Contacts of the helix formed by residues 1529 - 1559 (chain D) in PDB entry 5EK0
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 SER1529 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1528D GLN* 1.4 81.0 - - - +
1530D GLN* 1.3 56.6 + - - +
1531D HIS* 3.6 10.9 + - - +
1532D MET* 3.2 27.1 + - - +
1533D THR* 2.7 31.5 + - - -
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Residues in contact with GLN1530 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1529D SER* 1.3 71.6 + - - +
1531D HIS* 1.3 56.7 + - - +
1533D THR* 3.3 19.8 + - - +
1534D GLU* 3.1 47.4 + - + +
1589D GLU* 5.5 2.4 - - - +
1806D 5P2 5.0 7.5 - - - +
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Residues in contact with HIS1531 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1529D SER* 3.2 9.8 + - - +
1530D GLN* 1.3 74.8 - - - +
1532D MET* 1.3 65.9 + - + +
1534D GLU* 3.3 8.0 + - - +
1535D VAL* 2.8 59.2 + - + +
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Residues in contact with MET1532 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1523D VAL* 5.2 4.9 - - - +
1525D LYS* 5.9 4.3 - - - -
1528D GLN* 3.4 26.7 - - - +
1529D SER* 3.2 27.1 + - - +
1531D HIS* 1.3 86.1 - - + +
1533D THR* 1.3 59.3 + - - +
1535D VAL* 4.5 9.2 - - - -
1536D LEU* 3.0 51.4 + - + +
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Residues in contact with THR1533 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1528D GLN* 3.5 19.6 - - + +
1529D SER 2.7 19.7 + - - -
1530D GLN* 3.6 23.1 + - - +
1531D HIS 3.3 0.2 - - - -
1532D MET* 1.3 75.7 - - - +
1534D GLU* 1.4 57.1 + - - +
1536D LEU* 4.9 2.0 - - - -
1537D TYR* 3.0 75.8 + - + +
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Residues in contact with GLU1534 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1530D GLN* 3.1 32.1 + - + +
1531D HIS* 3.7 10.1 - - - +
1533D THR* 1.4 74.3 - - - +
1535D VAL* 1.4 63.8 + - + +
1537D TYR* 4.5 3.0 - - - -
1538D TRP* 3.1 38.4 + - + -
1805D PX4 3.0 33.1 + - - +
1806D 5P2 3.4 44.7 + - - +
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Residues in contact with VAL1535 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1531D HIS* 2.8 53.7 + - + +
1532D MET* 4.1 11.2 - - - +
1534D GLU* 1.4 68.9 - - + +
1536D LEU* 1.3 62.5 + - + +
1538D TRP* 3.2 8.2 + - - +
1539D ILE* 3.0 46.2 + - + +
1804D PX4 5.5 3.8 - - + -
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Residues in contact with LEU1536 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1520D THR* 3.4 26.9 - - - +
1523D VAL* 3.5 40.8 - - + +
1524D GLU* 4.2 14.4 - - + +
1528D GLN* 4.3 7.2 - - - +
1532D MET* 3.0 39.6 + - + +
1533D THR* 4.2 3.4 - - - +
1535D VAL* 1.3 77.1 - - + +
1537D TYR* 1.4 66.2 + - + +
1539D ILE* 3.3 23.3 + - + +
1540D ASN* 3.1 30.8 + - - +
1804D PX4 5.0 3.4 - - + -
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Residues in contact with TYR1537 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1524D GLU* 4.9 3.1 - - - -
1533D THR* 3.0 51.7 + - + +
1534D GLU* 5.1 2.9 - - - -
1536D LEU* 1.4 79.2 - - + +
1538D TRP* 1.4 56.1 + - - +
1540D ASN* 3.4 6.1 - - - +
1541D VAL* 3.2 27.7 + - - +
1589D GLU* 4.5 7.1 + - - -
1598D PHE* 3.5 24.5 - + - -
1602D ARG* 3.4 43.6 + - - -
