Contacts of the helix formed by residues 1648 - 1669 (chain X) in PDB entry 3HM6
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 LYS1648 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1611X ASN* 3.6 48.0 + - - +
1645X LEU* 3.0 18.3 + - + +
1647X GLY* 1.3 82.1 - - - +
1649X LEU* 1.3 59.8 + - - +
1650X GLU 3.3 3.1 - - - -
1651X TYR* 3.2 33.6 + - + +
1652X PHE 3.0 22.0 + - - -
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Residues in contact with LEU1649 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1642X THR 5.4 0.9 - - - +
1645X LEU 4.3 0.2 - - - +
1646X HIS* 3.4 32.8 - - + +
1648X LYS* 1.3 75.5 - - - +
1650X GLU* 1.3 53.1 + - - +
1651X TYR 3.4 0.2 - - - -
1652X PHE* 3.6 25.3 - - + +
1653X THR* 2.6 38.4 + - - -
1690X TRP* 5.7 2.0 - - + -
1693X ILE* 3.8 37.2 - - + -
2071X LEU* 3.7 23.8 - - + +
2074X LEU* 3.6 33.2 - - + -
2075X SER* 3.5 16.3 + - - +
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Residues in contact with GLU1650 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1648X LYS 3.3 0.8 - - - -
1649X LEU* 1.3 78.2 - - - +
1651X TYR* 1.3 57.9 + - - +
1653X THR* 3.6 2.6 + - - -
1654X ASP* 3.1 24.6 + - - +
2068X ASN* 3.4 49.0 + - - +
2071X LEU* 4.1 20.2 - - + +
2072X ALA* 5.7 4.5 - - + +
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Residues in contact with TYR1651 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1610X LEU 2.6 30.5 + - - -
1611X ASN* 3.3 22.8 - - - -
1612X SER 3.3 16.1 + - - -
1613X LYS* 3.4 13.5 + - + -
1616X LEU* 3.6 14.1 - - + +
1645X LEU* 4.0 23.8 - - + -
1648X LYS* 3.2 39.9 + - + +
1650X GLU* 1.3 78.0 - - - +
1652X PHE* 1.3 67.8 + - - +
1653X THR 3.1 0.2 - - - -
1654X ASP* 3.0 14.1 + - + +
1655X ILE* 2.8 45.5 + - + +
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Residues in contact with PHE1652 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1641X LEU 4.8 0.9 - - - -
1642X THR* 3.6 32.5 - - + -
1645X LEU* 4.2 29.6 - - + +
1648X LYS 3.0 13.8 + - - +
1649X LEU* 3.6 29.6 - - + +
1651X TYR* 1.3 77.9 - - - +
1653X THR* 1.3 56.7 + - - +
1655X ILE* 3.2 11.8 + - + +
1656X LEU* 2.9 29.8 + - + +
1686X LEU* 3.7 43.3 - - + -
1690X TRP* 3.7 39.9 - + + -
1693X ILE* 4.7 3.6 - - + -
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Residues in contact with THR1653 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1649X LEU 2.6 25.7 + - - -
1650X GLU 3.8 3.6 - - - -
1651X TYR 3.1 0.4 - - - -
1652X PHE* 1.3 76.1 - - - +
1654X ASP* 1.3 57.5 + - - +
1656X LEU* 3.4 6.7 + - + +
1657X ARG* 2.9 27.4 + - + +
1690X TRP* 3.0 33.0 + - + +
1953X TYR* 4.1 31.2 - - + +
2071X LEU* 3.2 26.4 - - + +
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Residues in contact with ASP1654 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1613X LYS* 2.8 37.5 + - - +
1650X GLU 3.1 14.5 + - - +
1651X TYR* 3.0 17.5 + - + +
1653X THR* 1.3 74.5 - - - +
1655X ILE* 1.3 66.7 + - - +
1657X ARG* 3.3 16.4 + - - +
1658X THR* 3.1 27.7 + - - -
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Residues in contact with ILE1655 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1613X LYS* 3.8 32.1 - - + -
