Contacts of the helix formed by residues 1548 - 1569 (chain A) in PDB entry 4LX2
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 ASP1548 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1495A PRO* 5.7 0.2 - - - +
1496A ARG* 3.9 18.8 + - - -
1545A ARG* 3.1 17.2 + - + +
1547A ASP* 1.3 82.6 + - - +
1549A PHE* 1.3 66.7 + - - +
1550A GLU* 3.5 10.9 + - - +
1551A THR* 2.6 32.2 + - - +
1552A VAL* 3.1 23.9 + - - +
1614A VAL* 4.5 0.2 - - - -
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Residues in contact with PHE1549 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1547A ASP 3.8 4.4 + - - -
1548A ASP* 1.3 74.5 + - - +
1550A GLU* 1.3 65.2 + - + +
1552A VAL* 3.3 5.3 + - - +
1553A SER* 2.8 33.8 + - - -
1611A LEU* 3.6 23.8 - - + -
1614A VAL* 3.8 22.2 - - + +
1615A LEU* 5.6 4.5 - - + +
1618A ILE* 4.2 12.5 - - + +
1668A SER* 4.2 3.4 - - - -
1669A PHE* 3.4 58.8 - + + -
1672A VAL* 3.4 36.8 - - + -
1673A MET* 4.5 8.7 - - + -
1686A VAL* 6.5 0.2 - - + -
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Residues in contact with GLU1550 (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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1495A PRO* 4.5 6.8 - - + +
1496A ARG* 2.7 57.3 + - - +
1548A ASP* 3.2 12.1 + - - +
1549A PHE* 1.3 87.6 - - + +
1551A THR* 1.3 58.0 + - - +
1554A PHE* 2.9 26.9 + - - +
1672A VAL* 3.9 29.3 - - + +
1675A GLN* 5.8 1.6 + - - -
1676A HIS* 3.2 19.3 + - + -
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Residues in contact with THR1551 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1495A PRO* 4.2 11.3 - - + +
1541A VAL* 3.8 26.0 - - + -
1542A LEU* 4.1 4.7 - - + +
1545A ARG* 2.9 49.8 + - + +
1548A ASP* 2.6 27.8 + - - +
1550A GLU* 1.3 80.1 - - - +
1552A VAL* 1.3 61.8 + - - +
1554A PHE* 3.3 0.7 + - - +
1555A TRP* 3.1 30.6 + - + +
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Residues in contact with VAL1552 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1542A LEU* 4.0 9.6 - - + -
1545A ARG 4.4 0.4 - - - +
1546A GLY* 3.3 34.8 - - - +
1548A ASP 3.1 15.6 + - - +
1549A PHE* 3.8 5.8 - - - +
1551A THR* 1.3 76.4 - - - +
1553A SER* 1.3 56.9 + - - +
1555A TRP 3.4 0.9 + - - -
1556A LEU* 2.9 29.2 + - - +
1607A ILE* 3.7 19.5 - - + +
1610A GLN* 4.1 10.3 - - + +
1611A LEU* 3.7 39.7 - - + +
1614A VAL* 4.6 4.0 - - + -
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Residues in contact with SER1553 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1549A PHE* 2.8 38.1 + - - -
1550A GLU 3.8 1.6 - - - -
1552A VAL* 1.3 73.9 - - - +
1554A PHE* 1.3 64.0 + - - +
1556A LEU* 3.7 1.9 - - - +
1557A SER* 2.8 30.5 + - - -
1611A LEU* 4.0 6.6 - - - +
1672A VAL* 4.3 1.3 - - - -
1673A MET* 3.8 12.8 - - - +
1676A HIS* 2.9 19.9 + - - -
1678A MET* 3.5 24.2 - - - +
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Residues in contact with PHE1554 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1493A LEU* 3.5 32.8 - - + -
1495A PRO* 3.6 34.1 - - + -
1500A VAL* 4.2 20.0 - - + -
1505A GLY 6.0 1.3 - - - -
1507A PRO* 3.8 12.1 - - + -
1550A GLU 2.9 19.0 + - - +
1551A THR 3.6 4.0 - - - +
1552A VAL 3.2 0.2 - - - -
1553A SER* 1.3 77.8 - - - +
1555A TRP* 1.3 86.3 + + - +
1557A SER* 3.4 1.4 + - - -
1558A ASN* 3.0 55.3 + - - -
1676A HIS* 3.4 30.1 - + + -
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Residues in contact with TRP1555 (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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1489A LEU 3.5 20.0 - - - -
1490A ILE* 3.7 39.7 + - + -
1493A LEU* 4.4 8.4 + - + -
1495A PRO* 5.1 1.4 - - + +
1507A PRO* 4.0 14.8 - - + -
1511A LEU* 5.4 4.5 - - + -
1538A ILE* 4.0 44.0 - - + -
1541A VAL* 3.8 29.3 - - + +
1542A LEU* 4.3 13.0 - - + -
1545A ARG* 4.8 4.0 - - - +
1551A THR* 3.1 28.7 + - + +
