Contacts of the helix formed by residues 1279 - 1312 (chain E) in PDB entry 5B2G
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 LYS1279 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1238A GLN* 4.4 26.5 - - + +
1239A ASP* 3.4 34.2 + - - +
1242A ALA* 4.0 14.5 - - + +
1301A TRP* 5.3 10.3 - - - -
1277E LYS* 3.2 3.9 - - + -
1278E ALA* 1.3 78.8 - - - +
1280E THR* 1.3 65.6 + - - +
1281E MET 3.1 2.2 - - - -
1282E ILE* 3.1 35.6 + - + +
1283E VAL* 3.5 9.4 + - - +
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Residues in contact with THR1280 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1241A GLN* 4.6 3.6 + - - +
1242A ALA* 3.4 30.1 + - - +
1245A ALA* 4.7 6.5 - - + -
100C VAL* 4.8 12.7 - - + +
1260E LEU* 4.1 33.9 - - + +
1277E LYS* 4.0 24.7 + - - +
1278E ALA 3.4 0.2 - - - -
1279E LYS* 1.3 78.4 - - - +
1281E MET* 1.3 63.0 + - - +
1283E VAL* 3.3 6.9 + - - +
1284E ALA* 3.1 24.9 + - - +
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Residues in contact with MET1281 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1170E GLN* 4.4 24.0 - - - +
1174E ILE* 5.0 7.6 - - + -
1260E LEU 3.7 24.9 - - - +
1261E SER* 4.3 18.2 - - - -
1263E VAL* 4.9 14.8 - - + -
1277E LYS 5.3 1.6 - - - +
1278E ALA* 3.6 21.5 - - - +
1279E LYS 3.1 0.6 - - - -
1280E THR* 1.3 82.0 - - - +
1282E ILE* 1.3 59.6 + - + +
1284E ALA* 3.7 4.6 - - - +
1285E GLY* 2.8 25.3 + - - -
1344E LEU* 3.8 29.8 - - + +
1347E SER* 6.1 0.2 - - - +
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Residues in contact with ILE1282 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1278E ALA 4.0 7.6 - - - +
1279E LYS* 3.1 32.5 + - + +
1281E MET* 1.3 74.5 - - - +
1283E VAL* 1.3 66.1 + - + +
1285E GLY* 3.3 1.1 + - - +
1286E VAL* 3.0 29.0 + - + +
1344E LEU 4.0 10.1 - - - +
1345E CYS* 4.0 22.6 - - + +
1347E SER* 4.0 19.1 - - - +
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Residues in contact with VAL1283 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1242A ALA* 4.0 16.6 - - + +
1245A ALA* 4.3 5.8 - - + -
1246A LEU* 3.9 41.3 - - + -
1249A ILE* 4.1 16.6 - - + -
1294A MET* 5.9 0.4 - - + -
1260E LEU* 4.1 15.9 - - + -
1279E LYS 3.5 12.1 + - - +
1280E THR* 3.3 10.3 + - - +
1282E ILE* 1.3 77.7 - - + +
1284E ALA* 1.3 57.8 + - - +
1286E VAL* 3.0 10.2 + - - +
1287E VAL* 2.9 30.8 + - + +
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Residues in contact with ALA1284 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1257E GLY* 3.6 24.0 - - - +
1260E LEU* 3.8 22.6 - - + +
1261E SER* 4.2 7.6 - - - +
1280E THR 3.1 8.6 + - - +
1281E MET* 3.9 8.5 - - - +
1282E ILE 3.5 0.2 - - - -
1283E VAL* 1.3 79.8 - - - +
1285E GLY* 1.3 56.6 + - - +
1287E VAL* 3.4 11.8 - - - +
1288E PHE* 3.0 37.8 + - + -
1344E LEU* 5.0 1.1 - - + -
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Residues in contact with GLY1285 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1281E MET 2.8 18.2 + - - -