1806D 5P2 3.4 82.4 - + + -
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Residues in contact with TRP1538 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1534D GLU* 3.1 34.2 + - + +
1535D VAL* 3.2 6.0 + - - +
1537D TYR* 1.4 72.8 - - - +
1539D ILE* 1.4 64.3 + - - +
1540D ASN 3.1 1.6 - - - -
1541D VAL* 3.2 32.1 + - + +
1542D VAL* 3.2 22.0 + - + +
1805D PX4 5.2 19.7 + - + -
1806D 5P2 3.2 65.2 + + + -
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Residues in contact with ILE1539 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1520D THR* 3.7 27.1 - - + -
1535D VAL* 3.0 33.5 + - + +
1536D LEU* 3.3 31.2 + - + +
1538D TRP* 1.4 74.4 - - + +
1540D ASN* 1.3 61.1 + - - +
1542D VAL* 3.4 19.3 - - + +
1543D PHE* 3.1 32.4 - - + -
1804D PX4 3.8 24.9 - - + -
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Residues in contact with ASN1540 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1517D ASN* 2.8 32.3 + - - +
1520D THR* 4.3 8.8 + - - -
1521D MET* 3.9 14.0 - - - +
1524D GLU* 6.0 0.2 + - - -
1536D LEU* 3.1 26.9 + - - +
1537D TYR* 3.4 7.9 - - - +
1538D TRP 3.1 0.4 - - - -
1539D ILE* 1.3 74.0 - - - +
1541D VAL* 1.4 53.2 + - - +
1543D PHE* 2.9 6.2 + - - +
1544D ILE* 2.8 42.0 + - + +
1602D ARG* 5.2 3.0 - - - +
1605D ARG* 5.6 0.8 - - - +
1608D ARG* 2.8 18.0 + - - +
1806D 5P2 2.8 29.1 + - + +
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Residues in contact with VAL1541 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1537D TYR 3.4 15.0 - - - +
1538D TRP* 3.2 23.6 + - + +
1540D ASN* 1.4 73.1 - - - +
1542D VAL* 1.4 53.9 + - - +
1544D ILE* 3.1 8.4 + - - +
1545D ILE* 2.8 52.8 + - + +
1582D MET* 4.0 19.5 - - + -
1806D 5P2 3.7 53.8 - - + -
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Residues in contact with VAL1542 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1538D TRP* 3.2 18.5 + - + +
1539D ILE* 3.4 13.2 - - + +
1540D ASN 3.2 0.2 - - - -
1541D VAL* 1.4 76.4 - - + +
1543D PHE* 1.4 54.6 + - + +
1545D ILE* 3.4 7.9 + - - +
1546D LEU* 2.8 49.7 + - + +
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Residues in contact with PHE1543 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1513D LEU* 3.3 52.7 - - + -
1516D LEU* 3.6 42.2 - - + -
1517D ASN* 3.3 33.0 - - + +
1520D THR* 4.1 3.6 - - + -
1539D ILE* 3.1 41.9 + - + -
1540D ASN 2.9 6.0 + - - +
1542D VAL* 1.4 75.4 - - + +
1544D ILE* 1.4 57.3 + - - +
1546D LEU* 3.6 8.3 - - + +
1547D PHE* 2.8 43.8 + + + -
1804D PX4 5.5 1.6 - - + -
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Residues in contact with ILE1544 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1540D ASN* 2.8 31.7 + - + +
1541D VAL 3.6 6.1 - - - +
1543D PHE* 1.4 70.2 - - - +
1545D ILE* 1.4 58.0 + - + +
1547D PHE* 3.6 3.1 + - - +
1548D THR* 2.7 32.3 + - - -
1575D VAL* 4.3 2.1 - - + +
1578D SER* 3.4 24.5 - - - +
1579D ILE* 3.9 22.2 - - + +
1582D MET* 3.5 37.5 - - + -
1608D ARG* 3.5 31.4 - - - +
1806D 5P2 3.8 18.8 - - + +
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Residues in contact with ILE1545 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1541D VAL* 2.8 35.2 + - + +
1542D VAL* 3.5 7.9 - - - +
1544D ILE* 1.4 77.3 - - + +
1546D LEU* 1.4 59.1 + - + +
