Contacts of the helix formed by residues 1401 - 1429 (chain A) in PDB entry 3MB3
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 SER1401 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1396A THR* 3.4 26.3 - - - +
1398A SER* 3.2 19.4 + - - -
1399A LYS 3.1 2.5 - - - +
1400A ARG* 1.3 78.6 - - - +
1402A ARG* 1.3 66.1 + - - +
1403A ILE* 3.1 15.6 + - - +
1404A TYR* 3.1 17.4 + - - +
1405A SER* 3.4 8.7 + - - -
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Residues in contact with ARG1402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1400A ARG 3.6 3.0 + - - -
1401A SER* 1.3 74.8 + - - +
1403A ILE* 1.3 77.3 + - + +
1405A SER* 3.4 9.5 + - - -
1406A MET* 3.1 32.8 + - + +
1409A ARG* 4.8 0.5 + - - -
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Residues in contact with ILE1403 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MB3 4.1 28.7 - - - +
1340A PRO* 3.7 27.4 - - + -
1341A PHE* 4.0 23.1 - - + -
1392A SER* 4.3 8.7 - - - +
1396A THR* 4.1 10.1 - - + +
1401A SER* 3.1 11.3 + - - +
1402A ARG* 1.3 85.7 - - + +
1404A TYR* 1.3 66.1 + - - +
1406A MET* 3.3 13.5 + - - +
1407A SER* 3.0 22.9 + - - -
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Residues in contact with TYR1404 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1392A SER* 5.3 1.8 - - - -
1393A LYS* 4.6 28.7 - - + -
1396A THR* 3.7 18.6 - - - +
1397A PRO 3.6 20.2 - - - -
1398A SER 3.2 26.2 - - - +
1399A LYS* 3.7 44.9 - - + -
1401A SER* 3.1 11.0 + - - +
1403A ILE* 1.3 79.5 - - - +
1405A SER* 1.3 61.9 + - - +
1407A SER* 3.3 6.3 + - - -
1408A LEU* 3.0 57.0 + - + +
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Residues in contact with SER1405 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1399A LYS 4.5 6.2 + - - -
1401A SER 3.4 11.5 + - - -
1402A ARG* 3.4 9.6 + - - -
1403A ILE 3.3 0.8 - - - -
1404A TYR* 1.3 80.2 - - - +
1406A MET* 1.3 61.3 + - - +
1408A LEU* 3.2 7.4 + - - +
1409A ARG* 2.9 52.6 + - - +
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Residues in contact with MET1406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1336A GLU 3.6 5.8 - - - +
1337A ASP* 2.8 52.4 - - - +
1339A GLU* 4.9 0.7 - - + -
1340A PRO* 3.1 24.9 - - + -
1341A PHE* 4.7 2.0 - - + -
1402A ARG* 3.1 25.4 + - + +
1403A ILE* 3.3 28.5 + - - +
1405A SER* 1.3 75.6 - - - +
1407A SER* 1.3 63.9 - - - +
1409A ARG* 3.2 26.4 + - - +
1410A LEU* 2.9 26.4 + - - +
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Residues in contact with SER1407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1341A PHE* 3.7 17.6 - - - -
1389A PHE* 3.7 24.1 + - - +
1392A SER* 3.7 25.6 + - - -
1393A LYS* 5.1 1.2 + - - +
1403A ILE 3.0 16.9 + - - -
1404A TYR* 3.5 5.4 - - - -
1406A MET* 1.3 78.1 - - - +
1408A LEU* 1.3 58.0 + - - +
1410A LEU* 3.8 2.2 - - - -
1411A SER* 2.8 30.4 + - - -
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Residues in contact with LEU1408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1393A LYS* 6.4 2.7 - - + -
1404A TYR* 3.0 48.3 + - + +
1405A SER* 3.2 9.4 + - - +
1407A SER* 1.3 76.2 - - - +
1409A ARG* 1.3 58.5 + - + +
1411A SER* 3.3 8.5 + - - -
1412A ALA* 2.9 30.0 + - - +
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Residues in contact with ARG1409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1337A ASP* 2.9 42.7 + - - +
1402A ARG 4.8 0.2 + - - -
1405A SER* 2.9 40.4 + - - +
1406A MET* 3.2 23.5 + - - +
1408A LEU* 1.3 76.3 - - + +
1410A LEU* 1.3 63.4 - - - +
1412A ALA* 3.3 7.2 + - - +
1413A PHE* 3.0 23.4 + - - +
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Residues in contact with LEU1410 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1332A ILE* 3.9 23.5 - - + +
1335A CYS* 3.5 32.5 - - - -
1337A ASP* 3.8 12.5 + - + +
1338A SER* 3.6 26.9 - - - +
1341A PHE* 3.9 15.9 - - + -
1363A PHE* 4.0 9.2 - - + -
1389A PHE* 4.0 15.5 - - + -
1406A MET 2.9 15.0 + - - +
1407A SER 3.9 3.1 - - - +
1409A ARG* 1.3 77.2 - - - +
1411A SER* 1.3 59.4 + - - +
1413A PHE* 3.4 10.8 + - + +
1414A PHE* 2.8 29.3 + - - +
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Residues in contact with SER1411 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1389A PHE* 3.6 34.6 - - - +
