Contacts of the helix formed by residues 1324 - 1350 (chain A) in PDB entry 5LUQ
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 PRO1324 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
681A LYS* 5.3 15.0 - - + +
1323A SER* 1.4 99.6 - - - +
1325A GLN* 1.3 92.1 + - - +
1326A GLU* 5.1 1.6 - - + +
1327A GLY* 3.5 0.7 - - - -
1328A GLU* 2.9 19.3 + - - +
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Residues in contact with GLN1325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
708A VAL* 4.6 18.8 - - + +
748A TYR* 3.9 26.6 + - + +
1324A PRO* 1.3 102.1 - - - +
1326A GLU* 1.3 60.2 + - + +
1328A GLU* 3.2 9.1 + - - +
1329A ARG* 2.9 28.1 + - - +
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Residues in contact with GLU1326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1247A PRO* 4.9 13.0 - - - +
1251A GLN* 5.5 1.8 + - - -
1323A SER* 3.8 11.2 - - - +
1324A PRO* 3.1 1.5 - - + -
1325A GLN* 1.3 77.4 - - + +
1327A GLY* 1.3 66.6 + - - +
1329A ARG* 3.1 34.0 + - - +
1330A TYR* 2.9 20.8 + - - +
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Residues in contact with GLY1327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1323A SER* 2.7 27.4 + - - +
1324A PRO 3.5 0.9 - - - -
1326A GLU* 1.3 72.4 - - - +
1328A GLU* 1.3 55.7 + - - +
1330A TYR* 3.0 13.8 - - - +
1331A ASN* 2.9 34.1 + - - +
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Residues in contact with GLU1328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
709A LYS* 2.2 37.5 + - - +
1324A PRO 2.9 12.4 + - - +
1325A GLN* 3.5 12.6 - - - +
1326A GLU 3.1 0.4 - - - -
1327A GLY* 1.3 74.6 - - - +
1329A ARG* 1.3 60.9 + - - +
1331A ASN* 3.1 14.8 + - - +
1332A TYR* 2.8 61.0 + - + +
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Residues in contact with ARG1329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1247A PRO* 3.5 24.5 + - - +
1250A LEU* 3.6 28.2 + - - +
1251A GLN* 2.9 43.8 - - - +
1255A CYS* 5.2 4.9 - - - -
1325A GLN 2.9 14.8 + - - +
1326A GLU* 3.6 36.6 + - - +
1328A GLU* 1.3 75.9 - - - +
1330A TYR* 1.3 52.9 + - - +
1332A TYR* 4.7 4.0 - - - +
1333A SER* 2.4 44.6 + - - +
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Residues in contact with TYR1330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1250A LEU* 4.8 29.2 - - + -
1305A ASP* 2.4 40.9 + - + +
1306A ILE 4.8 0.9 - - - -
1307A ILE 5.3 0.7 - - - -
1308A ALA* 2.8 27.2 + - - -
1326A GLU 2.9 12.4 + - - +
1327A GLY* 3.0 16.8 - - - +
1329A ARG* 1.3 81.1 - - - +
1331A ASN* 1.3 72.0 + - - -
1333A SER* 2.3 22.1 + - - -
1334A LYS* 2.9 46.8 + - + +
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Residues in contact with ASN1331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1306A ILE 4.1 12.0 - - - +
1307A ILE 5.5 0.7 - - - +
1327A GLY 2.9 22.2 + - - -
1328A GLU* 3.1 21.1 + - - +
1330A TYR* 1.3 88.2 - - - +
1332A TYR* 1.3 66.5 + - + +
1334A LYS* 2.6 29.1 + - - +
1335A CYS* 2.9 12.7 + - - +
1381A SER 5.1 4.0 - - - +
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Residues in contact with TYR1332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
709A LYS* 3.0 27.8 - - + +
1328A GLU* 2.8 50.9 + - + +
1329A ARG* 4.6 3.4 - - - +
1331A ASN* 1.3 78.5 - - + +
1333A SER* 1.3 53.9 + - - +
1335A CYS* 4.0 6.5 - - - +
1336A THR* 2.3 41.0 + - - +
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Residues in contact with SER1333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1250A LEU 4.5 6.4 + - - -
1254A LEU* 4.0 8.0 - - - +
1255A CYS* 3.3 33.0 - - - -
1329A ARG* 2.4 19.8 + - - -
1330A TYR* 2.3 32.4 + - - -
1332A TYR* 1.3 75.2 - - - +
1334A LYS* 1.3 67.8 + - - +