1548D THR* 3.0 11.0 + - - +
1549D ILE* 3.0 45.2 + - + +
1582D MET* 5.5 7.2 - - + -
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Residues in contact with LEU1546 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1509D PHE* 5.0 8.5 - - + -
1510D ILE* 5.3 0.7 - - - +
1513D LEU* 3.9 42.6 - - + +
1542D VAL* 2.8 44.2 + - + +
1543D PHE* 3.3 13.9 + - + +
1545D ILE* 1.4 73.6 - - + +
1547D PHE* 1.4 57.6 + - + +
1549D ILE* 3.4 15.8 - - + +
1550D GLU* 3.0 25.1 + - - +
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Residues in contact with PHE1547 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1510D ILE* 4.0 9.2 - - + -
1513D LEU* 3.7 31.6 - - + -
1514D ILE* 3.6 42.0 - - + -
1517D ASN* 3.7 21.1 - - + -
1543D PHE* 2.8 27.8 + + + +
1544D ILE* 4.2 4.3 - - - +
1546D LEU* 1.4 71.5 - - + +
1548D THR* 1.4 63.5 + - - +
1550D GLU* 3.4 18.2 - - - +
1551D ILE* 3.3 17.8 + - - +
1574D VAL* 6.3 2.0 - - + -
1575D VAL* 3.8 16.3 - - + +
1608D ARG* 4.0 32.1 - - + -
1611D ARG* 3.7 22.2 - - - +
----------------------------------------------------------
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Residues in contact with THR1548 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1544D ILE 2.7 21.8 + - - -
1545D ILE* 3.0 12.9 + - - +
1547D PHE* 1.4 73.0 - - - +
1549D ILE* 1.4 67.9 + - + +
1551D ILE* 3.2 9.5 + - + +
1552D ILE* 3.0 44.5 + - + +
1575D VAL* 3.3 8.6 - - + +
1579D ILE* 3.3 32.9 - - + +
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Residues in contact with ILE1549 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1545D ILE* 3.0 36.2 + - + +
1546D LEU* 3.4 16.8 - - + +
1548D THR* 1.4 78.7 - - + +
1550D GLU* 1.4 61.0 + - - +
1552D ILE* 3.5 15.4 + - + +
1553D LEU* 3.2 37.8 + - + +
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Residues in contact with GLU1550 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1506D PHE* 3.9 13.2 - - + -
1510D ILE* 3.6 36.1 - - + +
1546D LEU 3.0 14.5 + - - +
1547D PHE* 3.4 18.7 - - - +
1548D THR 3.2 0.2 - - - -
1549D ILE* 1.4 76.3 - - - +
1551D ILE* 1.4 59.9 + - - +
1553D LEU* 3.5 7.6 + - - +
1554D ARG* 2.8 57.6 + - - +
1571D ASP 5.4 0.3 - - - +
1611D ARG* 2.8 44.9 + - - -
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Residues in contact with ILE1551 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1547D PHE 3.3 7.9 + - - +
1548D THR* 3.2 14.8 + - + +
1550D GLU* 1.4 78.0 - - - +
1552D ILE* 1.4 62.4 + - + +
1554D ARG* 3.5 33.2 - - - +
1555D ILE* 2.8 46.5 + - + +
1562D PHE* 3.7 31.0 - - + -
1571D ASP* 4.1 19.7 - - + +
1572D PHE* 4.1 17.7 - - + +
1575D VAL* 3.7 24.5 - - + -
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Residues in contact with ILE1552 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1548D THR* 3.0 42.7 + - + +
1549D ILE* 3.8 16.8 - - + +
1551D ILE* 1.4 76.0 - - + +
1553D LEU* 1.4 57.1 + - + +
1555D ILE* 3.1 9.6 + - + +
1556D TYR* 2.9 46.2 + - + +
----------------------------------------------------------
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Residues in contact with LEU1553 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1497D ILE* 4.6 26.2 - - + -
1500D ILE* 5.4 6.7 - - + -
1501D VAL* 4.1 16.4 - - + -
1506D PHE* 4.0 26.0 - - + -