1552A VAL 4.3 0.2 - - - +
1554A PHE* 1.3 96.3 - + - +
1556A LEU* 1.3 60.7 + - - +
1558A ASN* 3.8 23.1 - - + -
1559A THR* 2.8 35.0 + - - -
1607A ILE* 4.3 2.5 - - - -
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Residues in contact with LEU1556 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1552A VAL 2.9 18.4 + - - +
1553A SER* 3.7 4.7 - - - +
1555A TRP* 1.3 78.1 - - - +
1557A SER* 1.3 62.4 + - - +
1559A THR* 3.8 0.7 - - - -
1560A CYS* 3.0 42.9 + - - -
1604A ALA* 3.6 29.8 - - + +
1607A ILE* 3.6 15.7 - - + +
1608A TYR* 4.1 23.3 - - + +
1611A LEU* 3.9 27.6 - - + -
1678A MET* 3.9 7.4 - - + -
1682A LEU* 3.9 22.7 - - + -
1827A PHE* 4.3 3.8 - - + -
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Residues in contact with SER1557 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1505A GLY* 6.0 0.9 - - - -
1553A SER 2.8 21.3 + - - -
1554A PHE 3.6 4.7 - - - -
1556A LEU* 1.3 77.1 - - - +
1558A ASN* 1.3 59.7 + - - +
1560A CYS* 3.4 5.6 + - - +
1561A ARG* 2.9 28.1 + - - +
1676A HIS* 3.5 30.9 - - - +
1677A GLY 4.6 2.2 - - - +
1678A MET* 3.4 39.1 - - - +
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Residues in contact with ASN1558 (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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1505A GLY* 3.3 19.4 - - - +
1507A PRO* 3.1 31.2 - - - +
1508A ALA* 3.2 20.1 + - + +
1538A ILE* 6.1 0.4 - - - -
1554A PHE* 3.0 51.3 + - - +
1555A TRP* 3.9 20.4 - - + -
1557A SER* 1.3 79.8 - - - +
1559A THR* 1.3 60.7 + - - +
1561A ARG* 4.3 1.1 - - - +
1562A PHE* 2.9 30.1 + - - +
1676A HIS 4.9 2.2 + - - -
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Residues in contact with THR1559 (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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1538A ILE* 3.7 21.6 - - - +
1555A TRP* 2.8 24.6 + - - -
1556A LEU* 3.8 3.6 - - - -
1558A ASN* 1.3 75.0 - - - +
1560A CYS* 1.3 62.5 + - - +
1562A PHE* 3.3 7.2 + - - +
1563A LEU* 3.0 22.2 + - + +
1600A LEU* 3.8 39.7 - - + +
1603A LEU* 4.3 6.5 - - + +
1604A ALA* 4.0 18.2 - - + +
1607A ILE* 3.5 14.3 - - + +
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Residues in contact with CYS1560 (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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1556A LEU* 3.0 25.3 + - - +
1557A SER* 3.6 6.3 - - - +
1559A THR* 1.3 73.9 - - - +
1561A ARG* 1.3 61.5 + - - +
1563A LEU* 3.1 11.8 + - - +
1564A HIS* 2.9 36.3 + - + +
1604A ALA* 4.4 6.1 - - - -
1679A ASP* 4.1 18.6 - - - +
1682A LEU* 3.9 16.4 - - + -
1827A PHE* 3.6 37.2 - - - -
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Residues in contact with ARG1561 (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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1504A PRO 5.6 1.2 + - - -
1505A GLY* 4.3 8.9 - - - +
1508A ALA* 3.7 20.9 - - + -
1509A TYR* 3.6 33.3 + - + -
1557A SER 2.9 18.3 + - - +
1558A ASN* 3.3 1.8 + - - -
1560A CYS* 1.3 75.6 - - - +
1562A PHE* 1.3 63.0 + - - +
1564A HIS* 3.2 22.4 + - - +
1565A CYS* 2.9 30.2 + - - +
1568A GLN* 4.7 2.2 + - - -
1677A GLY 5.0 6.7 + - - -
1679A ASP* 3.9 6.9 + - - -
1830A ASN* 2.8 47.8 + - - +
1831A PRO* 4.4 0.6 + - - +
1832A SER* 3.6 26.7 - - - +
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Residues in contact with PHE1562 (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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1508A ALA* 3.5 25.7 - - + +
1511A LEU* 3.9 12.8 - - + -
1512A PHE* 3.7 31.6 - - + -
1515A VAL* 4.0 8.3 - - + -
1530A LEU* 6.4 0.2 - - + -
1531A LEU* 3.7 22.0 - - + -
1534A THR* 4.1 18.2 - - + -
1538A ILE* 6.1 0.9 - - + -
1558A ASN 2.9 17.2 + - - +
1559A THR* 3.5 6.5 - - - +
1560A CYS 3.2 0.2 - - - -
1561A ARG* 1.3 77.8 - - - +
1563A LEU* 1.3 60.1 + - - +