1336A THR* 3.6 6.1 - - - -
1337A VAL* 2.9 29.3 + - - +
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Residues in contact with LYS1334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1250A LEU* 6.5 0.2 - - - -
1254A LEU* 4.2 33.2 - - + +
1302A ALA* 5.6 2.7 - - + +
1305A ASP* 2.6 48.9 + - - +
1306A ILE* 3.2 31.1 - - + +
1330A TYR* 2.9 56.5 + - + +
1331A ASN* 2.6 15.7 + - - +
1333A SER* 1.3 75.6 + - - +
1335A CYS* 1.3 56.2 + - - +
1337A VAL* 3.7 4.3 + - + +
1338A VAL* 3.0 30.5 + - - +
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Residues in contact with CYS1335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1306A ILE* 4.5 1.7 - - - +
1331A ASN 2.9 10.1 + - - +
1332A TYR* 4.0 9.2 - - - +
1334A LYS* 1.3 72.9 - - - +
1336A THR* 1.3 57.5 + - - +
1337A VAL 3.0 4.5 - - - -
1338A VAL* 2.7 29.7 + - - -
1339A VAL* 2.9 42.0 + - - +
1378A GLU* 5.1 9.0 - - - +
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Residues in contact with THR1336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1119A LYS* 6.3 0.9 - - - +
1255A CYS* 5.5 6.5 - - + +
1256A TRP* 6.3 4.7 - - + -
1259A LEU* 3.3 11.5 - - + +
1332A TYR* 2.3 32.1 + - - +
1333A SER* 3.1 8.3 + - - -
1335A CYS* 1.3 72.4 - - - +
1337A VAL* 1.3 57.3 + - + +
1339A VAL* 4.1 6.8 - - - +
1340A ARG* 3.1 26.5 - - + +
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Residues in contact with VAL1337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1254A LEU* 3.1 34.8 - - - +
1255A CYS* 4.0 4.5 - - - -
1258A ASP* 4.8 13.9 - - + +
1259A LEU* 3.5 30.5 - - + -
1302A ALA* 5.8 3.8 - - + -
1333A SER 2.9 12.1 + - - +
1334A LYS* 4.0 4.7 - - + +
1335A CYS 2.8 0.6 + - - -
1336A THR* 1.3 77.9 - - - +
1338A VAL* 1.3 59.7 + - + +
1339A VAL 3.3 0.2 - - - -
1340A ARG* 2.9 8.7 + - - +
1341A ILE* 2.9 45.6 + - + +
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Residues in contact with VAL1338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1299A GLU* 5.1 2.7 - - + +
1302A ALA* 4.0 19.7 - - + -
1306A ILE* 3.5 26.5 - - + -
1334A LYS 3.0 19.9 + - - +
1335A CYS* 2.7 18.3 + - - +
1337A VAL* 1.3 75.7 - - - +
1339A VAL* 1.3 65.9 + - + +
1341A ILE* 3.3 13.4 + - + +
1342A MSE 2.9 32.7 + - + +
1371A VAL* 4.8 17.3 - - + -
1378A GLU* 4.4 12.1 - - + +
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Residues in contact with VAL1339 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1335A CYS* 2.9 44.7 + - - +
1336A THR* 4.1 10.5 - - - +
1338A VAL* 1.3 81.0 - - + +
1340A ARG* 1.3 67.2 + - + +
1342A MSE 3.5 8.4 + - - +
1343A GLU* 2.8 29.6 + - - +
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Residues in contact with ARG1340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1166A LEU* 6.1 1.6 - - - +
1170A LYS* 5.5 1.2 - - - +
1259A LEU* 3.5 23.4 - - + +
1262A ALA* 5.7 2.7 - - + +
1263A ALA* 4.8 10.5 - - - +
1266A CYS* 4.9 9.7 - - - +
1267A TYR* 3.6 33.1 + - - -
1336A THR* 3.1 20.9 - - + +
1337A VAL 2.9 8.1 + - - +
1339A VAL* 1.3 82.4 - - + +
1341A ILE* 1.3 61.6 + - - +
1343A GLU* 3.1 41.0 + - - +
1344A PHE* 2.9 27.0 + - - +
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Residues in contact with ILE1341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1258A ASP* 6.1 2.2 - - + -
1259A LEU* 4.6 6.5 - - + -
1262A ALA* 5.3 7.2 - - + -
1295A ALA 5.2 4.5 - - - +
1298A LEU* 5.0 4.5 - - + +
1299A GLU* 3.2 48.0 - - + +
1302A ALA* 5.1 3.4 - - + -
1337A VAL* 2.9 35.6 + - + +
1338A VAL* 3.3 14.6 + - + +
1340A ARG* 1.3 74.6 - - - +
1342A MSE 1.3 60.4 + - + +
1344A PHE* 3.0 8.2 + - + +
1345A THR* 2.8 34.5 + - - +