1549D ILE* 3.2 31.0 + - + +
1550D GLU* 3.5 6.3 - - - +
1552D ILE* 1.4 78.6 - - + +
1554D ARG* 1.4 58.8 + - - +
1556D TYR* 3.5 8.2 - - - -
1557D VAL* 3.1 30.7 - - - +
----------------------------------------------------------
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Residues in contact with ARG1554 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1501D VAL* 4.0 17.9 - - + -
1506D PHE* 4.4 6.3 - - + -
1550D GLU* 2.8 62.1 + - - +
1551D ILE* 3.5 17.9 - - - +
1552D ILE 3.2 0.2 - - - -
1553D LEU* 1.4 74.4 - - - +
1555D ILE* 1.3 63.4 + - - +
1557D VAL* 3.6 7.3 - - - +
1558D HIS* 3.5 22.0 - - + +
1562D PHE* 3.4 21.8 - - + -
1567D TRP 4.8 0.4 - - - -
1568D SER* 2.8 43.0 + - - +
1571D ASP* 3.0 32.7 + - - +
1611D ARG* 4.3 0.2 - - - +
----------------------------------------------------------
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Residues in contact with ILE1555 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1551D ILE* 2.8 32.5 + - + +
1552D ILE* 3.7 7.9 - - + +
1554D ARG* 1.3 73.7 - - - +
1556D TYR* 1.3 79.7 + - + +
1557D VAL 3.2 0.6 + - - -
1558D HIS 3.7 0.5 - - - -
1559D ARG* 2.8 45.5 + - - +
1562D PHE* 3.6 29.4 - - + -
1563D PHE* 4.0 13.0 - - + -
1572D PHE* 3.8 34.8 - - + -
----------------------------------------------------------
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Residues in contact with TYR1556 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1494D TYR* 3.7 25.7 - + + -
1497D ILE* 3.4 17.6 - - + +
1552D ILE* 2.9 26.3 + - + +
1553D LEU* 3.5 5.0 - - - +
1555D ILE* 1.3 89.8 - - + +
1557D VAL* 1.4 65.1 + - - +
1559D ARG* 4.7 10.5 - - + +
----------------------------------------------------------
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Residues in contact with VAL1557 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1494D TYR* 3.7 13.1 + - - -
1497D ILE* 3.8 18.2 - - + +
1498D THR* 3.7 52.8 - - + +
1501D VAL* 4.0 9.4 - - + -
1502D GLU* 3.7 10.3 - - - +
1553D LEU 3.1 22.2 - - - +
1554D ARG* 3.6 8.1 - - - +
1555D ILE 3.2 0.4 + - - -
1556D TYR* 1.4 79.6 - - - +
1558D HIS* 1.4 82.7 + - + +
1559D ARG 3.4 4.2 - - - +
----------------------------------------------------------
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Residues in contact with HIS1558 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1501D VAL* 5.4 0.8 - - + +
1502D GLU* 2.8 41.6 + - - -
1554D ARG* 3.5 20.4 - - + +
1555D ILE 3.5 1.2 + - - -
1557D VAL* 1.4 79.7 - - + +
1559D ARG* 1.4 55.6 + - - +
1560D ILE 2.8 16.6 + - - -
1561D SER* 2.9 27.2 + - - -
1562D PHE* 3.5 34.9 + + + +
1568D SER* 6.0 2.2 - - - -
----------------------------------------------------------
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Residues in contact with ARG1559 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1494D TYR* 3.5 30.9 + - + +
1555D ILE* 2.8 24.1 + - - +
1556D TYR* 5.0 12.0 - - + +
1557D VAL 3.4 3.0 - - - +
1558D HIS* 1.4 73.3 - - - +
1560D ILE* 1.3 79.7 + - + +
1562D PHE* 4.7 0.8 - - - +
1563D PHE* 3.8 14.1 - - - -
----------------------------------------------------------
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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