1256D LEU* 3.2 10.6 + - + +
1257D GLN* 3.1 39.5 + - + +
1289D ILE* 5.6 1.6 - - + +
1292D ASN* 3.7 39.0 - - + +
1293D ILE* 3.9 22.2 - - + -
1296D LEU* 4.3 20.0 - - + -
----------------------------------------------------------
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Residues in contact with ASN1254 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1250D GLU 2.9 19.6 + - - +
1251D ASN* 3.7 8.5 - - - +
1253D VAL* 1.3 78.3 - - - +
1255D ASP* 1.3 59.8 + - - +
1257D GLN* 3.3 9.5 + - - +
1258D LEU* 3.0 53.4 + - - +
----------------------------------------------------------
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Residues in contact with ASP1255 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C ASP* 5.2 4.0 - - - +
1251D ASN* 3.0 23.9 + - - +
1252D TYR* 3.5 8.4 - - - +
1254D ASN* 1.3 77.3 - - - +
1256D LEU* 1.3 64.9 + - + +
1258D LEU* 3.4 19.9 + - - +
1259D VAL* 3.3 28.0 + - - +
1285D TRP* 5.1 0.4 - - - -
1365D ARG 5.4 0.9 - - - +
1374D PHE* 4.2 10.0 - - + -
1377D LYS* 3.3 45.2 + - + +
----------------------------------------------------------
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Residues in contact with LEU1256 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1252D TYR* 2.9 64.4 + - + +
1253D VAL* 3.2 13.7 + - + +
1255D ASP* 1.3 77.6 - - + +
1257D GLN* 1.3 62.2 + - - +
1258D LEU 3.5 0.2 + - - -
1259D VAL 3.5 5.2 + - - -
1260D THR* 3.5 5.5 + - - -
1285D TRP* 2.8 51.8 + - + +
1288D LEU* 4.0 27.6 - - + +
1289D ILE* 3.8 21.3 - - + -
1292D ASN* 4.4 4.7 - - + -
1377D LYS* 5.5 2.0 - - + -
1378D PRO* 4.3 5.6 - - + -
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Residues in contact with GLN1257 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1253D VAL* 3.1 28.4 + - + +
1254D ASN* 3.8 8.2 + - - +
1256D LEU* 1.3 74.3 - - - +
1258D LEU* 1.3 65.4 + - - +
1260D THR* 3.4 4.8 + - - +
1261D GLU* 3.1 23.9 + - - +
1289D ILE* 4.1 26.8 - - + +
1293D ILE* 3.6 28.0 - - - +
----------------------------------------------------------
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Residues in contact with LEU1258 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1254D ASN* 3.0 41.9 + - - +
1255D ASP* 3.6 19.5 - - - +
1256D LEU 3.3 0.2 - - - -
1257D GLN* 1.3 77.2 - - - +
1259D VAL* 1.3 54.4 + - + +
1261D GLU* 3.2 4.5 + - - +
1262D ILE* 2.8 48.6 + - + +
1365D ARG* 3.2 71.6 - - + +
1374D PHE* 5.3 6.5 - - + -
----------------------------------------------------------
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Residues in contact with VAL1259 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1255D ASP 3.3 13.6 + - - +
1256D LEU 3.7 1.8 - - - +
1258D LEU* 1.3 77.6 - - + +
1260D THR* 1.3 57.7 + - - +
1263D PHE* 2.9 40.2 + - + -
1264D GLN 2.9 9.5 + - - -
1282D PHE* 3.7 28.0 - - + -
1285D TRP* 3.6 34.3 - - + +
1371D LEU* 4.5 4.3 - - + -
1374D PHE* 3.5 37.9 - - + -
----------------------------------------------------------
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Residues in contact with THR1260 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1256D LEU 3.5 1.2 + - - -
1257D GLN* 3.4 8.8 + - - -
1258D LEU 3.3 0.6 - - - -
1259D VAL* 1.3 77.4 - - - +
1261D GLU* 1.3 63.3 + - - +
1264D GLN* 3.3 30.6 + - - +
1265D LYS* 3.1 48.4 + - + +
1285D TRP* 3.4 17.3 - - - -
1286D LYS* 5.9 0.3 - - - -
1289D ILE* 3.5 15.7 - - + +
----------------------------------------------------------
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Residues in contact with GLU1261 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1257D GLN 3.1 15.2 + - - +
1258D LEU* 3.2 5.1 + - - +
1260D THR* 1.3 83.4 - - - +
1262D ILE* 1.3 60.3 + - + +
1265D LYS* 4.3 11.6 - - + +
1266D PRO* 3.4 16.3 - - - +
1365D ARG* 2.6 44.6 + - - -
----------------------------------------------------------
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Residues in contact with ILE1262 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1258D LEU* 2.8 34.5 + - + +
1261D GLU* 1.3 80.9 - - + +
1263D PHE* 1.3 73.5 + - + +
1266D PRO* 3.4 5.4 - - - +
1360D LEU* 3.4 38.1 - - - +
1363D ASP* 3.7 18.6 - - + +
1365D ARG* 3.7 28.9 - - - +
1366D CYS* 3.1 37.7 - - - +
1374D PHE* 6.1 0.2 - - + -
----------------------------------------------------------
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Residues in contact with PHE1263 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1259D VAL* 2.9 23.4 + - + +
1261D GLU 3.6 0.6 - - - -
1262D ILE* 1.3 96.4 - - + +
1264D GLN* 1.3 65.2 + - - +
1265D LYS 3.6 0.9 - - - -
1266D PRO* 3.5 0.9 - - - +
1267D LEU* 3.0 30.7 + - + +
1282D PHE* 4.0 7.9 - - + -
1357D VAL* 4.2 6.5 - - + -
1360D LEU* 3.8 15.5 - - + -
1361D GLU* 3.8 28.3 - - + -
1366D CYS* 3.8 31.2 - - - -
1369D MET 4.8 0.2 - - - -
1370D PRO 4.5 1.3 - - - -
1371D LEU* 3.8 62.6 - - + -
1374D PHE* 4.2 11.9 - + - -
----------------------------------------------------------
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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