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Residues in contact with MSE1342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1338A VAL* 2.9 21.9 + - + +
1339A VAL* 3.8 7.2 - - - +
1341A ILE* 1.3 71.5 - - + +
1343A GLU* 1.3 59.4 + - - +
1344A PHE 2.9 4.7 - - - -
1345A THR* 3.3 7.5 + - - -
1346A THR* 2.7 39.4 + - - +
1371A VAL* 5.2 4.5 - - + +
1372A LEU* 3.3 58.6 - - + +
1375A THR* 5.8 4.0 - - - +
1378A GLU* 6.2 4.0 - - - -
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Residues in contact with GLU1343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1339A VAL 2.8 20.7 + - - +
1340A ARG* 3.1 43.3 + - - +
1342A MSE 1.3 76.1 - - - +
1344A PHE* 1.3 46.5 + - - -
1346A THR* 3.8 4.6 - - - +
1347A THR* 2.5 49.8 + - - +
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Residues in contact with PHE1344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1262A ALA* 3.9 11.7 - - + -
1265A GLU* 3.3 48.9 - - + -
1266A CYS* 3.2 38.8 - - - -
1269A THR* 4.3 4.3 - - + -
1340A ARG 2.9 15.6 + - - +
1341A ILE* 3.5 8.3 - - + +
1342A MSE 2.9 0.2 - - - -
1343A GLU* 1.3 76.9 - - - +
1345A THR* 1.3 60.7 + - - +
1346A THR 3.2 0.9 - - - -
1347A THR* 3.5 12.3 - - + -
1348A LEU* 2.8 71.5 + - + +
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Residues in contact with THR1345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1296A PHE* 5.2 6.6 - - + -
1299A GLU* 4.2 13.0 + - - -
1341A ILE* 2.8 21.4 + - - +
1342A MSE 3.9 8.0 - - - +
1344A PHE* 1.3 70.5 - - - +
1346A THR* 1.3 57.0 + - - +
1348A LEU* 3.7 6.9 - - - +
1349A LEU* 2.9 51.7 + - + +
1362A ASP* 5.3 3.4 - - - +
1368A LEU* 3.6 41.8 - - + +
1372A LEU* 5.7 2.9 - - + -
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Residues in contact with THR1346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1342A MSE 2.7 26.2 + - - +
1343A GLU* 3.8 6.3 - - - -
1345A THR* 1.3 73.4 - - - +
1347A THR* 1.3 63.6 + - - +
1349A LEU* 2.7 27.9 + - - -
1350A ASN* 2.9 29.3 + - + +
----------------------------------------------------------
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Residues in contact with THR1347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1266A CYS* 4.4 8.5 - - + -
1269A THR* 4.7 2.6 + - - +
1270A PHE* 3.3 34.3 - - + -
1343A GLU* 2.5 34.2 + - - +
1344A PHE* 3.5 23.5 + - + -
1346A THR* 1.3 79.3 - - - +
1348A LEU* 1.3 53.0 + - - +
1351A THR* 2.3 37.1 + - - -
1352A SER* 4.7 0.2 - - - -
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Residues in contact with LEU1348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1269A THR* 4.0 8.7 - - + -
1275A THR* 5.7 2.0 - - - -
1296A PHE* 5.6 10.8 - - + -
1344A PHE* 2.8 65.7 + - + +
1345A THR* 3.7 6.5 - - - +
1346A THR 2.8 1.8 + - - -
1347A THR* 1.3 71.7 - - - +
1349A LEU* 1.3 63.8 - - + +
1351A THR 2.8 2.1 + - - -
1352A SER* 2.4 55.9 + - - +
1353A PRO* 2.9 7.0 - - + +
1358A LEU* 6.1 4.9 - - + -
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Residues in contact with LEU1349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1345A THR* 2.9 39.6 + - + +
1346A THR* 2.7 9.2 + - - +
1348A LEU* 1.3 76.7 - - + +
1350A ASN* 1.3 59.9 + - + +
1351A THR 3.1 5.0 + - - -
1353A PRO* 3.2 21.6 - - + +
1356A TRP* 3.5 46.2 - - + -
1359A LEU* 3.6 41.1 - - + -
1362A ASP* 6.0 0.7 - - - +
1368A LEU* 5.2 4.3 - - + -
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Residues in contact with ASN1350 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1346A THR* 2.9 28.2 + - + +
1349A LEU* 1.3 76.0 - - + +
1351A THR* 1.3 67.2 + - + +
1356A TRP* 4.6 11.4 - - - -
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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