1616X LEU* 3.7 33.4 - - + -
1617X THR* 4.3 12.1 - - + -
1620X ILE* 4.5 8.3 - - + -
1645X LEU* 5.3 1.3 - - + -
1651X TYR* 2.8 35.2 + - + +
1652X PHE* 3.4 13.5 - - + +
1654X ASP* 1.3 75.5 - - - +
1656X LEU* 1.3 62.6 + - - +
1658X THR* 3.2 6.2 + - - -
1659X LEU* 3.0 43.4 + - + +
1686X LEU* 4.7 6.1 - - + -
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Residues in contact with LEU1656 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1652X PHE* 2.9 15.3 + - + +
1653X THR* 3.6 10.3 - - + +
1655X ILE* 1.3 76.6 - - - +
1657X ARG* 1.3 57.0 + - - +
1659X LEU* 3.5 5.5 + - - +
1660X LEU* 2.8 31.7 + - + +
1683X VAL* 4.2 15.7 - - + +
1686X LEU* 4.1 15.9 - - + +
1687X LEU* 3.9 39.0 - - + +
1690X TRP* 3.6 46.0 - - + +
1954X PHE* 4.2 15.0 - - + -
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Residues in contact with ARG1657 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1653X THR* 2.9 18.0 + - + +
1654X ASP* 3.5 17.1 + - - +
1655X ILE 3.2 0.2 - - - -
1656X LEU* 1.3 77.9 - - - +
1658X THR* 1.3 57.4 + - - +
1660X LEU* 3.6 7.5 + - - +
1661X SER* 3.1 28.4 + - - -
1953X TYR* 3.5 22.8 + - - +
1954X PHE* 6.2 0.4 - - - -
1957X LEU* 3.9 34.0 - - + +
1960X GLU* 4.3 15.2 + - - -
1961X GLN* 5.5 2.2 + - - +
1964X GLN* 6.0 1.8 - - - +
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Residues in contact with THR1658 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1613X LYS* 2.7 41.6 + - - -
1617X THR* 4.7 14.4 - - + -
1654X ASP* 3.1 7.3 + - - -
1655X ILE* 3.5 8.7 - - - -
1657X ARG* 1.3 74.4 - - - +
1659X LEU* 1.3 67.5 + - + +
1661X SER* 3.3 7.6 + - - -
1662X ASP* 3.1 36.2 + - - +
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Residues in contact with LEU1659 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1617X THR* 4.7 22.0 - - + +
1620X ILE* 4.0 32.5 - - + -
1655X ILE* 3.0 21.1 + - + +
1656X LEU* 3.9 2.7 - - - +
1658X THR* 1.3 74.2 - - + +
1660X LEU* 1.3 61.1 + - - +
1662X ASP* 3.3 14.3 + - - +
1663X LEU* 2.9 29.5 + - - +
1683X VAL* 3.6 27.0 - - + +
1686X LEU* 3.4 32.5 - - + -
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Residues in contact with LEU1660 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1656X LEU* 2.8 20.4 + - + +
1657X ARG* 3.7 5.4 - - - +
1658X THR 3.3 0.2 - - - -
1659X LEU* 1.3 77.1 - - - +
1661X SER* 1.3 55.6 - - - +
1663X LEU* 3.1 11.1 + - + +
1664X VAL* 2.8 44.8 + - + +
1675X MET* 4.5 2.7 - - + -
1676X LEU* 4.4 16.4 - - + -
1683X VAL* 4.1 7.1 - - + +
1687X LEU* 5.6 0.4 - - + -
1954X PHE* 4.0 28.5 - - + -
1957X LEU* 3.8 32.3 - - + -
1958X LEU* 4.0 20.4 - - + -
1961X GLN* 4.0 17.7 - - + -
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Residues in contact with SER1661 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1657X ARG* 3.1 16.8 + - - -
1658X THR* 3.4 12.3 - - - -
1660X LEU* 1.3 77.7 - - - +
1662X ASP* 1.3 62.8 + - - +
1664X VAL* 3.6 2.9 + - - +
1665X ALA* 3.3 21.3 + - - +
1961X GLN* 3.8 30.1 + - - +
1964X GLN* 5.6 0.5 + - - -
1965X HIS* 4.7 2.8 - - - -
