Contacts of the helix formed by residues 1548 - 1569 (chain B) in PDB entry 5JCZ
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1495B PRO* 5.8 0.3 - - - +
1545B ARG* 4.5 14.0 - - + +
1546B GLY 3.3 2.8 - - - -
1547B ASP* 1.3 77.7 - - - +
1549B PHE* 1.3 68.3 + - - +
1550B GLU* 4.0 11.4 + - - +
1551B THR* 2.9 34.7 + - - +
1552B VAL* 3.2 27.0 + - - +
1614B VAL* 4.5 0.7 - - - -
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Residues in contact with PHE1549 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1547B ASP 4.0 2.8 + - - -
1548B ASP* 1.3 74.8 + - - +
1550B GLU* 1.3 62.5 + - + +
1552B VAL* 3.4 4.4 + - - +
1553B SER* 2.8 34.6 + - - -
1611B LEU* 3.5 29.4 - - + -
1614B VAL* 4.0 18.8 - - + +
1615B LEU* 4.4 14.8 - - + -
1618B ILE* 5.1 4.7 - - + -
1668B SER 5.8 0.2 - - - -
1669B PHE* 3.5 65.7 - + + -
1672B VAL* 3.6 28.0 - - + -
1673B MET* 3.9 19.1 - - + -
1686B VAL* 5.5 3.1 - - + -
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Residues in contact with GLU1550 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1495B PRO* 4.6 10.0 - - + +
1496B ARG* 3.1 50.4 + - - +
1548B ASP* 3.3 12.6 + - - +
1549B PHE* 1.3 79.6 - - + +
1551B THR* 1.3 58.0 + - - +
1554B PHE* 2.9 27.8 + - - +
1672B VAL* 3.9 33.1 - - + +
1676B HIS* 3.1 23.6 + - + +
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Residues in contact with THR1551 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1495B PRO* 4.5 16.0 - - + +
1541B VAL* 3.8 22.4 - - + -
1542B LEU* 4.5 5.4 - - + -
1545B ARG* 3.7 37.9 - - + +
1548B ASP* 2.9 29.2 + - - +
1549B PHE 3.3 0.4 - - - -
1550B GLU* 1.3 78.7 - - - +
1552B VAL* 1.3 63.0 + - - +
1554B PHE* 3.2 1.9 + - - +
1555B TRP* 3.1 32.1 + - + +
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Residues in contact with VAL1552 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1542B LEU* 3.9 13.2 - - + -
1545B ARG 4.4 3.8 - - - +
1546B GLY 3.8 19.7 - - - +
1548B ASP 3.2 17.9 + - - +
1549B PHE* 3.8 3.1 - - - +
1551B THR* 1.3 75.4 - - - +
1553B SER* 1.3 58.0 + - - +
1555B TRP 3.9 0.2 - - - -
1556B LEU* 3.0 29.9 + - + +
1607B ILE* 3.6 33.1 - - + +
1610B GLN* 3.9 17.9 - - + +
1611B LEU* 3.7 25.6 - - + +
1614B VAL* 4.6 4.7 - - + -
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Residues in contact with SER1553 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1549B PHE* 2.8 26.5 + - - -
1550B GLU 3.8 1.3 - - - -
1552B VAL* 1.3 74.0 - - - +
1554B PHE* 1.3 60.9 + - - +
1556B LEU* 4.5 0.2 - - - -
1557B SER* 2.8 29.1 + - - -
1611B LEU* 3.8 12.1 - - - +
1672B VAL* 4.0 6.9 - - - +
1673B MET* 3.7 13.3 - - - +
1676B HIS* 3.0 19.8 + - - -
1678B MET* 3.3 25.9 - - - +
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Residues in contact with PHE1554 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1493B LEU* 3.6 24.5 - - + -
1495B PRO* 4.1 25.8 - - + -
1500B VAL* 3.5 33.9 - - + -
1505B GLY 5.9 2.0 - - - -
1507B PRO* 3.9 8.3 - - + -
1550B GLU 2.9 18.8 + - - +
1551B THR 3.6 4.0 - - - +
1553B SER* 1.3 78.3 - - - +
1555B TRP* 1.3 85.6 + + - +
1557B SER* 3.4 2.8 + - - -
1558B ASN* 2.6 59.7 + - - -
1676B HIS* 3.3 34.5 + + + -
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Residues in contact with TRP1555 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1489B LEU 3.3 22.9 - - - -
1490B ILE* 3.3 45.0 + - + -
1493B LEU* 4.4 12.5 + - + -
1495B PRO* 5.5 2.4 - - - +
1507B PRO* 4.4 9.4 - - + -
1508B ALA 6.0 0.2 - - - -
1511B LEU* 5.4 4.3 - - + -
1538B ILE* 4.5 30.1 - - + -
1541B VAL* 3.8 29.4 - - + +
1542B LEU* 4.3 15.7 - - + -
1551B THR* 3.1 29.0 + - + +
