Contacts of the helix formed by residues 1398 - 1420 (chain A) in PDB entry 3RYT
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 GLU1398 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1361A THR* 6.2 3.1 - - + -
1395A LEU* 2.8 17.4 + - + +
1397A GLY* 1.3 82.7 - - - +
1399A MET* 1.3 53.1 - - - +
1400A GLU* 3.0 9.0 - - - +
1401A TYR* 2.7 42.5 + - + -
1402A ALA* 3.2 9.4 + - - +
1837A SER* 3.4 2.5 - - - -
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Residues in contact with MET1399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1392A MET* 6.5 1.1 - - + -
1395A LEU 3.3 7.2 + - - +
1396A GLN* 4.6 6.7 - - - +
1398A GLU* 1.3 75.1 - - - +
1400A GLU* 1.3 57.4 + - - +
1401A TYR 3.1 0.2 - - - -
1402A ALA* 4.0 7.7 - - - +
1403A THR* 2.7 35.0 + - - +
1442A TRP* 6.0 2.7 - - + +
1445A PHE* 6.5 1.1 - - + -
1446A LEU* 5.6 7.2 - - + -
1833A LEU* 3.9 18.7 - - + +
1836A GLN 5.4 1.8 - - - +
1837A SER* 3.2 21.7 + - - +
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Residues in contact with GLU1400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1398A GLU* 3.0 3.3 - - - -
1399A MET* 1.3 78.4 - - - +
1401A TYR* 1.3 59.3 + - - +
1403A THR* 4.3 3.7 + - - -
1404A GLY* 4.2 7.6 + - - -
1830A SER* 4.4 22.9 + - - +
1833A LEU* 4.0 26.7 + - + +
1834A ALA* 4.6 8.1 - - + +
1837A SER* 4.9 0.8 - - - -
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Residues in contact with TYR1401 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1360A LEU 3.1 12.6 + - - -
1361A THR* 2.9 44.7 + - + -
1363A LYS* 3.6 18.3 - - + -
1366A LEU* 3.5 16.7 - - + +
1395A LEU* 3.6 39.9 - - + -
1398A GLU* 2.7 19.1 + - + +
1400A GLU* 1.3 78.0 - - - +
1402A ALA* 1.3 62.2 + - - +
1403A THR 3.0 4.3 - - - -
1404A GLY* 2.7 25.3 + - - -
1405A VAL* 3.3 28.1 + - + +
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Residues in contact with ALA1402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1392A MET* 4.7 21.5 - - + -
1395A LEU* 3.7 35.2 - - + +
1398A GLU 3.2 5.9 + - - +
1399A MET* 4.4 7.4 - - - +
1401A TYR* 1.3 83.2 - - - +
1403A THR* 1.3 57.1 + - - +
1404A GLY 3.3 0.2 - - - -
1405A VAL* 3.5 7.5 + - - +
1406A LEU* 3.0 28.4 + - - +
1438A MET* 4.6 5.5 - - + +
1442A TRP* 5.6 2.4 - - + -
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Residues in contact with THR1403 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1399A MET* 2.7 23.2 + - - +
1400A GLU 4.3 2.9 - - - -
1401A TYR 2.9 0.8 + - - -
1402A ALA* 1.3 76.1 - - - +
1404A GLY* 1.3 63.2 + - - +
1406A LEU* 3.9 6.8 - - + +
1407A LYS* 3.0 28.2 + - + +
1442A TRP* 3.0 32.3 + - + +
1715A TYR* 3.9 33.4 - - + +
1716A MET* 5.6 1.6 - - + -
1833A LEU* 3.5 20.4 - - + +
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Residues in contact with GLY1404 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1400A GLU 4.2 4.4 + - - -
1401A TYR* 2.7 11.8 + - - -
1403A THR* 1.3 77.5 - - - +
1405A VAL* 1.3 62.4 + - - -
1407A LYS* 3.5 16.0 + - - +
1408A GLN* 3.3 20.3 + - - +
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Residues in contact with VAL1405 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1363A LYS* 4.9 5.8 - - + +
1366A LEU* 4.0 23.6 - - + -
1367A LEU* 3.4 25.1 - - + -
1401A TYR* 3.3 46.4 + - + +
1402A ALA* 3.9 7.4 - - - +
1404A GLY* 1.3 74.0 - - - +
1406A LEU* 1.3 59.9 + - - +
