Contacts of the helix formed by residues 1721 - 1761 (chain B) in PDB entry 3KBU
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 ASP1721 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1719B GLY 3.3 0.6 - - - -
1720B GLN* 1.3 93.7 + - - +
1722B PHE* 1.3 65.7 + - - +
1723B ASP* 3.3 14.6 + - - +
1724B HIS* 3.0 20.7 + - - +
1725B VAL* 2.9 21.0 + - - +
1800B HIS* 4.2 14.8 - - - -
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Residues in contact with PHE1722 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1721B ASP* 1.3 74.3 - - - +
1723B ASP* 1.3 67.2 + - - +
1725B VAL* 3.5 4.9 - - + +
1726B THR* 2.8 36.0 + - - -
1797B TYR* 3.6 41.3 - + - -
1800B HIS* 3.8 22.2 - - + +
1801B ARG* 3.6 40.8 - - + -
1804B TYR* 3.7 48.0 - + + -
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Residues in contact with ASP1723 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1721B ASP* 3.3 13.9 + - - +
1722B PHE* 1.3 81.8 - - - +
1724B HIS* 1.3 60.7 + - - +
1726B THR* 3.5 7.1 - - - -
1727B LEU* 3.3 22.2 + - - +
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Residues in contact with HIS1724 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1717B GLU* 4.1 15.3 - - + -
1719B GLY* 3.5 9.5 - - - -
1720B GLN* 3.1 44.2 + - + +
1721B ASP* 3.0 23.2 + - - +
1723B ASP* 1.3 75.3 - - - +
1725B VAL* 1.3 54.3 + - - +
1726B THR 3.1 1.1 - - - -
1727B LEU* 3.1 13.3 + - + -
1728B LEU* 2.7 54.1 + - + +
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Residues in contact with VAL1725 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1718B MET 3.5 24.0 - - - +
1719B GLY* 4.5 4.4 - - - -
1721B ASP 2.9 11.7 + - - +
1722B PHE* 3.5 19.1 - - + +
1724B HIS* 1.3 73.3 - - - +
1726B THR* 1.3 64.1 + - - +
1728B LEU* 4.1 5.4 - - + -
1729B ARG* 2.8 32.2 + - + +
1793B LEU* 4.3 12.8 - - + +
1796B SER* 3.5 14.1 - - - +
1797B TYR* 3.9 34.5 - - + +
1800B HIS* 3.9 17.0 - - - +
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Residues in contact with THR1726 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1722B PHE* 2.8 31.6 + - - -
1723B ASP* 3.5 8.6 - - - -
1725B VAL* 1.3 78.3 - - - +
1727B LEU* 1.3 58.2 + - - +
1729B ARG* 3.8 13.9 + - - +
1730B ASP* 2.9 45.8 + - - +
1797B TYR* 3.4 25.0 + - + +
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Residues in contact with LEU1727 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1723B ASP 3.3 10.2 + - - +
1724B HIS* 3.1 17.3 + - + +
1726B THR* 1.3 78.8 - - - +
1728B LEU* 1.3 65.3 + - - +
1730B ASP* 3.2 10.7 + - + +
1731B LYS* 2.9 53.8 + - + +
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Residues in contact with LEU1728 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1717B GLU* 3.6 40.2 - - + +
1718B MET 4.2 2.5 - - - +
1719B GLY* 3.8 23.6 - - - +
1724B HIS* 2.7 37.5 + - + +
1725B VAL* 3.7 5.2 - - - +
1727B LEU* 1.3 72.9 - - - +
1729B ARG* 1.3 63.5 + - - +
1731B LYS* 3.4 10.7 + - + +
1732B PHE* 3.0 25.5 + - - +
1789B ARG* 4.9 4.0 - - - +
1793B LEU* 4.3 14.0 - - + +
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Residues in contact with ARG1729 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1725B VAL* 2.8 23.7 + - + +
