Contacts of the helix formed by residues 1672 - 1696 (chain C) in PDB entry 5Y3R
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 PHE1672 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1671C VAL* 1.3 90.9 - - + +
1673C THR* 1.3 59.3 + - - +
1675C TYR* 3.8 2.2 - - - +
1676C ILE* 2.9 37.6 + - + +
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Residues in contact with THR1673 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1654C GLN* 3.0 31.8 + - - +
1657C SER* 3.7 4.3 + - - +
1658C SER* 2.3 38.4 + - - +
1671C VAL 5.0 3.1 - - - +
1672C PHE* 1.3 78.1 - - - +
1674C THR* 1.3 58.0 + - - +
1676C ILE* 4.4 0.2 - - - -
1677C SER* 2.3 38.7 + - - -
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Residues in contact with THR1674 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1658C SER* 3.4 24.2 - - - -
1671C VAL* 3.0 27.1 + - - -
1673C THR* 1.3 82.2 - - - +
1675C TYR* 1.3 58.7 + - - +
1677C SER* 3.0 5.1 - - - -
1678C LEU* 2.9 40.7 + - + +
1721C HIS* 5.6 8.3 - - + -
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Residues in contact with TYR1675 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427C VAL* 4.2 8.3 + - - +
428C PRO* 3.3 24.4 + - + -
429C GLU* 4.1 6.4 - - - +
430C VAL* 3.5 24.2 - - + +
1591C LYS* 6.1 2.5 - - - -
1671C VAL* 2.7 21.8 + - + +
1672C PHE* 4.2 2.5 - - - +
1674C THR* 1.3 70.3 - - - +
1676C ILE* 1.3 69.4 + - + +
1677C SER 2.9 1.6 - - - -
1678C LEU* 4.1 18.2 - - + +
1679C LEU* 2.8 48.4 + - + +
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Residues in contact with ILE1676 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1591C LYS* 6.2 0.2 - - - +
1654C GLN* 3.2 38.1 - - - +
1672C PHE* 2.9 25.1 + - + +
1673C THR* 3.8 0.4 - - - -
1675C TYR* 1.3 84.9 - - + +
1677C SER* 1.3 55.5 + - - +
1679C LEU* 3.1 27.1 - - + +
1680C ALA* 2.8 25.8 + - + +
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Residues in contact with SER1677 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1654C GLN* 2.6 14.1 + - - +
1655C ILE* 3.4 28.7 - - - +
1658C SER* 2.6 17.7 + - - -
1673C THR 2.3 22.9 + - - -
1674C THR* 3.0 13.9 - - - -
1675C TYR 2.9 0.6 - - - -
1676C ILE* 1.3 74.2 - - - +
1678C LEU* 1.3 54.1 + - - -
1679C LEU 3.1 1.1 - - - -
1680C ALA* 2.3 25.7 + - - -
1681C ASP* 2.7 20.6 + - - +
1721C HIS* 6.2 0.2 - - - -
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Residues in contact with LEU1678 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430C VAL* 5.6 4.0 - - + -
1655C ILE* 5.6 0.4 - - + -
1674C THR* 2.9 31.0 + - + +
1675C TYR* 3.3 22.6 + - + +
1677C SER* 1.3 69.9 - - - +
1679C LEU* 1.3 50.5 + - - +
1681C ASP* 2.4 26.8 - - - +
1682C THR* 2.0 38.0 + - - -
1721C HIS* 4.8 23.8 - - + +
1723C PRO* 5.9 3.4 - - + -
1724C MET* 3.5 22.4 - - + -
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Residues in contact with LEU1679 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430C VAL* 5.8 2.9 - - - -
1590C THR 5.5 2.5 - - - +
1591C LYS* 4.3 38.4 - - + +
1675C TYR* 2.8 38.4 + - + +
1676C ILE* 3.1 43.1 - - + +
1678C LEU* 1.3 72.7 - - - +
1680C ALA* 1.3 65.7 + - + +
1682C THR* 3.0 8.4 - - - +
1683C LYS* 2.9 34.5 + - + +
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Residues in contact with ALA1680 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1651C LYS* 3.7 26.7 - - + +
1654C GLN* 5.4 1.1 - - + -
1655C ILE* 3.5 19.3 - - + -
1676C ILE* 2.8 19.9 + - + +
1677C SER* 2.3 18.0 + - - +
1679C LEU* 1.3 68.1 - - + +
1681C ASP* 1.3 57.1 + - - +
1683C LYS* 2.3 41.1 + - - +
1684C LEU* 2.8 10.6 + - - -