1408A GLN* 2.9 8.4 + - - +
1409A LEU* 2.8 48.0 + - + +
1438A MET* 5.4 4.9 - - + -
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Residues in contact with LEU1406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1392A MET* 6.1 1.1 - - + -
1402A ALA 3.0 18.8 + - - +
1403A THR* 3.9 5.8 - - + +
1404A GLY 3.3 0.2 - - - -
1405A VAL* 1.3 76.1 - - - +
1407A LYS* 1.3 58.4 + - + +
1409A LEU* 3.3 6.8 + - + +
1410A LEU* 2.9 49.4 + - + +
1435A ALA* 3.6 28.3 - - + +
1438A MET* 3.6 24.9 - - + +
1439A LEU* 3.8 17.7 - - + +
1442A TRP* 3.7 43.5 - - + +
1716A MET* 5.1 4.0 - - + -
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Residues in contact with LYS1407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1403A THR* 3.0 26.2 + - + +
1404A GLY* 3.7 13.7 - - - +
1405A VAL 3.2 0.4 - - - -
1406A LEU* 1.3 78.9 - - + +
1408A GLN* 1.3 57.6 + - - +
1410A LEU* 4.5 2.9 - - - -
1411A SER* 2.9 27.7 + - - -
1715A TYR* 3.1 32.3 + - + +
1716A MET* 5.2 7.4 - - + -
1719A PHE* 3.4 48.4 - - + -
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Residues in contact with GLN1408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1367A LEU* 3.7 32.5 - - + -
1404A GLY 3.3 9.3 + - - +
1405A VAL* 2.9 11.0 + - - +
1407A LYS* 1.3 77.6 - - - +
1409A LEU* 1.3 63.5 + - + +
1411A SER* 3.5 9.6 + - - -
1412A ASP* 3.4 42.7 + - - +
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Residues in contact with LEU1409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1367A LEU* 3.6 26.0 - - + +
1370A ILE* 3.5 46.7 - - + -
1371A ARG* 5.9 0.7 - - + +
1405A VAL* 2.8 28.4 + - + +
1406A LEU* 3.8 4.5 - - - +
1408A GLN* 1.3 77.7 - - + +
1410A LEU* 1.3 59.0 + - - +
1412A ASP* 3.9 5.4 + - - +
1413A LEU* 3.2 27.5 + - - +
1435A ALA* 3.7 22.6 - - + +
1438A MET* 3.8 21.3 - - + -
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Residues in contact with LEU1410 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1406A LEU* 2.9 45.2 + - + +
1407A LYS* 4.0 6.5 - - - +
1409A LEU* 1.3 75.1 - - - +
1411A SER* 1.3 66.7 + - - +
1413A LEU* 3.9 12.7 - - + +
1414A ILE* 3.2 29.2 + - + +
1428A LEU* 5.4 5.4 - - + -
1435A ALA* 3.6 30.1 - - + +
1436A GLU* 4.2 7.0 - - + +
1439A LEU* 3.8 27.6 - - + -
1716A MET* 4.7 12.3 - - + -
1719A PHE* 4.4 14.4 - - + -
1720A LEU* 6.1 3.1 - - + -
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Residues in contact with SER1411 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1407A LYS 2.9 18.5 + - - -
1408A GLN* 3.6 18.6 + - - -
1409A LEU 3.3 0.2 - - - -
1410A LEU* 1.3 74.5 - - - +
1412A ASP* 1.3 63.5 + - - +
1414A ILE* 2.9 20.6 + - - +
1415A GLU* 2.9 26.8 + - - +
1723A GLN* 4.0 23.7 + - - -
1726A LYS* 4.2 8.0 + - - -
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Residues in contact with ASP1412 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1408A GLN* 3.4 32.9 + - - +
1409A LEU* 4.3 6.0 - - - +
1411A SER* 1.3 81.3 + - - +
1413A LEU* 1.3 55.9 + - - +
1415A GLU* 3.0 11.8 + - - +
1416A LYS* 2.7 45.2 + - + +
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Residues in contact with LEU1413 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1374A GLU* 4.6 8.1 - - - +
1409A LEU 3.2 17.5 + - - +
1410A LEU* 3.9 12.8 - - + +
1411A SER 3.2 0.2 - - - -
1412A ASP* 1.3 79.3 - - - +
1414A ILE* 1.3 58.8 + - + +