1726B THR* 3.8 10.0 - - - +
1728B LEU* 1.3 72.8 - - - +
1730B ASP* 1.3 87.5 + - - +
1732B PHE* 3.2 4.2 + - - +
1733B ARG* 3.0 50.8 + - - +
1790B MET* 5.7 6.6 - - + +
1793B LEU* 4.4 28.8 - - + +
1794B ALA* 5.1 8.3 - - + +
1797B TYR* 3.3 58.6 + - + -
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Residues in contact with ASP1730 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1726B THR* 2.9 32.7 + - - +
1727B LEU* 3.2 14.4 + - + +
1729B ARG* 1.3 99.8 + - - +
1731B LYS* 1.3 62.5 + - - +
1733B ARG* 3.2 18.6 + - - +
1734B ASP* 3.1 28.1 + - - +
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Residues in contact with LYS1731 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1727B LEU* 2.9 44.7 + - + +
1728B LEU* 3.7 12.3 - - + +
1730B ASP* 1.3 76.4 - - - +
1732B PHE* 1.3 57.8 + - - +
1734B ASP* 3.3 13.3 - - - +
1735B PHE* 2.8 26.9 + - - +
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Residues in contact with PHE1732 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1712B VAL* 4.6 8.3 - - + -
1713B ALA* 4.0 12.3 - - - -
1728B LEU 3.0 17.3 + - - +
1729B ARG 3.2 4.2 + - - +
1731B LYS* 1.3 76.7 - - - +
1733B ARG* 1.3 59.3 + - - +
1735B PHE* 3.6 28.5 - + + -
1736B ALA* 2.8 25.5 + - + +
1786B ILE* 3.3 44.6 - - + -
1789B ARG* 3.2 37.9 - - + -
1790B MET* 3.7 19.3 - - + -
1793B LEU* 3.8 18.2 - - + -
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Residues in contact with ARG1733 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1729B ARG* 3.0 47.4 + - + +
1730B ASP* 3.2 27.5 + - - +
1732B PHE* 1.3 76.4 - - - +
1734B ASP* 1.3 62.4 + - - +
1736B ALA* 3.3 6.7 + - + +
1737B ARG* 3.1 45.9 + - - +
1790B MET* 4.7 27.9 - - + +
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Residues in contact with ASP1734 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1730B ASP* 3.1 14.6 + - - +
1731B LYS* 3.3 15.5 - - - +
1733B ARG* 1.3 77.9 - - - +
1735B PHE* 1.3 60.2 + - - +
1737B ARG* 3.4 14.7 + - - +
1738B GLU* 2.9 43.6 + - - +
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Residues in contact with PHE1735 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1709B LYS* 3.6 38.8 - - + -
1712B VAL* 3.6 37.2 - - + -
1713B ALA 4.8 0.9 - - - -
1731B LYS 2.8 18.0 + - - +
1732B PHE* 3.6 34.8 - + + +
1733B ARG 3.3 0.2 - - - -
1734B ASP* 1.3 71.1 - - - +
1736B ALA* 1.3 69.1 + - - +
1738B GLU* 4.4 3.3 - - - +
1739B THR* 2.7 52.8 + - - -
1786B ILE* 4.1 19.7 - - + -
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Residues in contact with ALA1736 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1732B PHE* 2.8 21.4 + - + +
1733B ARG* 3.5 8.5 - - - +
1735B PHE* 1.3 80.4 - - - +
1737B ARG* 1.3 57.4 + - - +
1739B THR* 3.9 1.0 - - - -
1740B GLY* 2.9 26.5 + - - -
1786B ILE* 3.7 30.6 - - + +
1790B MET* 4.3 13.7 - - - -
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Residues in contact with ARG1737 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1733B ARG* 3.1 37.7 + - - +
1734B ASP* 3.4 14.7 + - - +
1736B ALA* 1.3 81.0 - - - +