1565A CYS* 3.2 5.1 + - - +
1566A LEU* 3.0 39.0 + - + +
1596A TYR* 3.8 27.6 - + - -
1600A LEU* 3.7 22.2 - - + -
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Residues in contact with LEU1563 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1559A THR 3.0 13.1 + - - +
1560A CYS* 3.3 12.8 - - - +
1562A PHE* 1.3 77.0 - - - +
1564A HIS* 1.3 66.2 + - + +
1566A LEU* 3.2 4.1 + - - +
1567A LYS* 3.1 46.9 + - + +
1597A ARG* 3.8 40.8 - - + +
1600A LEU* 3.6 16.0 - - + +
1601A SER* 3.3 26.7 - - - +
1827A PHE* 4.6 22.4 - - + +
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Residues in contact with HIS1564 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1560A CYS* 2.9 34.8 + - + +
1561A ARG* 3.6 27.6 - - - +
1563A LEU* 1.3 79.2 - - + +
1565A CYS* 1.3 53.6 + - - +
1567A LYS* 3.2 3.2 + - - +
1568A GLN* 2.8 38.6 + - - +
1679A ASP* 2.7 37.3 + - - -
1827A PHE* 4.1 11.9 - - + -
1828A PRO 3.3 26.0 - - - -
1829A PHE* 3.5 17.0 - - + -
1830A ASN* 3.3 27.4 + - - +
1831A PRO* 5.2 0.4 - - + -
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Residues in contact with CYS1565 (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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1508A ALA 4.8 1.1 - - - -
1509A TYR* 3.7 38.8 - - - -
1512A PHE* 3.8 34.4 - - + -
1561A ARG* 2.9 25.0 + - - -
1562A PHE* 3.5 9.2 - - - +
1564A HIS* 1.3 75.3 - - - +
1566A LEU* 1.3 63.7 + - - +
1568A GLN* 4.4 4.3 - - - -
1569A TYR* 3.0 42.1 + - + +
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Residues in contact with LEU1566 (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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1512A PHE* 3.9 24.0 - - + -
1515A VAL* 4.7 3.4 - - + -
1531A LEU* 5.3 0.4 - - + -
1562A PHE* 3.0 34.7 + - + +
1563A LEU* 3.2 6.5 + - - +
1565A CYS* 1.3 77.2 - - - +
1567A LYS* 1.3 57.1 + - - +
1569A TYR 4.0 0.5 - - - -
1570A SER* 3.1 26.5 + - - -
1588A LEU* 4.8 3.7 - - + +
1593A LEU* 3.7 30.7 - - + +
1596A TYR* 4.0 20.2 - - + -
1597A ARG* 3.9 24.5 + - + -
1600A LEU* 3.6 26.2 - - + -
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Residues in contact with LYS1567 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1563A LEU* 3.1 40.4 + - + +
1564A HIS* 3.6 8.6 + - - +
1565A CYS 3.1 0.2 - - - -
1566A LEU* 1.3 74.4 - - - +
1568A GLN* 1.3 65.2 + - - +
1569A TYR 3.1 1.8 - - - -
1570A SER* 2.7 23.9 + - - -
1575A PHE* 3.2 52.7 - - + +
1597A ARG* 3.7 22.0 - - - +
1601A SER* 5.3 2.1 + - - -
1827A PHE 4.3 15.2 + - - -
1829A PHE* 3.8 22.9 - - + +
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Residues in contact with GLN1568 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1509A TYR* 6.1 0.2 - - - -
1561A ARG* 4.7 3.5 + - - -
1564A HIS 2.8 21.2 + - - +
1565A CYS* 4.0 4.7 - - - +
1567A LYS* 1.3 74.0 - - - +
1569A TYR* 1.3 78.5 + - + +
1570A SER 3.8 0.3 + - - -
1575A PHE 3.8 5.5 - - - +
1576A MET* 4.2 6.9 - - - +
1578A HIS 5.4 1.0 + - - -
1579A ASN* 2.9 51.8 + - - +
1583A GLN* 3.5 12.5 + - - +
1587A CYS* 4.2 1.6 - - - -
1829A PHE* 3.8 13.7 - - + -
1831A PRO* 3.5 14.1 - - + +
1832A SER* 2.9 50.0 + - - +
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Residues in contact with TYR1569 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1509A TYR* 5.7 2.2 - + - -
1512A PHE* 3.3 33.9 - + + -
1565A CYS* 3.0 29.0 + - - +
1566A LEU 4.0 3.1 - - - -
1568A GLN* 1.3 102.6 + - + +
1570A SER* 1.3 57.8 + - - +
1571A GLY 3.3 2.2 - - - -
1579A ASN* 5.0 0.2 - - - -
1583A GLN* 3.3 61.4 + - + +
1586A HIS* 3.8 26.6 + - + +
1587A CYS* 3.2 6.9 - - - -
1588A LEU* 2.9 30.6 + - - +
1832A SER* 4.9 1.3 + - - -
1834A LEU 3.6 10.4 + - - -
1836A LEU* 3.8 23.8 + - + +
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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