1416A LYS* 4.5 10.4 - - - +
1417A ASN* 3.2 44.7 + - - +
1428A LEU* 4.5 6.7 - - + -
1431A THR* 5.1 2.7 - - - +
1433A SER* 3.3 24.5 - - - +
1435A ALA* 3.9 14.4 - - + -
1436A GLU* 3.4 39.7 - - + +
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Residues in contact with ILE1414 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1410A LEU* 3.2 16.1 + - + +
1411A SER* 2.9 9.2 + - - +
1413A LEU* 1.3 79.8 - - + +
1415A GLU* 1.3 66.6 + - - +
1417A ASN* 3.5 4.6 + - - +
1418A LEU* 3.0 44.2 + - + +
1427A LEU* 5.2 7.2 - - + -
1428A LEU* 6.1 8.3 - - + -
1719A PHE* 5.6 1.1 - - + -
1720A LEU* 4.8 10.8 - - + -
1723A GLN* 4.0 27.4 - - + +
1727A HIS* 4.2 16.6 - - + +
1738A TRP* 4.1 24.0 - - + -
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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
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1411A SER* 2.9 26.6 + - - +
1412A ASP* 3.0 13.2 + - - +
1414A ILE* 1.3 75.0 - - - +
1416A LYS* 1.3 56.2 + - + +
1418A LEU* 3.1 4.0 + - - +
1419A GLU* 2.7 40.1 + - + +
1723A GLN* 3.7 7.8 + - - -
1726A LYS* 3.3 22.1 + - - +
1727A HIS* 3.2 37.0 + - - -
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Residues in contact with LYS1416 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1374A GLU* 5.2 12.5 + - - +
1412A ASP* 2.7 30.4 + - + +
1413A LEU* 4.5 10.1 - - - +
1415A GLU* 1.3 73.7 - - + +
1417A ASN* 1.3 67.4 + - - +
1419A GLU* 3.5 6.1 + - - +
1420A SER* 3.0 29.8 + - - -
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Residues in contact with ASN1417 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1413A LEU* 3.2 32.2 + - - +
1414A ILE 3.5 3.5 + - - +
1415A GLU 3.1 1.0 - - - -
1416A LYS* 1.3 84.3 - - - +
1418A LEU* 1.3 59.9 + - - +
1419A GLU 3.4 0.2 - - - -
1420A SER* 4.0 0.9 - - - -
1421A LYS 3.9 0.2 + - - -
1422A ASN* 3.0 48.4 + - + +
1427A LEU* 3.4 42.2 + - + +
1431A THR* 4.6 10.3 - - - +
1436A GLU* 5.5 0.2 + - - -
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Residues in contact with LEU1418 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1414A ILE* 3.0 35.1 + - + +
1415A GLU* 4.0 5.2 - - - +
1417A ASN* 1.3 75.5 - - - +
1419A GLU* 1.3 62.8 + - - +
1420A SER 3.2 1.7 + - - -
1421A LYS* 3.7 10.3 + - - +
1422A ASN 3.9 18.8 - - - +
1424A PRO* 4.4 14.8 - - + -
1427A LEU* 4.0 19.1 - - + -
1727A HIS* 3.9 25.1 - - + +
1729A ILE* 4.2 15.5 - - + -
1738A TRP* 4.5 4.0 - - + -
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Residues in contact with GLU1419 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1415A GLU* 2.7 18.8 + - + +
1416A LYS* 3.9 7.0 - - - +
1417A ASN 3.4 0.2 - - - -
1418A LEU* 1.3 77.1 - - - +
1420A SER* 1.3 60.0 + - - +
1421A LYS* 3.4 3.0 - - - +
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Residues in contact with SER1420 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1416A LYS 3.0 17.9 + - - -
1417A ASN 4.0 0.2 + - - -
1418A LEU 3.2 0.4 - - - -
1419A GLU* 1.3 80.1 - - - +
1421A LYS* 1.3 64.8 + - - +
1422A ASN* 3.0 16.8 - - - -
1295B LYS* 3.8 28.9 + - - +
1296B GLU* 5.1 4.8 - - - +
1299B ALA* 3.0 20.6 - - - +
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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
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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