1738B GLU* 1.3 59.2 + - + +
1740B GLY* 3.4 1.4 + - - -
1741B ALA* 2.9 30.0 + - + +
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Residues in contact with GLU1738 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1709B LYS* 5.6 2.5 - - - +
1734B ASP* 2.9 30.0 + - - +
1735B PHE* 4.4 2.9 - - - +
1737B ARG* 1.3 73.6 - - + +
1739B THR* 1.3 67.0 + - - +
1741B ALA* 3.2 5.1 + - - +
1742B ILE* 2.9 44.8 + - + +
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Residues in contact with THR1739 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1705B TRP* 3.6 12.1 - - + -
1709B LYS* 3.5 40.0 + - + +
1735B PHE* 2.7 44.4 + - + -
1736B ALA 3.9 2.5 - - - -
1738B GLU* 1.3 75.5 - - - +
1740B GLY* 1.3 53.9 + - - +
1742B ILE* 5.8 0.2 - - - -
1743B GLY* 2.8 33.4 + - - -
1779B TRP* 3.8 2.2 - - + -
1782B LEU* 4.2 8.5 - - + -
1786B ILE* 3.8 22.9 - - + -
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Residues in contact with GLY1740 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1736B ALA 2.9 18.2 + - - -
1737B ARG* 3.7 1.6 - - - -
1739B THR* 1.3 74.1 - - - +
1741B ALA* 1.3 64.6 + - - +
1744B GLN* 3.0 27.9 + - - +
1779B TRP* 4.0 11.8 - - - -
1783B LEU* 4.6 11.4 - - - -
1786B ILE* 5.2 1.0 - - - +
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Residues in contact with ALA1741 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1737B ARG* 2.9 23.2 + - + +
1738B GLU* 3.8 5.6 - - - +
1740B GLY* 1.3 75.0 - - - +
1742B ILE* 1.3 64.7 + - + +
1744B GLN* 4.0 3.4 - - - +
1745B GLU* 3.3 20.7 + - - +
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Residues in contact with ILE1742 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1705B TRP* 3.5 25.8 - - + +
1709B LYS* 6.2 2.2 - - - +
1738B GLU* 2.9 32.9 + - + +
1739B THR 4.3 0.2 - - - +
1741B ALA* 1.3 76.3 - - + +
1743B GLY* 1.3 66.7 + - - +
1745B GLU* 3.4 9.3 + - - +
1746B ARG* 3.2 35.9 + - + +
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Residues in contact with GLY1743 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1702B LEU* 5.6 0.7 - - - -
1705B TRP* 3.7 17.0 - - - -
1739B THR 2.8 23.6 + - - -
1742B ILE* 1.3 76.0 - - - +
1744B GLN* 1.3 62.6 + - - +
1746B ARG* 3.1 5.8 + - - +
1747B VAL* 2.9 28.1 + - - +
1779B TRP* 3.5 17.0 - - - -
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Residues in contact with GLN1744 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1740B GLY 3.0 19.1 + - - +
1741B ALA* 4.0 3.8 - - - +
1743B GLY* 1.3 74.8 - - - +
1745B GLU* 1.3 63.8 + - - +
1747B VAL* 4.5 8.6 - - - +
1748B ASP* 2.9 62.4 + - - +
1779B TRP* 2.7 36.8 + - + +
1783B LEU* 4.7 4.0 - - - +
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Residues in contact with GLU1745 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1741B ALA 3.3 14.2 + - - +
1742B ILE* 3.9 8.7 - - - +
1743B GLY 3.2 1.0 - - - -
1744B GLN* 1.3 80.5 - - - +
1746B ARG* 1.3 66.0 + - + +
1748B ASP* 3.3 7.7 + - + +
1749B ASN* 3.1 39.5 + - - +
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Residues in contact with ARG1746 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1698B GLU* 4.7 2.0 + - - +