1282E ILE 3.7 2.2 - - - -
1283E VAL 3.0 0.4 - - - -
1284E ALA* 1.3 75.1 - - - +
1286E VAL* 1.3 63.8 + - - +
1288E PHE 3.3 1.4 + - - -
1289E LEU* 3.0 25.1 + - - +
1341E GLY* 3.4 8.5 - - - -
1344E LEU* 3.6 25.8 - - - +
1345E CYS* 3.9 9.0 - - - -
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Residues in contact with VAL1286 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1246A LEU* 6.5 0.9 - - + -
1294A MET* 5.9 6.7 - - + -
1282E ILE* 3.0 22.3 + - + +
1283E VAL* 3.0 10.6 + - - +
1285E GLY* 1.3 73.4 - - - +
1287E VAL* 1.3 61.6 + - + +
1289E LEU* 3.0 14.1 + - + +
1290E LEU* 2.9 47.3 + - + +
1345E CYS* 4.0 12.6 - - - -
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Residues in contact with VAL1287 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1249A ILE* 3.8 35.0 - - + -
1294A MET* 5.8 3.6 - - + -
1253E VAL* 2.9 43.8 - - + +
1254E ALA* 4.3 1.1 - - - +
1256E LEU* 4.8 1.3 - - + -
1257E GLY* 3.6 15.7 - - - +
1283E VAL* 2.9 22.0 + - + +
1284E ALA* 3.4 11.7 - - - +
1286E VAL* 1.3 77.1 - - + +
1288E PHE* 1.3 62.2 + - - +
1290E LEU* 3.2 14.2 + - + +
1291E ALA* 3.1 18.7 + - - +
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Residues in contact with PHE1288 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1174E ILE* 5.1 1.6 - - - -
1177E ALA* 3.4 32.8 - - + -
1178E VAL* 5.1 2.2 - - + -
1181E TRP* 5.4 0.2 - - + -
1254E ALA* 3.3 31.9 - - + -
1257E GLY* 3.2 29.2 - - - -
1258E VAL* 3.4 16.2 - - + -
1261E SER* 4.1 8.1 - - - -
1284E ALA 3.0 22.7 + - - -
1285E GLY 3.6 6.1 - - - +
1286E VAL 3.3 0.2 - - - -
1287E VAL* 1.3 75.8 - - - +
1289E LEU* 1.3 62.1 + - - +
1291E ALA* 3.3 4.2 + - - +
1292E GLY* 3.1 20.4 + - - -
1337E LEU* 3.1 38.5 - - + +
1340E GLY 4.6 0.4 - - - -
1341E GLY* 4.2 5.4 - - - +
1344E LEU* 3.5 22.4 - - + -
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Residues in contact with LEU1289 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1285E GLY 3.0 13.8 + - - +
1286E VAL* 3.0 16.0 + - + +
1288E PHE* 1.3 76.6 - - - +
1290E LEU* 1.3 60.7 + - + +
1293E LEU* 3.1 27.3 + - - +
1337E LEU 4.4 0.2 - - - -
1338E LEU* 3.0 50.7 - - + +
1341E GLY* 3.7 7.2 - - - -
1342E GLY* 3.7 7.2 - - - +
1345E CYS* 3.8 27.8 - - + -
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Residues in contact with LEU1290 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1249A ILE* 6.5 0.2 - - + -
1253A VAL* 6.5 0.7 - - + -
1290A LEU* 4.2 40.8 - - + -
1294A MET* 4.6 19.7 - - + -
1253E VAL* 4.5 10.5 - - + -
1286E VAL* 2.9 33.3 + - + +
1287E VAL* 3.5 13.9 - - + +
1289E LEU* 1.3 79.1 - - + +
1291E ALA* 1.3 59.5 + - - +
1293E LEU* 3.3 16.0 + - + +
1294E MET* 2.9 36.7 + - - +
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Residues in contact with ALA1291 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1250E SER* 3.5 15.9 + - - +
1253E VAL* 4.3 4.4 - - + +
1254E ALA* 3.6 25.6 - - + +
1287E VAL 3.1 12.8 + - - +
1288E PHE 3.3 5.6 + - - +