1407A SER 2.8 18.7 + - - -
1408A LEU* 3.6 12.8 - - - -
1410A LEU* 1.3 77.1 - - - +
1412A ALA* 1.3 52.1 + - - +
1414A PHE* 3.1 3.1 + - - +
1415A GLU* 2.8 47.7 + - - +
----------------------------------------------------------
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Residues in contact with ALA1412 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1408A LEU 2.9 17.9 + - - +
1409A ARG* 3.6 8.3 - - - +
1411A SER* 1.3 74.5 - - - +
1413A PHE* 1.3 57.0 + - - +
1415A GLU* 3.5 6.4 + - - +
1416A GLU* 3.0 39.6 + - + +
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Residues in contact with PHE1413 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1328A LEU* 3.9 19.5 - - + -
1331A LEU* 4.4 25.6 - - + -
1332A ILE* 4.2 22.0 - - + -
1335A CYS* 6.1 1.3 - - - -
1409A ARG 3.0 13.2 + - - +
1410A LEU* 3.4 15.9 - - + +
1412A ALA* 1.3 74.6 - - - +
1414A PHE* 1.3 68.6 + - - +
1416A GLU* 3.3 12.1 + - - +
1417A HIS* 3.1 55.2 + + - -
----------------------------------------------------------
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Residues in contact with PHE1414 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1328A LEU* 4.0 24.7 - - + -
1329A LEU* 5.5 2.2 - - + -
1332A ILE* 4.0 17.5 - - + -
1381A LEU* 4.4 5.8 - - + -
1382A CYS* 4.2 17.0 - - - -
1385A VAL* 3.6 46.9 - - + -
1386A ARG* 4.8 2.9 - - + -
1389A PHE* 4.1 11.4 - + + -
1410A LEU 2.8 17.6 + - - +
1411A SER 3.4 6.7 - - - +
1413A PHE* 1.3 77.7 - - - +
1415A GLU* 1.3 83.4 + - + +
1417A HIS* 3.0 4.0 + - - +
1418A ILE* 2.8 55.3 + - + +
----------------------------------------------------------
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Residues in contact with GLU1415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1386A ARG* 2.8 53.6 + - - +
1389A PHE* 5.4 0.7 - - - -
1411A SER* 2.8 34.9 + - - +
1412A ALA* 3.9 5.6 - - - +
1414A PHE* 1.3 83.2 - - - +
1416A GLU* 1.3 61.3 + - - +
1417A HIS 3.3 0.3 + - - -
1418A ILE* 3.7 7.9 - - - +
1419A SER* 2.9 29.1 + - - -
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Residues in contact with GLU1416 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1412A ALA* 3.0 27.1 + - + +
1413A PHE* 3.5 14.9 - - - +
1414A PHE 3.2 0.4 - - - -
1415A GLU* 1.3 78.8 - - - +
1417A HIS* 1.3 79.0 + - + +
1419A SER* 4.1 10.9 + - - -
1420A SER* 4.2 6.2 + - - -
----------------------------------------------------------
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Residues in contact with HIS1417 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1328A LEU* 3.7 28.0 - - + -
1331A LEU* 6.0 4.6 - - + +
1413A PHE* 3.1 55.7 + + - +
1414A PHE 3.0 2.6 + - - -
1416A GLU* 1.3 96.3 + - + +
1418A ILE* 1.3 65.6 + - - +
1419A SER 3.4 0.4 + - - -
1420A SER* 3.6 12.4 + - - -
1421A VAL* 3.4 15.9 + - - +
----------------------------------------------------------
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Residues in contact with ILE1418 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1325A CYS* 4.0 21.3 - - - -
1328A LEU* 4.2 9.4 - - + +
1378A PRO* 5.5 1.6 - - + -
1381A LEU* 4.8 2.5 - - + -
1382A CYS* 3.4 30.1 - - - -
1386A ARG* 4.6 4.3 - - - +
1414A PHE* 2.8 50.2 + - + +
1415A GLU* 3.7 18.6 - - - +
1417A HIS* 1.3 76.0 - - - +
1419A SER* 1.3 70.9 + - - +
1421A VAL* 2.8 35.2 + - + +
1422A LEU* 2.9 20.5 + - + +
----------------------------------------------------------
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Residues in contact with SER1419 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1415A GLU 2.9 16.5 + - - -
1416A GLU* 4.1 8.9 + - - -
1418A ILE* 1.3 80.3 - - - +
1420A SER* 1.3 56.7 + - - +
1422A LEU* 3.2 7.3 + - - +
1423A SER* 2.7 37.9 + - - -
----------------------------------------------------------
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Residues in contact with SER1420 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1416A GLU 4.2 8.7 + - - -
1417A HIS* 3.6 9.7 + - - -
1418A ILE 3.2 0.8 - - - -
1419A SER* 1.3 76.8 - - - +
1421A VAL* 1.3 61.6 + - - +
1423A SER* 4.4 6.3 - - - -
1424A ASP* 2.9 44.3 + - - -