1701B ASP* 4.1 11.9 - - - +
1702B LEU* 3.6 50.8 - - + +
1705B TRP* 3.5 37.7 - - - +
1742B ILE* 3.2 26.6 + - + +
1743B GLY* 3.1 7.0 + - - +
1745B GLU* 1.3 80.4 - - + +
1747B VAL* 1.3 61.9 + - - +
1749B ASN* 3.1 12.0 + - - +
1750B VAL* 3.1 25.7 + - + +
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Residues in contact with VAL1747 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1702B LEU* 4.0 22.4 - - + -
1706B ILE* 4.9 0.4 - - + -
1743B GLY 2.9 19.5 + - - +
1744B GLN* 4.0 10.3 - - - +
1746B ARG* 1.3 73.6 - - - +
1748B ASP* 1.3 58.6 + - - +
1750B VAL* 3.3 1.9 + - - +
1751B ASN* 2.9 53.6 + - - +
1775B LEU* 4.5 11.7 - - + -
1776B ASN* 3.6 12.8 - - - +
1779B TRP* 3.7 46.0 - - + +
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Residues in contact with ASP1748 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1744B GLN* 2.9 55.0 + - - +
1745B GLU* 3.5 7.1 - - + +
1747B VAL* 1.3 79.0 - - - +
1749B ASN* 1.3 59.2 + - - +
1751B ASN* 3.4 7.2 + - - +
1752B ALA* 3.0 28.3 + - - +
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Residues in contact with ASN1749 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1745B GLU* 3.1 35.7 + - - +
1746B ARG* 3.1 10.0 + - - +
1748B ASP* 1.3 75.5 - - - +
1750B VAL* 1.3 63.0 + - + +
1752B ALA* 3.3 6.3 + - - +
1753B PHE* 2.8 29.8 + - - +
1756B ARG* 4.8 1.6 + - - -
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Residues in contact with VAL1750 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1695B LEU* 3.9 9.2 - - + -
1698B GLU* 4.6 26.0 - - + +
1699B THR* 3.7 20.4 - - - +
1702B LEU* 3.8 16.4 - - + -
1746B ARG* 3.1 17.4 + - + +
1747B VAL 3.9 0.7 - - - +
1749B ASN* 1.3 73.9 - - + +
1751B ASN* 1.3 66.9 + - - +
1753B PHE* 3.6 5.9 - - - +
1754B ILE* 2.9 33.3 + - + +
1775B LEU* 3.6 26.5 - - + -
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Residues in contact with ASN1751 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1747B VAL* 2.9 36.8 + - - +
1748B ASP* 3.6 9.8 + - - +
1750B VAL* 1.3 77.9 - - - +
1752B ALA* 1.3 56.3 + - - +
1754B ILE* 3.2 7.0 + - - +
1755B GLU* 2.9 34.1 + - + +
1772B LYS* 2.9 35.4 - - - +
1775B LEU* 4.7 5.4 - - - +
1776B ASN* 2.9 33.5 + - - +
----------------------------------------------------------
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Residues in contact with ALA1752 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1748B ASP 3.0 17.9 + - - +
1749B ASN* 3.8 6.7 - - - +
1751B ASN* 1.3 72.7 - - - +
1753B PHE* 1.3 65.8 + - - +
1755B GLU* 3.3 6.3 + - - +
1756B ARG* 2.9 42.2 + - + +
----------------------------------------------------------
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Residues in contact with PHE1753 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1691B HIS* 3.8 21.3 - + + -
1694B GLN* 3.6 28.0 - - + -
1695B LEU* 3.7 42.4 - - + -
1698B GLU* 3.7 22.7 - - - +
1749B ASN 2.8 21.7 + - - +
1750B VAL* 3.6 6.5 - - - +
1752B ALA* 1.3 73.6 - - - +
1754B ILE* 1.3 64.2 + - - +
1756B ARG* 3.2 30.5 + - + +
1757B LEU* 3.1 40.1 + - + +
----------------------------------------------------------