1554B PHE* 1.3 100.5 - + + +
1556B LEU* 1.3 60.1 + - - +
1557B SER 3.3 0.2 - - - -
1558B ASN* 3.9 22.0 - - + +
1559B THR* 2.6 35.7 + - - -
1607B ILE* 3.9 3.4 - - - +
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Residues in contact with LEU1556 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1552B VAL* 3.0 18.8 + - + +
1553B SER 3.8 4.3 - - - +
1555B TRP* 1.3 78.0 - - - +
1557B SER* 1.3 63.6 + - - +
1559B THR* 4.0 0.9 - - - -
1560B CYS* 3.1 43.6 + - - -
1604B ALA* 3.6 26.5 - - - +
1607B ILE* 3.6 18.8 - - + +
1608B TYR* 3.9 20.9 - - + +
1611B LEU* 3.9 18.8 - - + -
1678B MET* 3.9 22.2 - - + -
1682B LEU* 4.0 20.9 - - + -
1827B PHE* 4.4 1.3 - - + -
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Residues in contact with SER1557 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1505B GLY* 5.8 2.0 - - - -
1553B SER 2.8 18.0 + - - -
1554B PHE 3.5 9.0 - - - -
1555B TRP 3.3 0.2 - - - -
1556B LEU* 1.3 79.4 - - - +
1558B ASN* 1.3 60.2 + - - +
1560B CYS* 3.5 5.4 + - - +
1561B ARG* 3.1 27.3 + - - +
1676B HIS* 3.8 24.7 - - - +
1677B GLY 4.6 2.5 - - - +
1678B MET* 3.3 36.1 + - - +
1679B ASP* 5.7 0.8 - - - +
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Residues in contact with ASN1558 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1505B GLY* 3.2 21.2 - - - +
1507B PRO* 3.2 27.6 - - - +
1508B ALA* 3.2 17.4 + - + +
1538B ILE* 5.9 0.7 - - - -
1554B PHE* 2.6 62.4 + - - +
1555B TRP* 3.9 20.6 - - + -
1557B SER* 1.3 78.9 - - - +
1559B THR* 1.3 61.4 + - - +
1561B ARG* 4.3 1.8 - - - -
1562B PHE* 2.8 27.6 + - - +
1676B HIS 5.4 1.4 + - - -
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Residues in contact with THR1559 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1538B ILE* 3.6 23.3 - - + +
1555B TRP* 2.6 25.8 + - - -
1556B LEU 4.0 2.7 - - - -
1558B ASN* 1.3 77.1 - - - +
1560B CYS* 1.3 57.6 + - - +
1562B PHE* 3.4 7.9 + - - +
1563B LEU* 3.0 27.5 + - + +
1600B LEU* 4.1 36.5 - - + +
1603B LEU* 4.2 12.1 - - + -
1604B ALA* 4.5 8.1 - - + -
1607B ILE* 3.6 16.7 - - + +
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Residues in contact with CYS1560 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1556B LEU* 3.1 28.0 + - - +
1557B SER* 3.7 5.6 - - - +
1559B THR* 1.3 81.1 - - - +
1561B ARG* 1.3 56.0 + - - +
1563B LEU* 3.2 9.7 + - - +
1564B HIS* 2.8 38.6 + - + +
1604B ALA* 4.4 7.9 - - - -
1679B ASP* 3.7 18.6 - - - +
1682B LEU* 3.9 25.8 - - - -
1827B PHE* 3.9 23.6 - - - -
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Residues in contact with ARG1561 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1505B GLY* 4.1 10.8 - - - +
1508B ALA* 3.6 15.7 - - + -
1509B TYR* 3.6 43.6 + - + -
1557B SER 3.1 17.9 + - - +
1558B ASN* 3.8 6.1 - - - +
1559B THR 3.3 0.2 - - - -
1560B CYS* 1.3 73.0 - - - +
1562B PHE* 1.3 60.2 + - - +
1564B HIS* 3.1 27.1 + - + +
1565B CYS* 2.9 32.1 + - - -
1568B GLN* 4.6 2.2 + - - -
1679B ASP* 4.4 1.8 + - - -
1830B ASN 2.8 30.7 + - - -
1831B PRO* 4.1 0.6 - - - +
1832B SER* 3.7 15.3 + - - +
130D HIS* 3.5 20.7 + - - +
131D LEU* 3.5 20.0 - - - +
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Residues in contact with PHE1562 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1508B ALA* 3.5 26.4 - - + +
1511B LEU* 3.7 27.6 - - + -
1512B PHE* 3.7 20.2 - - + -
1515B VAL* 4.3 6.7 - - + -
1531B LEU* 3.9 25.8 - - + -
1534B THR* 4.4 21.3 - - + -
1535B ILE* 6.1 1.1 - - + -
1538B ILE* 5.9 3.6 - - + -
1558B ASN 2.8 18.5 + - - +
1559B THR* 3.6 6.1 - - - +
1561B ARG* 1.3 74.8 - - - +
1563B LEU* 1.3 60.8 + - - +
1565B CYS* 3.5 3.8 + - - +