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Residues in contact with ASP1662 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1658X THR* 3.1 26.0 + - - +
1659X LEU* 3.7 15.8 - - - +
1660X LEU 3.3 0.2 - - - -
1661X SER* 1.3 76.3 + - - +
1663X LEU* 1.3 60.7 + - - +
1665X ALA* 3.4 5.7 + - - +
1666X GLN* 3.0 47.9 + - - +
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Residues in contact with LEU1663 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1659X LEU 2.9 16.8 + - - +
1660X LEU* 3.1 10.3 + - + +
1662X ASP* 1.3 76.9 - - - +
1664X VAL* 1.3 56.3 + - - +
1666X GLN* 3.3 14.5 + - - +
1667X TYR* 2.9 63.3 + - + +
1675X MET* 3.8 25.1 - - + -
1676X LEU* 3.9 24.9 - - + +
1681X THR* 5.8 2.0 - - + +
1683X VAL* 3.9 32.1 - - + -
1684X GLU* 5.5 2.0 - - + -
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Residues in contact with VAL1664 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1660X LEU* 2.8 25.5 + - + +
1661X SER 3.9 0.7 - - - +
1662X ASP 3.3 0.2 - - - -
1663X LEU* 1.3 75.2 - - - +
1665X ALA* 1.3 59.4 + - - +
1667X TYR* 4.2 0.2 - - - +
1668X VAL* 2.9 40.2 + - + +
1675X MET* 3.8 28.7 - - + -
1958X LEU* 5.6 0.4 - - + -
1961X GLN* 3.7 33.2 - - + +
1965X HIS* 3.7 22.0 - - + +
1976X TRP* 3.6 25.6 - - + -
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Residues in contact with ALA1665 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1661X SER 3.3 15.0 + - - +
1662X ASP* 3.4 6.7 + - - +
1664X VAL* 1.3 78.6 - - - +
1666X GLN* 1.3 64.7 + - + +
1668X VAL* 3.8 2.6 + - - +
1669X ALA* 3.7 16.5 + - - +
1965X HIS* 3.8 24.0 + - + +
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Residues in contact with GLN1666 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1621X HIS* 6.4 0.2 - - - -
1662X ASP* 3.0 35.2 + - - +
1663X LEU* 3.5 19.6 - - - +
1665X ALA* 1.3 77.2 - - + +
1667X TYR* 1.3 61.2 - - + +
1669X ALA* 3.4 14.4 + - - +
1670X LYS* 3.3 34.4 + - - +
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Residues in contact with TYR1667 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1663X LEU* 2.9 52.2 + - + +
1664X VAL 4.2 0.9 - - - +
1666X GLN* 1.3 74.5 - - + +
1668X VAL* 1.3 59.0 + - - +
1669X ALA 3.2 2.0 - - - -
1670X LYS* 3.1 46.1 + - + +
1671X ASN 3.7 17.9 - - - -
1672X PRO* 3.0 32.0 - - + -
1674X LEU* 3.7 18.4 + - + -
1675X MET* 3.7 41.1 - - + -
1676X LEU 5.1 1.4 + - - -
1684X GLU* 5.4 3.1 + - - -
1976X TRP* 5.8 0.2 - - + -
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Residues in contact with VAL1668 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1664X VAL* 2.9 33.2 + - + +
1665X ALA* 4.0 6.7 - - - +
1667X TYR* 1.3 76.6 - - - +
1669X ALA* 1.3 60.8 + - + +
1670X LYS 3.3 5.1 + - - +
1672X PRO* 4.2 15.7 - - + +
1965X HIS* 3.7 28.5 - - + +
1967X ILE* 3.3 31.9 - - + -
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Residues in contact with ALA1669 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1665X ALA 3.7 8.4 + - - +
1666X GLN* 3.4 10.6 + - - +
1667X TYR 3.2 0.8 - - - -
1668X VAL* 1.3 77.8 - - + +
1670X LYS* 1.3 64.7 + - + +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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