Contacts of the helix formed by residues 1665 - 1678 (chain B) in PDB entry 5EK0
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 THR1665 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1525A LYS* 4.1 29.9 + - + +
1526A GLU* 4.3 7.1 + - - -
1652B THR* 3.7 6.1 - - - -
1664B GLY* 1.3 77.3 - - - +
1666B LEU* 1.4 63.0 + - + +
1667B GLY 3.2 2.7 - - - +
1668B GLU* 3.6 23.3 - - - +
1669B SER* 2.9 30.5 + - - -
1802B PX4 3.4 22.2 + - - +
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Residues in contact with LEU1666 (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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1521A MET 5.3 0.4 - - - +
1522A MET* 3.8 46.6 + - + +
1524A GLU 5.6 0.9 - - - +
1525A LYS* 5.0 2.8 - - - +
1645B TYR* 4.2 2.5 - - + -
1648B ALA* 3.9 6.7 - - + +
1649B ILE* 3.7 43.5 - - + +
1652B THR* 3.8 12.7 + - + +
1665B THR* 1.4 75.6 - - + +
1667B GLY* 1.3 57.9 + - - +
1669B SER* 3.8 1.0 - - - -
1670B PHE* 2.9 57.0 + - + +
1802B PX4 3.9 15.9 - - + -
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Residues in contact with GLY1667 (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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1665B THR* 3.2 5.5 - - - +
1666B LEU* 1.3 78.3 - - - +
1668B GLU* 1.3 60.1 + - - +
1670B PHE 3.7 0.2 + - - -
1671B TYR* 3.4 15.8 + - - +
1802B PX4 3.2 67.3 + - - +
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Residues in contact with GLU1668 (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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1660B PRO 3.7 7.3 - - - +
1661B GLU* 3.0 31.7 - - - +
1662B TRP 2.9 22.2 - - - +
1664B GLY 4.1 0.2 - - - +
1665B THR* 3.2 35.9 + - - +
1667B GLY* 1.3 76.8 - - - +
1669B SER* 1.3 57.7 + - - +
1671B TYR* 3.2 6.5 + - - +
1672B THR* 3.1 22.7 + - - -
1802B PX4 3.4 39.2 - - - -
1688C ARG* 4.2 6.9 + - - -
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Residues in contact with SER1669 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1648B ALA* 3.6 16.2 - - - -
1651B ALA* 4.1 9.0 - - - -
1652B THR* 2.7 33.1 + - - -
1662B TRP 3.9 4.5 - - - -
1663B PHE* 3.2 25.0 + - - +
1665B THR 2.9 9.5 + - - -
1666B LEU 4.0 3.6 - - - -
1668B GLU* 1.3 74.8 - - - +
1670B PHE* 1.3 62.4 + - - +
1672B THR 4.6 0.2 - - - +
1673B LEU* 3.2 31.0 + - - +
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Residues in contact with PHE1670 (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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1641B THR* 4.6 4.5 - - + -
1644B PHE* 3.7 35.8 - + + -
1645B TYR* 3.5 62.4 - + - -
1648B ALA* 3.6 17.9 - - + -
1666B LEU* 2.9 32.2 + - + +
1667B GLY 3.9 3.4 - - - +
1668B GLU 3.3 0.4 - - - -
1669B SER* 1.3 75.3 - - - +
1671B TYR* 1.3 60.4 + - - +
1673B LEU* 4.9 1.8 - - - -
1674B PHE* 3.3 14.7 + - - +
1802B PX4 3.4 70.6 - - + +
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Residues in contact with TYR1671 (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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1667B GLY 3.4 11.4 + - - +
1668B GLU* 3.2 11.3 + - - +
1670B PHE* 1.3 76.7 - - - +
1672B THR* 1.3 59.2 + - - +
1674B PHE* 3.0 7.3 + + - +
1675B GLN* 2.9 26.4 + - + +
1802B PX4 3.7 23.1 - - + +
1682C TRP* 3.5 7.4 - + - -
1683C SER* 3.2 30.7 + - - -
1687C VAL* 3.3 26.0 - - + +
1688C ARG* 3.5 35.6 - - - +
1691C MET* 3.5 23.5 - - + +
1698C TRP* 4.1 15.9 - + + -
1702C ILE* 4.0 25.4 - - + -
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Residues in contact with THR1672 (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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1662B TRP* 2.7 33.7 + - + -