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Residues in contact with ASP1681 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1655C ILE* 3.1 38.1 - - + +
1677C SER 2.7 13.8 + - - -
1678C LEU* 2.4 42.7 - - - +
1680C ALA* 1.3 71.3 - - - +
1682C THR* 1.3 75.8 + - - -
1684C LEU* 3.6 8.5 - - - +
1685C ASP* 2.6 40.3 + - - +
1717C LEU* 4.3 11.3 - - + +
1721C HIS* 5.0 3.5 - - - -
1724C MET* 3.1 17.1 - - + +
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Residues in contact with THR1682 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430C VAL* 5.2 14.4 - - + +
1678C LEU 2.0 26.2 + - - -
1679C LEU* 3.0 11.2 - - - +
1680C ALA 2.8 0.2 + - - -
1681C ASP* 1.3 84.4 + - - +
1683C LYS* 1.3 68.7 + - - +
1685C ASP* 2.8 31.0 + - + +
1686C LEU* 3.1 12.9 + - + +
1724C MET* 3.2 16.7 - - - +
1727C ARG* 5.8 4.9 - - - +
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Residues in contact with LYS1683 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1590C THR 3.4 20.3 + - - -
1591C LYS* 2.2 43.0 + - - +
1593C VAL* 3.9 3.2 - - - +
1594C SER* 2.9 29.5 + - - +
1651C LYS* 3.4 27.2 - - + +
1679C LEU* 2.9 26.4 + - + +
1680C ALA* 2.3 29.4 + - - +
1682C THR* 1.3 66.5 - - - +
1684C LEU* 1.3 51.9 + - + +
1685C ASP 2.7 0.9 + - - -
1686C LEU* 2.2 43.0 + - + +
1687C HIS* 2.8 30.1 + - + +
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Residues in contact with LEU1684 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1648C LEU* 3.5 26.2 - - + +
1651C LYS* 4.1 6.7 - - + -
1652C ILE* 3.4 27.1 - - + +
1655C ILE* 3.4 30.1 - - + -
1680C ALA 2.8 12.0 + - - +
1681C ASP 3.7 4.7 - - - +
1683C LYS* 1.3 69.4 - - - +
1685C ASP* 1.3 65.2 + - - +
1687C HIS* 3.1 34.1 - - + +
1688C LEU* 2.9 38.3 + - + +
1713C VAL* 4.3 1.1 - - + -
1717C LEU* 3.5 19.5 - - + -
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Residues in contact with ASP1685 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1681C ASP* 2.6 24.8 + - - +
1682C THR* 2.8 26.7 + - + +
1684C LEU* 1.3 79.7 - - - +
1686C LEU* 1.3 68.4 + - + +
1688C LEU* 3.6 1.4 - - - +
1689C LYS* 2.8 54.1 + - + +
1717C LEU* 6.0 0.9 - - - +
1724C MET* 4.8 11.5 - - - +
1727C ARG* 4.4 25.0 + - - +
1728C GLU* 5.4 0.9 + - - -
1731C PRO* 6.0 0.9 - - - -
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Residues in contact with LEU1686 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1594C SER* 5.0 4.3 - - - +
1598C ASN* 3.1 46.0 - - - +
1601C LEU* 4.8 4.2 - - + +
1682C THR* 3.1 14.5 + - + +
1683C LYS* 2.2 29.5 + - + +
1685C ASP* 1.3 72.5 - - + +
1687C HIS* 1.3 56.9 + - + +
1689C LYS* 2.7 27.8 + - + -
1690C GLY* 2.8 15.9 + - - -
1810C PRO* 4.2 30.7 - - + +
1811C ARG* 6.3 0.2 - - + -
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Residues in contact with HIS1687 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1594C SER* 3.8 15.7 - - - -
1597C LEU* 5.1 14.7 - - + +
1598C ASN* 5.4 1.6 - - - -
1640C GLU* 5.1 10.1 + - + +
1643C MET* 6.3 3.6 - - + -
1647C ALA* 6.4 0.2 - - + -
1648C LEU* 4.1 16.2 - - + +
1651C LYS* 3.8 11.4 - - + -
1683C LYS* 2.8 58.1 + - + +
1684C LEU* 3.1 27.3 - - + +
1686C LEU* 1.3 74.9 - - + +
1688C LEU* 1.3 58.9 + - + +
1691C GLN* 2.6 41.5 + - + +
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Residues in contact with LEU1688 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1648C LEU* 5.3 6.7 - - + -
1684C LEU* 2.9 32.1 + - + +
1685C ASP* 3.8 2.5 - - - +
1687C HIS* 1.3 78.6 - - + +
1689C LYS* 1.3 50.4 + - + +
1691C GLN* 4.6 1.8 - - - -
1692C ALA* 2.4 38.0 + - - +
1695C LEU* 5.5 0.5 - - - +
1710C LEU* 3.5 39.0 - - + +
