Contacts of the helix formed by residues 1324 - 1351 (chain C) in PDB entry 5Y3R
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 C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
746C ARG* 3.4 27.1 - - - +
1323C SER* 1.3 85.7 - - - +
1325C GLN* 1.3 59.3 + - - +
1327C GLY* 3.1 4.9 + - - -
1328C GLU* 2.9 25.1 + - - +
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Residues in contact with GLN1325 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
712C LYS* 5.7 2.4 + - - -
1118C GLU* 4.9 12.8 + - - +
1323C SER 3.6 0.2 - - - -
1324C PRO* 1.3 81.0 - - - +
1326C GLU* 1.3 69.6 + - + +
1328C GLU* 2.1 63.5 + - - +
1329C ARG* 3.0 13.8 + - - +
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Residues in contact with GLU1326 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1247C PRO* 4.2 31.3 - - - +
1250C LEU* 5.9 0.2 - - - +
1323C SER* 3.2 31.9 - - - +
1325C GLN* 1.3 80.4 - - + +
1327C GLY* 1.3 52.5 + - - +
1329C ARG* 4.9 0.2 - - - +
1330C TYR* 2.7 43.0 + - + +
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Residues in contact with GLY1327 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1323C SER* 3.2 5.7 + - - -
1324C PRO* 3.1 7.1 + - - -
1326C GLU* 1.3 79.4 - - - +
1328C GLU* 1.3 62.7 + - - +
1330C TYR* 4.1 4.9 - - - -
1331C ASN* 2.9 40.6 + - - +
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Residues in contact with GLU1328 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1118C GLU* 5.9 0.7 - - - -
1324C PRO 2.9 8.7 + - - +
1325C GLN* 2.1 57.6 + - - +
1327C GLY* 1.3 74.3 - - - +
1329C ARG* 1.3 109.3 + - - +
1332C TYR* 2.6 46.9 + - + +
1386C ILE* 5.2 2.0 - - - +
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Residues in contact with ARG1329 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1117C ASP* 4.4 11.9 + - - +
1118C GLU* 3.9 23.6 + - - -
1250C LEU* 4.2 27.6 - - + +
1254C LEU 5.9 2.5 - - - +
1255C CYS* 5.9 15.0 - - - +
1325C GLN* 3.0 9.3 + - - +
1326C GLU 4.9 0.2 - - - +
1328C GLU* 1.3 106.6 + - - +
1330C TYR* 1.3 53.1 + - - +
1332C TYR* 3.0 47.7 + - - -
1333C SER* 2.3 44.6 + - - -
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Residues in contact with TYR1330 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1245C ARG 5.6 5.6 - - - -
1250C LEU* 4.7 12.0 - - + +
1305C ASP* 3.8 20.0 + - - +
1326C GLU* 2.7 24.5 + - + +
1327C GLY* 4.1 3.4 - - - +
1329C ARG* 1.3 75.5 - - - +
1331C ASN* 1.3 72.1 + - - +
1333C SER* 2.2 24.6 + - - -
1334C LYS* 2.9 52.1 + - + +
1382C ILE* 6.5 0.4 - - + -
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Residues in contact with ASN1331 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1327C GLY* 2.9 28.6 + - - +
1330C TYR* 1.3 85.8 - - - +
1332C TYR* 1.3 68.7 + - - +
1333C SER 3.1 1.1 - - - -
1334C LYS* 4.4 2.7 - - - +
1335C CYS* 3.0 29.8 + - - +
1381C SER 3.6 21.6 + - - +
1382C ILE* 4.1 4.5 - - - +
1383C GLY* 3.5 19.8 + - - +
1386C ILE* 4.0 5.8 - - + -
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Residues in contact with TYR1332 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1254C LEU 6.0 0.9 - - - -
