Contacts of the helix formed by residues 1434 - 1461 (chain B) in PDB entry 5NPK
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 THR1434 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1430B LEU 5.2 0.9 - - - +
1431B ARG* 3.0 25.7 + - + +
1432B ARG 3.2 0.7 - - - +
1433B LEU* 1.3 83.7 - - - +
1435B GLY* 1.3 65.0 + - - +
1436B LEU* 4.4 2.7 + - - +
1437B GLU* 3.3 27.4 + - - +
1438B ARG* 3.6 6.2 + - - +
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Residues in contact with GLY1435 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1434B THR* 1.3 70.5 - - - +
1436B LEU* 1.3 69.6 + - - +
1437B GLU 3.3 0.5 + - - -
1438B ARG* 3.3 15.4 + - - +
1439B ASP* 3.7 13.6 + - - +
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Residues in contact with LEU1436 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1434B THR* 3.4 3.1 + - - +
1435B GLY* 1.3 77.8 - - - +
1437B GLU* 1.3 58.5 + - - +
1439B ASP* 3.1 16.4 + - - +
1440B LYS* 2.9 35.5 + - + +
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Residues in contact with GLU1437 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1431B ARG* 3.7 3.1 - - + +
1432B ARG* 3.1 62.4 + - + +
1434B THR* 3.3 19.8 + - - +
1435B GLY 3.2 0.6 - - - -
1436B LEU* 1.3 76.3 - - + +
1438B ARG* 1.3 63.5 + - - +
1440B LYS* 3.2 16.5 + - - +
1441B ILE* 3.0 30.8 + - + +
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Residues in contact with ARG1438 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1385B ARG* 3.6 25.5 + - - +
1388B LEU* 3.9 35.0 - - + +
1389B ASP* 3.1 34.9 + - - +
1432B ARG 4.5 1.2 + - - +
1434B THR 3.6 6.2 + - - +
1435B GLY* 3.3 10.8 + - - +
1436B LEU 3.3 0.6 - - - -
1437B GLU* 1.3 78.4 - - - +
1439B ASP* 1.3 68.3 + - - +
1441B ILE* 3.3 3.4 + - - +
1442B GLU* 2.8 48.2 + - + +
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Residues in contact with ASP1439 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1435B GLY 3.7 13.7 + - - +
1436B LEU* 3.1 16.5 + - - +
1438B ARG* 1.3 80.5 - - - +
1440B LYS* 1.3 60.7 + - + +
1442B GLU* 3.2 7.4 + - - +
1443B ALA* 2.8 30.7 + - - +
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Residues in contact with LYS1440 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1436B LEU* 2.9 27.3 + - + +
1437B GLU* 3.6 24.0 - - - +
1439B ASP* 1.3 75.4 - - + +
1441B ILE* 1.3 59.9 + - + +
1443B ALA* 3.4 5.4 + - - +
1444B GLU* 3.0 30.4 + - - +
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Residues in contact with ILE1441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1381B LEU* 4.0 23.2 - - + +
1384B LEU* 4.3 15.3 - - + -
1385B ARG* 3.9 26.2 - - + +
1388B LEU* 3.6 28.0 - - + -
1428B MET* 5.3 0.9 - - - -
1432B ARG* 3.4 36.3 - - + +
1437B GLU* 3.0 20.8 + - - +
1438B ARG* 3.7 8.3 - - - +
1440B LYS* 1.3 77.9 - - + +
1442B GLU* 1.3 57.0 + - - +
1444B GLU* 3.5 7.7 + - - +
1445B TYR* 3.0 26.7 + - - +
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Residues in contact with GLU1442 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1385B ARG* 2.7 37.0 + - - -
1438B ARG* 2.8 48.8 + - - +
1439B ASP* 3.7 8.5 - - - +
1441B ILE* 1.3 78.7 - - - +
1443B ALA* 1.3 57.1 + - - +
1445B TYR* 3.2 4.6 + - - +
1446B ASN* 3.0 55.0 + - - +
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Residues in contact with ALA1443 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1439B ASP 2.8 18.4 + - - +
1440B LYS* 3.9 5.6 - - - +