1713C VAL* 4.5 12.6 - - + -
1714C LEU* 4.4 32.3 - - + +
1717C LEU* 5.6 1.8 - - + -
1731C PRO* 4.6 14.0 - - + +
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Residues in contact with LYS1689 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1685C ASP* 2.8 40.7 + - + +
1686C LEU* 2.7 16.5 + - + +
1688C LEU* 1.3 72.7 - - - +
1690C GLY* 1.3 61.2 - - - +
1692C ALA* 2.9 8.5 + - - +
1693C VAL* 2.8 32.0 + - - +
1727C ARG* 3.2 54.4 + - - +
1730C PRO* 5.2 4.5 - - - +
1731C PRO* 3.8 25.8 - - + -
1810C PRO 5.5 7.0 - - - +
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Residues in contact with GLY1690 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1601C LEU* 4.6 24.6 - - - +
1686C LEU* 2.8 14.5 + - - +
1689C LYS* 1.3 73.7 - - - +
1691C GLN* 1.3 52.5 + - - -
1693C VAL* 2.5 33.9 + - - +
1694C THR* 3.0 11.1 + - - +
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Residues in contact with GLN1691 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1597C LEU* 5.9 4.9 - - - +
1601C LEU* 5.5 3.2 - - - +
1636C ASP* 2.9 30.1 + - - +
1637C SER* 3.2 20.0 - - - +
1639C LEU* 4.4 3.8 - - - +
1640C GLU* 3.4 27.7 - - + +
1686C LEU 4.1 0.2 + - - -
1687C HIS* 2.6 26.2 + - + +
1688C LEU* 4.5 2.0 - - - -
1690C GLY* 1.3 74.8 - - - +
1692C ALA* 1.3 56.1 + - - +
1694C THR* 3.0 34.8 - - - +
1695C LEU* 3.0 36.1 + - + +
1710C LEU* 6.4 1.1 - - + -
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Residues in contact with ALA1692 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1688C LEU 2.4 32.3 + - - +
1689C LYS* 2.9 10.0 + - - +
1691C GLN* 1.3 77.7 - - - +
1693C VAL* 1.3 56.4 + - + +
1695C LEU* 3.2 20.2 + - + +
1696C LEU* 2.9 30.8 + - + +
1700C THR* 5.7 2.7 - - - +
1731C PRO* 5.2 2.9 - - + -
1732C GLY* 5.1 14.1 - - - +
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Residues in contact with VAL1693 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1605C PHE* 5.1 21.8 - - + -
1689C LYS 2.8 17.4 + - - +
1690C GLY* 2.5 23.1 + - - +
1692C ALA* 1.3 70.2 - - + +
1694C THR* 1.3 57.8 + - - +
1695C LEU 3.1 1.3 - - - -
1696C LEU* 3.0 45.1 - - + +
1697C PRO* 3.1 6.2 - - - +
1809C ASP* 5.4 14.1 - - - +
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Residues in contact with THR1694 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1633C TRP* 2.2 44.4 + - - +
1636C ASP* 3.1 16.8 - - - +
1637C SER* 3.4 9.8 + - - +
1690C GLY 3.0 7.2 + - - +
1691C GLN* 3.0 44.2 - - - +
1693C VAL* 1.3 76.0 - - - +
1695C LEU* 1.3 60.8 + - + +
1697C PRO* 3.1 21.2 - - - +
1698C PHE* 4.6 7.3 + - - -
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Residues in contact with LEU1695 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1637C SER* 5.1 9.6 - - - +
1688C LEU 5.5 0.2 - - - +
1691C GLN* 3.0 22.8 + - + +
1692C ALA* 3.3 23.3 - - + +
1693C VAL 3.1 0.4 - - - -
1694C THR* 1.3 82.6 - - + +
1696C LEU* 1.3 52.8 + - - +
1697C PRO 3.1 0.7 - - - -
1698C PHE* 2.4 32.5 + - + +
1699C PHE* 3.0 27.0 + - - +
1700C THR* 3.7 26.5 - - - +
1703C THR* 3.1 31.6 - - + +
1704C GLY* 4.5 7.4 - - - +
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Residues in contact with LEU1696 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1692C ALA* 2.9 21.6 + - + +
1693C VAL* 3.0 41.5 - - + +
1695C LEU* 1.3 75.3 - - - +
1697C PRO* 1.3 63.6 - - + +
1698C PHE 3.3 2.6 + - - +
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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
------------------------------------------------------------
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