1290E LEU* 1.3 76.9 - - - +
1292E GLY* 1.3 58.3 + - - +
1294E MET* 2.8 22.3 + - - +
1295E VAL* 2.8 17.7 + - - +
1337E LEU* 3.6 20.0 - - + -
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Residues in contact with GLY1292 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1288E PHE 3.1 11.9 + - - -
1291E ALA* 1.3 77.7 - - - +
1293E LEU* 1.3 61.3 + - - +
1295E VAL* 3.2 1.4 + - - -
1296E ILE* 3.0 22.0 + - - +
1334E SER* 3.2 28.8 - - - -
1337E LEU* 3.4 16.2 - - - +
1338E LEU* 4.1 9.4 - - - -
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Residues in contact with LEU1293 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1289E LEU 3.1 19.9 + - - +
1290E LEU* 3.4 17.5 - - + +
1292E GLY* 1.3 77.1 - - - +
1294E MET* 1.3 59.9 + - + +
1295E VAL 3.7 0.2 + - - -
1296E ILE* 3.7 21.8 + - + +
1297E VAL* 3.5 20.4 + - + +
1338E LEU* 3.7 13.9 - - + +
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Residues in contact with MET1294 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1286A VAL* 5.6 9.2 - - + -
1287A VAL* 6.1 3.6 - - + -
1290A LEU* 5.0 15.5 - - + -
1246E LEU* 3.4 38.4 - - + +
1249E ILE* 3.6 23.1 - - + -
1250E SER* 3.3 35.7 - - - +
1253E VAL* 4.9 8.5 - - - -
1290E LEU* 2.9 19.6 + - - +
1291E ALA* 2.8 12.4 + - - +
1293E LEU* 1.3 78.5 - - + +
1295E VAL* 1.3 58.5 + - - +
1296E ILE 3.5 0.2 - - - -
1297E VAL* 4.1 5.7 - - - +
1298E PRO* 3.0 23.4 - - - +
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Residues in contact with VAL1295 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1184E VAL* 3.3 30.1 - - + -
1187E CYS* 5.3 1.6 - - - -
1247E VAL* 6.0 3.6 - - + +
1250E SER* 3.1 27.1 - - - +
1291E ALA 2.8 13.5 + - - +
1292E GLY* 3.2 2.2 + - - -
1294E MET* 1.3 74.8 - - - +
1296E ILE* 1.3 66.2 + - - +
1297E VAL 3.2 1.8 - - - -
1298E PRO* 3.3 8.3 - - + +
1299E VAL* 3.2 24.0 - - + +
1330E GLY* 3.4 34.5 - - - +
1334E SER* 3.7 13.7 - - - +
1337E LEU* 4.6 4.0 - - + -
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Residues in contact with ILE1296 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1292E GLY 3.0 17.9 + - - +
1293E LEU* 3.8 18.2 - - + +
1294E MET 3.5 0.2 - - - -
1295E VAL* 1.3 77.4 - - - +
1297E VAL* 1.3 63.9 - - + +
1299E VAL* 4.0 2.2 - - - -
1300E SER* 2.4 43.5 + - - +
1331E TRP* 5.4 7.9 - - + +
1334E SER* 3.5 18.2 - - - +
1338E LEU* 3.5 29.2 - - + -
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Residues in contact with VAL1297 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1246E LEU* 4.0 20.2 - - + -
1293E LEU 3.5 17.7 + - - +
1294E MET* 4.1 6.3 - - + +
1296E ILE* 1.3 82.2 - - + +
1298E PRO* 1.3 71.1 - - + +
1300E SER* 3.3 7.3 + - - -
1301E TRP* 2.9 39.0 + - + +
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Residues in contact with PRO1298 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1193E TRP* 4.3 9.4 - - + -
1243E ALA* 4.1 26.0 - - + +
1246E LEU* 4.6 7.9 - - + -
1247E VAL* 4.1 20.2 - - + -