1255C CYS 5.4 6.9 + - - -
1259C LEU* 4.7 12.1 - - - +
1328C GLU* 2.6 28.9 + - + +
1329C ARG* 3.0 45.9 + - - -
1331C ASN* 1.3 75.4 - - - +
1333C SER* 1.3 63.3 + - - +
1335C CYS* 4.1 1.2 - - - +
1336C THR* 2.1 72.8 + - + +
1340C ARG* 5.8 0.7 + - - -
1386C ILE* 3.5 21.6 - - + +
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Residues in contact with SER1333 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1250C LEU* 4.9 8.2 - - - +
1254C LEU* 5.2 9.9 - - - -
1329C ARG* 2.3 30.8 + - - -
1330C TYR* 2.2 32.2 + - - -
1332C TYR* 1.3 84.4 - - - +
1334C LYS* 1.3 67.4 + - - +
1336C THR* 2.5 31.1 + - - -
1337C VAL* 2.7 20.1 + - - -
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Residues in contact with LYS1334 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1241C LEU* 6.2 1.0 - - - +
1250C LEU* 4.6 14.5 - - - +
1302C ALA* 5.1 3.5 - - + +
1305C ASP* 3.0 52.0 - - - +
1306C ILE* 4.8 1.1 - - + -
1330C TYR* 2.9 68.8 + - + +
1331C ASN* 3.3 1.5 + - - +
1333C SER* 1.3 86.7 + - - +
1335C CYS* 1.3 58.4 + - - +
1337C VAL* 3.0 13.5 - - + +
1338C VAL* 3.0 26.2 + - - +
1382C ILE* 3.5 30.7 - - + +
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Residues in contact with CYS1335 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1331C ASN 3.0 10.8 + - - +
1332C TYR* 4.1 2.7 - - - +
1333C SER 2.7 3.2 + - - -
1334C LYS* 1.3 69.2 - - - +
1336C THR* 1.3 66.3 + - - +
1337C VAL 2.9 2.3 + - - -
1338C VAL* 3.0 11.9 + - + +
1339C VAL* 2.9 31.4 + - + +
1378C GLU* 5.4 0.9 - - - -
1382C ILE* 3.4 16.4 - - - -
1383C GLY* 2.9 53.2 - - - -
1386C ILE* 5.1 3.8 - - + -
1391C VAL* 5.3 11.0 - - + -
1392C MET* 4.9 3.8 - - - -
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Residues in contact with THR1336 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1259C LEU* 3.5 25.1 - - + +
1332C TYR* 2.1 69.5 + - + +
1333C SER* 2.5 10.7 + - - -
1335C CYS* 1.3 72.1 - - - +
1337C VAL* 1.3 53.1 + - - +
1339C VAL* 3.0 10.7 - - + +
1340C ARG* 2.9 43.6 + - + +
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Residues in contact with VAL1337 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1254C LEU* 5.9 2.7 - - + +
1258C ASP* 4.7 17.7 - - + +
1298C LEU 4.9 3.8 - - - +
1299C GLU* 5.0 2.9 - - + -
1302C ALA* 3.7 26.7 - - + -
1305C ASP* 5.6 1.1 - - - +
1333C SER* 2.7 28.7 + - - +
1334C LYS* 3.0 14.4 - - + +
1336C THR* 1.3 73.5 - - - +
1338C VAL* 1.3 70.3 + - - +
1339C VAL 2.9 0.7 + - - -
1340C ARG* 5.2 0.2 - - - -
1341C ILE* 2.9 51.9 + - + +
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Residues in contact with VAL1338 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1299C GLU* 4.5 9.4 - - + +
1302C ALA* 5.9 3.1 - - + -
1334C LYS 3.0 9.5 + - - +
1335C CYS* 3.0 28.5 + - + +
1337C VAL* 1.3 78.9 - - + +
1339C VAL* 1.3 67.0 + - + +
1342C MET* 2.8 64.5 + - + +
1371C VAL* 4.2 20.0 - - + -
1372C LEU* 5.8 4.3 - - + -
1378C GLU* 4.1 19.3 - - - +
1382C ILE* 4.4 5.8 - - + -
1395C LEU* 6.2 1.1 - - + -
1398C VAL* 5.9 0.9 - - + -
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Residues in contact with VAL1339 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1335C CYS* 2.9 19.4 + - + +