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Residues in contact with ILE1754 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1695B LEU* 3.6 29.6 - - + -
1699B THR* 4.9 2.2 - - - +
1750B VAL* 2.9 38.1 + - + +
1751B ASN* 3.4 4.5 - - - +
1753B PHE* 1.3 76.1 - - - +
1755B GLU* 1.3 59.9 + - - +
1757B LEU* 3.2 7.8 + - - +
1758B ILE* 2.9 39.2 + - + +
1768B ILE* 3.3 24.2 - - + +
1771B TRP* 5.0 2.7 - - + -
1772B LYS* 3.8 49.4 - - + +
1775B LEU* 5.2 2.2 - - + -
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Residues in contact with GLU1755 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1751B ASN* 2.9 23.6 + - + +
1752B ALA* 3.3 7.1 + - - +
1754B ILE* 1.3 72.7 - - - +
1756B ARG* 1.3 54.1 + - - +
1758B ILE* 3.2 19.5 + - - +
1759B ASP* 2.7 61.9 + - - +
1772B LYS* 2.5 38.1 + - - +
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Residues in contact with ARG1756 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1749B ASN 4.8 1.6 + - - -
1752B ALA* 2.9 28.7 + - - +
1753B PHE* 3.3 47.5 - - + +
1755B GLU* 1.3 74.5 - - - +
1757B LEU* 1.3 61.2 + - + +
1759B ASP* 4.4 3.5 - - - +
1760B ALA* 3.0 31.4 + - - +
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Residues in contact with LEU1757 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1688B ASN* 5.1 4.7 - - - +
1691B HIS* 3.8 44.6 - - + +
1692B LEU* 4.8 0.9 - - - +
1695B LEU* 4.0 19.5 - - + -
1753B PHE* 3.1 31.3 + - + +
1754B ILE* 3.5 5.6 - - - +
1756B ARG* 1.3 77.0 - - + +
1758B ILE* 1.3 68.3 + - - +
1760B ALA* 3.2 5.5 + - + +
1761B GLY 3.0 18.4 + - - +
1762B HIS* 3.7 28.4 - - + +
1768B ILE* 4.0 26.9 - - + -
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Residues in contact with ILE1758 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1754B ILE* 2.9 41.2 + - + +
1755B GLU* 3.9 19.1 - - - +
1757B LEU* 1.3 71.6 - - - +
1759B ASP* 1.3 74.9 + - - +
1761B GLY* 3.0 15.4 + - - -
1762B HIS* 4.5 4.8 + - - -
1765B ALA* 4.2 32.1 - - + +
1768B ILE* 4.2 14.8 - - + -
1769B ALA* 4.5 12.6 - - + +
1772B LYS* 5.8 0.2 - - + -
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Residues in contact with ASP1759 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1755B GLU* 2.7 45.8 + - - +
1756B ARG* 4.4 2.9 - - - +
1758B ILE* 1.3 82.4 - - - +
1760B ALA* 1.3 59.6 + - - +
1761B GLY* 3.3 1.2 + - - -
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Residues in contact with ALA1760 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1684B ARG* 5.1 4.3 + - - -
1688B ASN* 5.8 3.8 - - - +
1756B ARG 3.0 20.9 + - - +
1757B LEU* 3.8 5.2 - - + +
1759B ASP* 1.3 76.3 - - - +
1761B GLY* 1.3 64.8 + - - +
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Residues in contact with GLY1761 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1684B ARG* 3.5 12.4 + - - -
1688B ASN* 3.2 17.8 + - - +
1757B LEU 3.0 6.5 + - - +
1758B ILE 3.0 10.4 + - - -
1759B ASP 3.2 1.1 - - - -
1760B ALA* 1.3 84.7 - - - +
1762B HIS* 1.3 60.0 + - - +
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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