1566B LEU* 3.2 36.7 + - + +
1600B LEU* 3.5 39.3 - - + -
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Residues in contact with LEU1563 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1559B THR* 3.0 14.8 + - + +
1560B CYS* 3.4 14.4 - - - +
1561B ARG 3.2 0.2 - - - -
1562B PHE* 1.3 77.0 - - - +
1564B HIS* 1.3 66.7 + - + +
1566B LEU* 3.3 5.3 + - + +
1567B LYS* 3.1 54.9 + - - +
1597B ARG* 3.6 42.8 - - + +
1600B LEU* 4.2 15.7 - - + +
1601B SER* 4.1 27.8 - - - +
1604B ALA* 5.5 4.9 - - + -
1827B PHE* 6.2 5.6 - - + -
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Residues in contact with HIS1564 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1560B CYS* 2.8 28.8 + - + -
1561B ARG* 3.1 53.6 + - - +
1563B LEU* 1.3 81.6 - - + +
1565B CYS* 1.3 51.4 + - - +
1567B LYS* 3.3 2.3 + - - +
1568B GLN* 2.8 38.4 + - - +
1679B ASP* 3.0 31.5 + - - -
1828B PRO 3.2 28.0 - - - -
1829B PHE* 3.5 14.5 - - - -
1830B ASN 3.4 26.3 + - - +
1831B PRO 5.0 0.2 - - - -
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Residues in contact with CYS1565 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1508B ALA 4.7 1.6 - - - -
1509B TYR* 3.8 39.3 - - - -
1512B PHE* 3.7 37.2 - - + -
1561B ARG* 2.9 23.8 + - - -
1562B PHE 3.7 7.9 - - - +
1563B LEU 3.2 0.2 - - - -
1564B HIS* 1.3 76.0 - - - +
1566B LEU* 1.3 59.0 + - - +
1568B GLN* 4.4 3.6 - - - -
1569B TYR* 2.9 48.9 + - + +
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Residues in contact with LEU1566 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1512B PHE* 3.6 28.0 - - + -
1515B VAL* 4.6 4.7 - - + -
1531B LEU* 4.9 6.3 - - + -
1562B PHE* 3.2 33.7 + - + +
1563B LEU* 3.3 6.0 + - - +
1565B CYS* 1.3 76.9 - - - +
1567B LYS* 1.3 57.3 + - - +
1569B TYR 3.9 0.5 - - - -
1570B SER* 3.1 27.2 + - - -
1588B LEU* 5.0 4.0 - - + +
1593B LEU* 4.2 25.8 - - + -
1596B TYR* 5.4 3.4 - - + +
1597B ARG* 4.0 29.5 + - + +
1600B LEU* 3.6 31.2 - - + -
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Residues in contact with LYS1567 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1563B LEU* 3.1 43.8 + - + +
1564B HIS* 5.1 1.7 + - - +
1566B LEU* 1.3 75.1 - - - +
1568B GLN* 1.3 65.7 + - - +
1569B TYR 3.2 0.2 - - - -
1570B SER* 2.7 24.4 + - - -
1575B PHE* 3.1 43.7 - - + +
1597B ARG* 3.8 19.3 - - - +
1601B SER* 6.2 0.4 - - - -
1827B PHE* 5.8 2.2 + - - +
1828B PRO 5.1 5.1 + - - -
1829B PHE* 3.5 43.5 - - + +
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Residues in contact with GLN1568 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1509B TYR* 5.9 0.5 - - - -
1561B ARG* 4.6 2.9 + - - -
1564B HIS 2.8 22.4 + - - +
1565B CYS* 4.0 4.6 - - - +
1567B LYS* 1.3 73.2 - - - +
1569B TYR* 1.3 76.7 + - + +
1575B PHE 3.7 9.9 - - - -
1576B MET* 3.5 11.1 - - - +
1578B HIS 5.2 1.0 + - - -
1579B ASN* 2.8 50.9 + - - +
1583B GLN* 3.4 18.8 + - - +
1587B CYS* 3.9 0.3 - - - -
1829B PHE* 3.8 1.7 - - - -
1831B PRO* 3.4 20.7 - - + +
1832B SER* 2.9 45.3 + - - +
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Residues in contact with TYR1569 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1509B TYR* 5.8 2.1 - + - -
1512B PHE* 3.3 33.6 - + + -
1565B CYS* 2.9 26.2 + - + -
1566B LEU 3.9 4.0 - - - -
1568B GLN* 1.3 102.0 + - + +
1570B SER* 1.3 56.5 + - - +
1571B GLY 3.4 2.7 - - - -
1583B GLN* 3.2 61.3 + - + +
1586B HIS* 3.7 22.4 + - + +
1587B CYS* 3.6 12.6 - - - -
1588B LEU* 3.0 29.5 + - - +
1832B SER* 5.5 1.0 + - - -
1834B LEU 3.5 11.8 + - - -
1836B LEU* 3.9 19.8 + - + +
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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