1336C THR* 3.0 22.2 - - + +
1338C VAL* 1.3 87.8 - - + +
1340C ARG* 1.3 80.9 + - + +
1342C MET* 3.3 5.5 - - - +
1343C GLU* 2.8 38.4 + - - +
1391C VAL* 5.7 11.0 - - + +
1394C HIS* 6.4 1.3 - - + -
1395C LEU* 5.7 9.0 - - + -
1398C VAL* 4.9 18.2 - - + +
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Residues in contact with ARG1340 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1166C LEU* 3.8 24.0 - - - +
1258C ASP* 5.5 1.3 - - + +
1259C LEU* 3.2 61.0 + - + +
1262C ALA* 3.1 17.7 - - + +
1263C ALA* 5.4 5.0 - - - +
1332C TYR* 5.8 0.4 + - - -
1336C THR* 2.9 27.3 + - + +
1337C VAL* 4.2 0.4 - - - +
1339C VAL* 1.3 83.0 - - + +
1341C ILE* 1.3 60.4 + - + +
1343C GLU* 2.4 54.1 + - + +
1344C PHE 3.0 4.9 + - - -
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Residues in contact with ILE1341 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1258C ASP* 5.1 27.4 - - + +
1261C LEU* 6.1 1.8 - - + -
1262C ALA* 4.6 4.9 - - + +
1295C ALA* 3.9 30.5 - - + +
1296C PHE* 5.8 0.7 - - - -
1298C LEU* 4.9 4.3 - - + -
1299C GLU* 3.1 39.0 - - + +
1337C VAL* 2.9 37.6 + - + +
1340C ARG* 1.3 76.0 - - + +
1342C MET* 1.3 51.6 - - - +
1344C PHE* 3.6 1.4 + - - +
1345C THR* 2.1 38.1 + - - +
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Residues in contact with MET1342 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1299C GLU* 3.3 20.9 - - - +
1338C VAL* 2.8 47.3 + - + +
1339C VAL* 3.3 5.8 - - - +
1341C ILE* 1.3 76.3 - - - +
1343C GLU* 1.3 59.4 + - - +
1345C THR* 3.3 12.8 - - + +
1346C THR* 2.9 33.0 + - - +
1368C LEU* 4.1 14.4 - - + +
1371C VAL* 3.9 21.1 - - + -
1372C LEU* 4.8 6.5 - - + -
1398C VAL* 3.8 20.6 - - + -
1402C LEU* 3.7 33.2 - - + -
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Residues in contact with GLU1343 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1262C ALA* 4.3 6.5 - - + -
1263C ALA* 5.5 1.1 - - + +
1266C CYS* 3.9 6.3 - - - -
1339C VAL* 2.8 32.9 + - - +
1340C ARG* 2.4 53.1 + - - +
1342C MET* 1.3 69.0 - - - +
1344C PHE* 1.3 50.9 + - - +
1346C THR* 3.8 1.5 - - - -
1347C THR* 2.3 37.0 + - - -
1394C HIS* 4.9 15.0 + - - -
1398C VAL* 5.2 4.7 - - - +
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Residues in contact with PHE1344 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1262C ALA* 3.0 27.6 - - - +
1265C GLU* 2.9 48.7 - - + -
1266C CYS* 3.2 19.3 - - - -
1269C THR* 3.5 18.2 - - + -
1275C THR* 3.3 24.0 - - + -
1292C LYS* 4.7 9.6 - - + -
1340C ARG 3.0 4.8 + - - +
1341C ILE 4.7 1.3 - - - +
1343C GLU* 1.3 79.5 - - - +
1345C THR* 1.3 69.5 + - - +
1347C THR* 3.2 5.2 - - - -
1348C LEU* 2.9 49.7 + - + +
1358C LEU* 5.0 0.9 - - + -
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Residues in contact with THR1345 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1296C PHE* 6.1 1.6 - - + -
1299C GLU* 4.0 5.6 + - - +
1341C ILE* 2.1 36.5 + - - +
1342C MET* 3.3 12.8 - - + -
1344C PHE* 1.3 80.6 - - - +
1346C THR* 1.3 59.7 + - - +
1348C LEU* 3.2 8.0 + - - +
1349C LEU* 2.9 42.7 + - + +