1294E MET 3.0 24.0 - - - +
1295E VAL* 3.3 11.9 - - + +
1297E VAL* 1.3 93.8 - - + +
1299E VAL* 1.3 64.8 + - + +
1301E TRP* 3.8 13.8 - - + +
1302E THR* 3.0 35.1 + - - +
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Residues in contact with VAL1299 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1187E CYS* 4.3 5.6 - - - -
1193E TRP* 4.0 19.7 - - + -
1247E VAL* 6.1 0.2 - - + -
1295E VAL* 3.2 24.7 - - + +
1296E ILE 4.3 1.3 - - - +
1297E VAL 3.4 0.4 - - - -
1298E PRO* 1.3 77.8 - - + +
1300E SER* 1.3 59.6 + - - +
1302E THR* 3.3 14.9 + - - -
1303E ALA* 3.7 12.3 - - - +
1327E LEU* 3.1 40.4 - - + +
1330E GLY* 4.0 19.1 - - - -
1331E TRP* 3.9 23.6 - - + +
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Residues in contact with SER1300 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1296E ILE* 2.4 36.9 + - - +
1297E VAL* 3.7 3.6 - - - -
1298E PRO 3.1 0.4 - - - -
1299E VAL* 1.3 78.9 - - - +
1301E TRP* 1.3 60.2 + - - +
1303E ALA* 3.3 6.1 + - - +
1304E HIS* 2.9 23.3 + - - +
1331E TRP* 3.5 24.3 + - - -
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Residues in contact with TRP1301 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1279A LYS* 5.4 11.0 - - - +
1239E ASP* 3.5 49.8 - - + -
1240E LEU* 4.7 2.2 - - + -
1242E ALA* 6.0 1.3 - - + -
1243E ALA* 3.8 25.1 - - + -
1246E LEU* 5.2 4.9 - - + +
1297E VAL* 2.9 42.9 + - + +
1298E PRO* 3.9 8.7 - - + -
1300E SER* 1.3 75.4 - - - +
1302E THR* 1.3 79.6 + - + +
1303E ALA 3.2 0.4 - - - -
1304E HIS* 3.5 17.9 - - + -
1305E ASN* 3.1 45.2 + - - +
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Residues in contact with THR1302 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1193E TRP* 3.9 21.3 - - + -
1213E LEU* 6.1 0.2 - - + -
1240E LEU* 4.7 14.1 - - + -
1243E ALA* 5.4 2.5 - - + -
1298E PRO* 3.0 22.3 + - + +
1299E VAL 3.3 8.7 + - - -
1301E TRP* 1.3 99.9 - - + +
1303E ALA* 1.3 60.9 + - - +
1305E ASN* 3.7 4.8 + - - +
1306E ILE* 3.0 34.8 + - - +
1327E LEU* 3.4 18.9 - - - +
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Residues in contact with ALA1303 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1299E VAL 3.7 6.5 - - - +
1300E SER 3.3 9.5 + - - +
1301E TRP 3.2 0.2 - - - -
1302E THR* 1.3 80.5 + - - +
1304E HIS* 1.3 62.8 + - - +
1306E ILE* 3.5 10.6 + - - +
1307E ILE* 3.2 32.7 + - + +
1323E MET* 3.6 27.1 - - - +
1327E LEU* 4.1 6.5 - - + -
1331E TRP* 3.6 17.9 - - + -
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Residues in contact with HIS1304 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1300E SER 2.9 15.7 + - - +
1301E TRP* 3.6 17.7 - - + +
1302E THR 3.3 0.4 - - - -
1303E ALA* 1.3 79.3 - - - +
1305E ASN* 1.3 65.6 + - - +
1306E ILE 3.2 0.4 - - - -
1307E ILE* 3.5 6.6 + - - +
1308E GLN* 2.9 46.4 + - + +
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Residues in contact with ASN1305 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1194E ARG* 6.1 2.7 - - - +