1442B GLU* 1.3 76.1 - - - +
1444B GLU* 1.3 61.8 + - - +
1446B ASN* 3.6 7.3 + - - +
1447B GLU* 3.1 24.8 + - - +
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Residues in contact with GLU1444 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1377B ARG* 2.9 50.3 + - - +
1381B LEU* 3.8 11.7 - - + +
1440B LYS 3.0 18.8 + - - +
1441B ILE* 3.9 6.0 - - - +
1442B GLU 3.3 0.2 - - - -
1443B ALA* 1.3 74.8 - - - +
1445B TYR* 1.3 59.4 + - - +
1447B GLU* 3.4 5.8 + - + +
1448B LEU* 2.9 34.1 + - + +
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Residues in contact with TYR1445 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1378B ALA* 3.7 18.2 - - + -
1381B LEU* 3.7 28.9 - - + +
1382B GLU* 2.6 44.9 + - + +
1385B ARG* 3.6 40.2 + - - +
1441B ILE 3.0 19.0 + - - +
1442B GLU* 3.2 6.7 + - - +
1444B GLU* 1.3 77.0 - - - +
1446B ASN* 1.3 70.6 + - - +
1448B LEU* 3.1 5.1 + - - +
1449B LEU* 3.0 54.4 + - + +
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Residues in contact with ASN1446 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1385B ARG* 5.5 0.2 + - - -
1442B GLU* 3.0 43.0 + - - +
1443B ALA* 4.2 6.0 - - - +
1445B TYR* 1.3 86.2 - - - +
1447B GLU* 1.3 63.8 + - - +
1449B LEU* 3.2 15.6 + - - +
1450B ASN* 3.2 28.9 + - - +
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Residues in contact with GLU1447 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1443B ALA 3.1 18.4 + - - +
1444B GLU* 3.8 6.5 - - + +
1446B ASN* 1.3 77.3 - - - +
1448B LEU* 1.3 56.5 + - - +
1450B ASN* 3.4 10.9 + - - +
1451B TYR* 3.0 28.4 + - + +
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Residues in contact with LEU1448 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1374B ALA* 3.8 30.7 - - + +
1377B ARG* 3.4 34.1 - - + -
1378B ALA* 3.6 19.1 - - + +
1381B LEU* 3.6 17.5 - - + -
1444B GLU* 2.9 21.2 + - + +
1445B TYR* 3.1 6.0 + - - +
1447B GLU* 1.3 75.0 - - - +
1449B LEU* 1.3 59.7 + - - +
1451B TYR* 3.5 14.9 - - + +
1452B ILE* 2.8 40.3 + - + +
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Residues in contact with LEU1449 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1378B ALA* 5.1 3.4 - - + -
1382B GLU* 5.2 0.9 - - - +
1445B TYR* 3.0 62.2 + - + +
1446B ASN* 3.2 16.5 + - - +
1448B LEU* 1.3 77.9 - - - +
1450B ASN* 1.3 65.6 + - - +
1452B ILE* 3.4 15.5 + - + +
1453B SER* 3.1 23.0 + - - -
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Residues in contact with ASN1450 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1446B ASN* 3.2 18.1 + - - +
1447B GLU* 3.7 10.2 - - + +
1449B LEU* 1.3 78.4 - - - +
1451B TYR* 1.3 63.3 + - - +
1453B SER* 3.4 6.8 + - - -
1454B GLU* 3.1 37.9 + - - +
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Residues in contact with TYR1451 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1370B ASN* 3.5 31.0 + - + +
1374B ALA* 4.1 17.5 - - + -
1447B GLU* 3.0 20.1 + - + +
1448B LEU* 3.2 15.9 + - + +
1450B ASN* 1.3 74.9 - - - +
1452B ILE* 1.3 64.7 + - - +
1454B GLU* 3.2 17.0 + - + +
1455B LEU* 3.0 57.8 + - + +
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Residues in contact with ILE1452 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1371B LEU* 3.8 16.4 - - + -
1374B ALA* 3.6 40.8 - - + +
1375B LYS* 3.8 15.9 - - + +
1378B ALA* 4.1 16.6 - - + -
1448B LEU* 2.8 27.6 + - + +
1449B LEU* 3.8 13.7 - - + +
1451B TYR* 1.3 71.2 - - - +
1453B SER* 1.3 64.2 + - - +
1455B LEU* 3.2 5.1 + - - +