1368C LEU* 5.1 15.5 - - + -
1402C LEU* 4.2 11.7 - - + -
1406C LEU* 6.1 0.4 - - + -
----------------------------------------------------------
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Residues in contact with THR1346 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1342C MET* 2.9 18.5 + - - +
1343C GLU* 4.4 0.9 - - - -
1345C THR* 1.3 71.8 - - - +
1347C THR* 1.3 66.9 + - - +
1349C LEU* 3.7 7.6 - - - -
1350C ASN* 2.9 27.9 + - + +
1398C VAL* 5.6 0.9 - - - +
1401C ASN* 3.2 40.4 - - + +
1402C LEU* 3.2 28.8 + - - +
1405C ALA* 3.6 10.1 - - + -
----------------------------------------------------------
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Residues in contact with THR1347 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1266C CYS* 2.6 41.9 - - + +
1269C THR* 3.5 18.6 - - + +
1270C PHE* 4.6 5.6 - - + -
1343C GLU 2.3 30.4 + - - -
1344C PHE* 3.2 14.4 - - + -
1345C THR 3.1 0.2 - - - -
1346C THR* 1.3 76.7 - - - +
1348C LEU* 1.3 53.5 + - - +
1350C ASN* 3.9 1.9 - - - +
1351C THR* 2.7 43.0 + - + +
----------------------------------------------------------
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Residues in contact with LEU1348 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1269C THR* 3.5 6.5 - - + -
1275C THR* 3.5 24.5 - - - +
1276C VAL* 5.6 0.4 - - + -
1296C PHE* 6.5 0.7 - - + -
1344C PHE* 2.9 55.8 + - + +
1345C THR* 3.4 8.1 - - - +
1347C THR* 1.3 74.4 - - - +
1349C LEU* 1.3 65.0 + - + +
1351C THR* 2.6 29.0 + - - +
1353C PRO 4.8 8.1 - - - +
1354C GLU* 4.5 4.1 - - - +
1358C LEU* 3.7 31.6 - - + -
1359C LEU* 5.6 6.5 - - + -
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Residues in contact with LEU1349 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1345C THR* 2.9 26.9 + - + +
1346C THR* 3.4 12.8 + - - +
1348C LEU* 1.3 72.2 - - - +
1350C ASN* 1.3 58.9 + - - +
1354C GLU* 2.7 31.5 - - - +
1359C LEU* 3.5 27.8 - - + -
1402C LEU* 3.7 27.1 - - + +
1405C ALA* 3.3 29.3 - - + +
1406C LEU* 3.6 35.4 - - + -
1408C MET* 5.4 2.8 - - - +
1410C PRO* 3.6 6.7 - - + -
----------------------------------------------------------
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Residues in contact with ASN1350 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1346C THR* 2.9 21.3 + - + +
1347C THR* 4.0 1.6 - - - +
1349C LEU* 1.3 80.0 - - - +
1351C THR* 1.3 68.3 + - + +
1352C SER* 3.2 3.8 + - - -
1354C GLU* 4.3 2.6 - - - +
1401C ASN* 5.7 5.3 + - - +
1405C ALA* 3.6 15.0 - - + +
1408C MET* 5.9 6.8 - - - +
----------------------------------------------------------
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Residues in contact with THR1351 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1269C THR* 3.6 29.1 - - - +
1270C PHE* 4.3 11.7 - - + -
1347C THR* 2.7 25.5 + - + +
1348C LEU* 2.6 44.8 + - - +
1350C ASN* 1.3 71.9 - - + +
1352C SER* 1.3 66.9 + - - +
1353C PRO* 3.1 21.8 + - + +
1354C GLU* 3.2 14.4 + - - +
----------------------------------------------------------
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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