1663B PHE* 3.5 32.5 - - + -
1668B GLU 3.1 5.6 + - - -
1669B SER 4.5 0.2 - - - -
1671B TYR* 1.3 73.6 - - - +
1673B LEU* 1.3 57.8 + - - +
1675B GLN* 3.0 6.2 + - - +
1676B VAL* 2.8 34.0 + - + +
1686B ILE* 3.9 23.3 - - + -
1688C ARG* 3.2 29.2 + - - +
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Residues in contact with LEU1673 (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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1644B PHE* 3.5 15.4 - - + +
1647B PHE* 3.4 39.9 - - + +
1648B ALA* 3.5 10.8 - - + +
1651B ALA* 4.3 8.1 - - + -
1663B PHE* 4.8 3.1 - - + -
1669B SER 3.2 22.2 + - - +
1672B THR* 1.3 74.4 - - - +
1674B PHE* 1.4 56.6 - - - +
1676B VAL* 4.3 1.3 - - - -
1677B MET* 3.2 20.3 + - - +
1700B PHE* 4.1 14.1 - - + -
1701B PHE* 4.0 26.0 - - + -
1704B PHE* 3.2 39.7 - - + -
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Residues in contact with PHE1674 (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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1644B PHE* 3.6 8.9 - + + -
1670B PHE 3.3 15.0 + - - +
1671B TYR* 3.0 10.9 + + - +
1673B LEU* 1.4 76.2 - - - +
1675B GLN* 1.4 62.7 + - - +
1677B MET* 3.1 33.7 + - + +
1678B THR* 3.1 34.6 + - + +
1802B PX4 3.8 25.4 - - + -
1804B PX4 4.8 2.7 - - + -
1682C TRP* 3.6 33.0 - + - -
1702C ILE* 3.6 26.2 - - + -
1705C ILE* 3.9 22.4 - - + -
1706C PHE* 4.0 23.8 - + - -
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Residues in contact with GLN1675 (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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1671B TYR* 2.9 14.2 + - + +
1672B THR* 3.0 9.6 + - - +
1674B PHE* 1.4 76.4 - - - +
1676B VAL* 1.4 59.6 + - - +
1678B THR* 2.9 20.7 + - - -
1680B GLU* 2.8 41.9 + - + +
1681B SER* 3.6 1.4 - - - -
1686B ILE* 3.4 19.0 - - + +
1682C TRP* 3.7 11.9 - - + -
1683C SER* 2.7 35.7 + - - +
1684C MET* 3.4 27.5 - - - +
1688C ARG* 3.1 22.7 + - - -
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Residues in contact with VAL1676 (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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1672B THR* 2.8 25.4 + - + +
1673B LEU* 4.0 6.1 - - - +
1675B GLN* 1.4 74.1 - - - +
1677B MET* 1.4 56.2 + - - +
1679B LEU* 3.0 28.2 + - - +
1682B TRP* 4.0 18.4 - - + +
1686B ILE* 4.2 24.0 - - + -
1687B VAL* 5.0 0.7 - - + -
1701B PHE* 4.3 23.1 - - + -
1704B PHE* 3.7 26.0 - - + -
1705B ILE* 3.7 22.4 - - + +
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Residues in contact with MET1677 (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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1640B MET* 4.1 13.9 - - - -
1644B PHE* 3.5 26.5 - - + -
1673B LEU 3.2 15.1 + - - +
1674B PHE* 3.1 40.9 + - + +
1676B VAL* 1.4 72.9 - - - +
1678B THR* 1.3 56.8 + - - +
1679B LEU* 3.0 14.7 + - - +
1704B PHE* 4.2 0.4 - - - -
1705B ILE* 5.7 0.4 - - - -
1708B VAL* 3.6 38.9 - - + +
1712B MET* 3.8 24.0 - - + -
1802B PX4 5.1 4.3 - - + -
1804B PX4 3.6 34.9 - - + +
1706C PHE* 5.6 1.3 - - + -
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Residues in contact with THR1678 (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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1674B PHE* 3.1 35.5 + - + +
1675B GLN 2.9 17.8 + - - -
1677B MET* 1.3 73.5 - - - +
1679B LEU* 1.4 61.9 + - - +
1680B GLU* 3.1 7.8 + - - +
1804B PX4 3.9 28.1 - - + +
1679C LEU* 3.9 35.8 - - + +
1682C TRP* 2.8 31.0 + - - +
1705C ILE* 4.6 0.2 - - + -
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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