----------------------------------------------------------
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Residues in contact with VAL1421 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1321A TRP* 3.8 21.4 - - + +
1324A GLN* 3.4 42.2 - - + +
1325A CYS* 4.1 9.9 - - - -
1328A LEU* 5.2 3.8 - - + -
1378A PRO* 4.6 6.1 - - + -
1417A HIS* 3.4 17.0 - - + +
1418A ILE* 2.8 28.4 + - + +
1420A SER* 1.3 79.3 - - - +
1422A LEU* 1.3 58.6 + - - +
1424A ASP* 4.0 2.6 - - - +
1425A TYR* 3.2 24.4 + - - +
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Residues in contact with LEU1422 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1378A PRO* 4.0 27.4 - - + -
1379A MET* 4.1 31.0 - - + +
1382A CYS* 4.2 20.2 - - + -
1386A ARG* 5.1 10.1 - - - +
1418A ILE* 2.9 26.5 + - + +
1419A SER* 3.7 7.9 - - - +
1421A VAL* 1.3 75.0 - - - +
1423A SER* 1.3 59.9 + - - +
1424A ASP 3.2 0.2 - - - -
1425A TYR* 3.0 6.0 + - + +
1426A LYS* 2.8 41.0 + - + +
----------------------------------------------------------
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Residues in contact with SER1423 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1419A SER* 2.7 23.1 + - - -
1420A SER* 4.1 7.0 - - - -
1422A LEU* 1.3 71.4 - - - +
1424A ASP* 1.3 64.1 + - - +
1426A LYS* 3.6 6.9 + - - +
1427A SER* 3.2 26.2 + - - -
----------------------------------------------------------
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Residues in contact with ASP1424 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1316A TYR* 5.2 10.2 - - + +
1317A ASP 5.3 0.4 - - - +
1324A GLN* 4.5 17.0 + - - +
1420A SER* 2.9 31.8 + - - +
1421A VAL* 4.0 4.3 - - - +
1423A SER* 1.3 78.0 - - - +
1425A TYR* 1.3 60.7 + - - +
1427A SER* 3.7 6.7 + - - -
1428A ALA* 3.0 29.3 + - - +
----------------------------------------------------------
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Residues in contact with TYR1425 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1317A ASP 5.9 1.3 - - - -
1318A ILE* 4.1 18.4 - - + -
1321A TRP* 3.9 24.0 - + + -
1376A GLU* 4.8 5.1 + - - -
1377A SER* 3.7 13.4 - - - -
1378A PRO* 3.7 28.7 - - + -
1379A MET* 3.7 32.0 - - + +
1421A VAL 3.2 14.9 + - - +
1422A LEU* 3.0 11.0 + - - +
1424A ASP* 1.3 74.1 - - - +
1426A LYS* 1.3 68.4 - - + +
1428A ALA* 3.0 5.9 + - - +
1429A LEU* 2.9 69.0 + - + +
----------------------------------------------------------
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Residues in contact with LYS1426 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1379A MET* 4.3 34.0 - - - +
1422A LEU* 2.8 31.0 + - + +
1423A SER* 4.0 6.5 - - - +
1425A TYR* 1.3 77.4 - - + +
1427A SER* 1.3 61.2 + - - +
1429A LEU* 3.3 27.1 - - + +
1430A ARG* 3.9 4.7 + - - +
----------------------------------------------------------
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Residues in contact with SER1427 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1423A SER 3.2 15.9 + - - -
1424A ASP* 3.7 7.6 + - - -
1426A LYS* 1.3 75.6 - - - +
1428A ALA* 1.3 62.4 + - - +
1429A LEU 3.1 1.6 - - - -
1430A ARG* 2.8 34.2 + - - +
1431A PHE* 5.0 0.7 - - - +
----------------------------------------------------------
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Residues in contact with ALA1428 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1316A TYR* 3.8 30.2 - - + +
1317A ASP 4.1 16.8 - - - +
1318A ILE* 4.5 12.8 - - + +
1424A ASP 3.0 23.1 + - - +
1425A TYR* 3.5 6.1 - - - +
1427A SER* 1.3 76.2 + - - +
1429A LEU* 1.3 60.0 + - - +
1430A ARG 3.1 4.4 + - - -
1431A PHE* 3.9 15.3 + - - +
----------------------------------------------------------
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Residues in contact with LEU1429 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1318A ILE* 3.5 35.0 - - + -
1379A MET* 6.3 0.2 - - + -
1425A TYR* 2.9 54.8 + - + +
1426A LYS* 3.3 18.8 - - + +
1427A SER 3.1 0.4 - - - -
1428A ALA* 1.3 75.0 - - - +
1430A ARG* 1.3 56.2 + - - +
1431A PHE 3.9 1.6 + - - -
----------------------------------------------------------
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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