1239E ASP* 3.4 23.6 + - - -
1301E TRP* 3.1 30.6 + - - +
1302E THR* 3.7 5.8 + - - +
1303E ALA 3.4 0.2 - - - -
1304E HIS* 1.3 84.3 - - - +
1306E ILE* 1.3 59.7 + - + +
1308E GLN* 3.6 21.5 - - - +
1309E ASP* 3.3 19.6 + - - +
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Residues in contact with ILE1306 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1193E TRP 4.4 0.4 - - - +
1194E ARG* 3.7 43.1 - - + +
1302E THR* 3.0 27.1 + - - +
1303E ALA* 3.9 5.8 - - - +
1304E HIS 3.2 0.8 - - - -
1305E ASN* 1.3 80.9 - - + +
1307E ILE* 1.3 61.7 + - + +
1309E ASP* 3.2 7.7 + - - +
1310E PHE* 3.2 22.3 + - - +
1321E ARG* 3.6 32.8 - - + +
1322E GLU* 3.8 0.7 - - - -
1323E MET* 3.6 38.6 - - + +
1327E LEU* 4.3 5.2 - - + -
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Residues in contact with ILE1307 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1303E ALA* 3.2 20.7 + - + +
1304E HIS* 4.1 7.0 - - - +
1306E ILE* 1.3 76.1 - - + +
1308E GLN* 1.3 64.4 + - - +
1309E ASP 3.1 1.8 - - - -
1310E PHE* 3.2 22.3 + - + +
1311E TYR* 3.6 31.1 + - + +
1323E MET* 4.1 26.7 - - + -
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Residues in contact with GLN1308 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1304E HIS* 2.9 33.4 + - + +
1305E ASN* 3.6 24.0 - - - +
1307E ILE* 1.3 77.7 - - - +
1309E ASP* 1.3 60.0 + - - +
1311E TYR* 3.9 9.1 + - - +
1312E ASN* 3.6 17.0 + - - +
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Residues in contact with ASP1309 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1305E ASN 3.3 16.3 + - - +
1306E ILE* 3.2 14.5 + - - +
1307E ILE 3.1 0.6 - - - -
1308E GLN* 1.3 78.9 - - - +
1310E PHE* 1.3 61.8 + - - +
1312E ASN* 3.3 25.9 + - - +
1315E VAL* 4.2 7.0 - - - +
1321E ARG* 3.2 25.6 + - + +
227F ARG* 2.4 48.2 + - - -
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Residues in contact with PHE1310 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1306E ILE 3.2 11.1 + - - +
1307E ILE* 3.2 15.2 + - + +
1309E ASP* 1.3 77.2 - - - +
1311E TYR* 1.3 89.5 + + - +
1312E ASN 3.3 5.7 + - - +
1315E VAL* 4.7 5.0 - - - +
1320E LYS* 5.8 9.2 - - + -
1321E ARG 5.2 10.8 - - - +
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Residues in contact with TYR1311 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1307E ILE* 3.6 26.7 + - + +
1308E GLN* 3.9 8.3 + - - +
1309E ASP 3.5 0.2 - - - -
1310E PHE* 1.3 100.0 - + - +
1312E ASN* 1.3 64.0 + - - +
1313E PRO* 3.0 12.1 - - - +
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Residues in contact with ASN1312 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1308E GLN 3.6 13.3 + - - +
1309E ASP* 3.3 26.0 + - - +
1310E PHE 3.1 2.8 - - - +
1311E TYR* 1.3 76.2 - - - +
1313E PRO* 1.3 70.2 - - - +
1314E LEU* 3.2 28.6 + - - +
1315E VAL* 3.0 32.5 - - + +
227F ARG* 4.9 2.4 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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