1456B GLU* 3.0 49.6 + - - +
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Residues in contact with SER1453 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1449B LEU 3.1 17.9 + - - -
1450B ASN* 3.7 7.4 - - - -
1452B ILE* 1.3 77.4 - - - +
1454B GLU* 1.3 65.9 + - - +
1456B GLU* 3.4 13.5 + - - +
1457B THR* 3.0 29.3 + - - -
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Residues in contact with GLU1454 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1450B ASN* 3.1 28.9 + - - +
1451B TYR* 3.2 22.7 + - + +
1453B SER* 1.3 75.7 - - - +
1455B LEU* 1.3 65.4 + - + +
1457B THR* 3.3 8.8 + - - -
1458B ILE* 3.3 27.9 + - + +
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Residues in contact with LEU1455 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1367B THR* 3.6 29.9 - - + +
1370B ASN* 3.7 13.2 - - + +
1371B LEU* 3.6 41.5 - - + +
1374B ALA* 4.5 2.5 - - + -
1451B TYR* 3.0 60.7 + - + +
1452B ILE 3.2 3.8 + - - +
1454B GLU* 1.3 75.7 - - - +
1456B GLU* 1.3 62.0 + - - +
1458B ILE* 3.3 15.1 + - + +
1459B LEU* 3.1 27.3 + - - +
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Residues in contact with GLU1456 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1371B LEU* 3.9 19.7 - - + +
1375B LYS* 3.2 26.2 + - - -
1452B ILE* 3.0 28.2 + - - +
1453B SER* 3.8 12.5 - - - +
1455B LEU* 1.3 73.2 - - - +
1457B THR* 1.3 61.1 + - - +
1459B LEU* 3.3 7.3 + - - +
1460B ALA* 2.9 31.8 + - - +
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Residues in contact with THR1457 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1453B SER* 3.0 17.8 + - - -
1454B GLU* 3.5 11.5 - - - -
1455B LEU 3.3 0.2 - - - -
1456B GLU* 1.3 77.2 - - - +
1458B ILE* 1.3 62.2 + - + +
1460B ALA* 3.3 6.6 + - - +
1461B ASP* 3.3 23.7 + - + +
1464B VAL* 4.0 20.3 - - + +
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Residues in contact with ILE1458 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1367B THR* 4.0 23.8 - - + +
1454B GLU* 3.3 18.3 + - + +
1455B LEU* 3.5 17.9 - - + +
1456B GLU 3.3 0.6 - - - -
1457B THR* 1.3 77.0 - - - +
1459B LEU* 1.3 60.0 + - - +
1461B ASP 3.0 22.2 - - - +
1464B VAL* 3.7 21.3 - - + +
1465B LEU* 3.8 35.2 - - + +
1468B LEU* 3.7 28.5 - - + -
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Residues in contact with LEU1459 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1364B ARG* 4.0 22.7 - - + +
1367B THR* 3.6 20.9 - - + -
1368B GLN* 3.7 39.3 - - + +
1371B LEU* 3.7 30.3 - - + -
1455B LEU 3.1 14.2 + - - +
1456B GLU* 3.3 5.4 + - - +
1458B ILE* 1.3 77.7 - - + +
1460B ALA* 1.3 59.4 + - - +
1461B ASP 3.8 0.6 + - - -
1465B LEU* 5.0 2.5 - - + -
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Residues in contact with ALA1460 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1456B GLU 2.9 16.8 + - - +
1457B THR* 3.9 7.6 - - - +
1458B ILE 3.2 0.4 - - - -
1459B LEU* 1.3 79.5 - - - +
1461B ASP* 1.3 58.2 + - + +
1462B GLU 4.2 1.0 + - - -
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Residues in contact with ASP1461 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1457B THR* 3.3 8.0 + - + +
1458B ILE 3.0 15.8 - - - +
1459B LEU 3.5 1.1 - - - -
1460B ALA* 1.3 81.0 - - + +
1462B GLU* 1.3 64.2 + - - +
1463B GLU* 2.9 29.2 + - - +
1464B VAL* 3.1 30.7 + - + +
1465B LEU 3.1 10.7 + - - -
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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