Contacts of the helix formed by residues 1658 - 1676 (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 THR1658 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1626B GLY* 3.6 10.3 - - - -
1630B HIS* 3.5 40.6 - - + +
1656B THR* 4.2 10.8 - - + +
1657B TYR* 1.3 78.6 - - - +
1659B LEU* 1.3 64.6 + - - +
1660B ASP* 3.3 17.4 + - - +
1661B SER* 3.0 28.8 + - - +
1662B ILE* 3.3 12.8 + - - +
1664B ARG* 4.7 1.9 + - - -
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Residues in contact with LEU1659 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1626B GLY 3.7 15.8 + - - +
1627B MET* 4.1 22.9 - - - -
1630B HIS* 4.8 3.4 + - - +
1658B THR* 1.3 76.9 - - - +
1660B ASP* 1.3 60.1 + - - +
1662B ILE* 3.2 10.4 + - + +
1663B LEU* 2.9 34.8 + - + +
1719B TYR* 4.4 7.0 - - + -
1720B ASN* 3.5 36.3 - - + +
1723B GLN* 3.7 33.9 - - + -
1724B LEU* 4.5 14.4 - - + -
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Residues in contact with ASP1660 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1658B THR* 3.2 9.1 + - - +
1659B LEU* 1.3 76.9 - - - +
1661B SER* 1.3 60.5 + - - +
1663B LEU* 3.6 19.6 - - - +
1664B ARG* 2.9 48.4 + - + +
1723B GLN* 5.3 2.3 - - - +
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Residues in contact with SER1661 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1622B MET* 4.4 5.0 - - - +
1656B THR 4.5 2.8 + - - -
1657B TYR* 3.7 25.3 - - - -
1658B THR* 3.0 32.7 + - - +
1659B LEU 3.2 0.4 - - - -
1660B ASP* 1.3 78.7 - - - +
1662B ILE* 1.3 57.5 + - - +
1664B ARG* 3.3 27.5 + - - +
1665B GLN* 3.0 28.1 + - - +
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Residues in contact with ILE1662 (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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1619B LEU* 4.4 11.0 - - + -
1622B MET* 3.7 37.2 - - + +
1623B ILE* 4.0 8.7 - - + -
1626B GLY* 4.1 6.5 - - - -
1627B MET* 3.9 30.1 - - + -
1658B THR 3.5 13.5 - - - +
1659B LEU* 3.2 10.7 + - + +
1661B SER* 1.3 76.2 - - - +
1663B LEU* 1.3 58.0 + - - +
1665B GLN* 3.3 6.3 + - - +
1666B LEU* 2.9 35.2 + - + +
1694B ILE* 4.0 27.1 - - + -
1724B LEU* 4.7 7.2 - - + -
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Residues in contact with LEU1663 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1659B LEU* 2.9 29.3 + - + +
1660B ASP* 3.6 21.8 - - - +
1662B ILE* 1.3 76.9 - - - +
1664B ARG* 1.3 57.9 + - + +
1666B LEU* 3.4 6.9 + - + +
1667B ASN* 3.0 35.3 + - - +
1723B GLN* 4.0 29.2 - - + +
1724B LEU* 3.6 31.0 - - + -
1727B TRP* 4.2 27.8 + - + -
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Residues in contact with ARG1664 (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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1658B THR* 4.7 1.8 + - - -
1660B ASP* 2.9 32.8 + - + +
1661B SER* 3.6 34.4 + - - +
1663B LEU* 1.3 74.5 - - + +
1665B GLN* 1.3 65.5 + - - +
1667B ASN* 3.3 12.6 + - - +
1668B SER* 3.0 22.3 + - - -
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Residues in contact with GLN1665 (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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1618B ILE* 3.7 15.8 - - + +
1619B LEU* 4.1 10.3 - - + -
1622B MET* 3.8 30.6 - - + +
1661B SER 3.0 15.7 + - - +
1662B ILE 3.3 4.9 + - - +
1664B ARG* 1.3 74.4 - - - +
1666B LEU* 1.3 65.4 + - - +
1668B SER* 3.2 14.0 + - - -
1669B PHE* 3.0 65.0 + - + -
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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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1619B LEU* 4.0 32.5 - - + -
1662B ILE* 2.9 20.4 + - + +
1663B LEU* 3.6 8.7 - - + +
1665B GLN* 1.3 76.5 - - - +
1667B ASN* 1.3 62.0 + - - +
1669B PHE* 3.3 6.2 + - + +
1670B HIS* 3.0 25.6 + - - +
1690B MET* 4.2 18.7 - - + +
1691B PHE* 3.8 25.8 - - + -
1694B ILE* 4.3 11.4 - - + -
1724B LEU* 4.1 22.0 - - + -
1727B TRP* 3.7 28.1 - - + -
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Residues in contact with ASN1667 (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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1663B LEU* 3.0 22.4 + - - +
1664B ARG* 3.5 14.3 - - - +
1666B LEU* 1.3 76.3 - - - +
1668B SER* 1.3 55.8 + - - +
1670B HIS* 4.0 2.2 - - - +
1671B SER* 2.9 33.2 + - - -
1727B TRP* 2.6 33.6 + - - +
1731B LYS* 3.3 21.9 - - - +
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Residues in contact with SER1668 (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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1664B ARG 3.0 12.8 + - - -
1665B GLN* 3.5 21.6 + - - -
1667B ASN* 1.3 75.3 - - - +
1669B PHE* 1.3 66.8 + - - +
1671B SER* 3.9 4.2 - - - -
1672B VAL* 3.1 36.5 + - - +
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Residues in contact with PHE1669 (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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1549B PHE* 3.5 47.8 - + + -
1615B LEU* 3.8 19.1 - - + -
1618B ILE* 3.8 24.2 - - + -
1619B LEU* 4.0 17.7 - - + -
1665B GLN* 3.0 53.6 + - + -
1666B LEU* 3.5 8.7 - - + +
1668B SER* 1.3 80.6 - - - +
1670B HIS* 1.3 62.1 + - - +
1672B VAL 3.4 0.3 + - - -
1673B MET* 3.2 31.2 + - + +
1690B MET* 3.4 29.4 - - + -
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Residues in contact with HIS1670 (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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1666B LEU 3.0 16.4 + - - +
1667B ASN* 4.0 3.8 - - - +
1669B PHE* 1.3 76.6 - - - +
1671B SER* 1.3 65.5 + - - +
1673B MET* 3.4 12.4 + - + +
1674B CYS* 3.0 53.8 + - - -
1683B ILE* 3.9 20.7 - - + +
1687B VAL* 4.6 2.9 - - + +
1690B MET* 5.6 0.8 - - + +
1727B TRP* 4.0 15.9 - + + -
1731B LYS* 4.0 34.1 + - + +
1733B LEU* 4.0 29.4 - - + +
129D ARG* 4.9 5.2 + - - -
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Residues in contact with SER1671 (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 ASN 2.9 20.0 + - - -
1668B SER* 3.9 5.2 - - - -
1670B HIS* 1.3 80.3 - - - +
1672B VAL* 1.3 59.0 + - - +
1674B CYS* 3.5 6.2 + - - +
1675B GLN* 3.0 30.0 + - - +
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Residues in contact with VAL1672 (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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1549B PHE* 3.6 26.7 - - + -
1550B GLU* 3.9 28.9 - - + +
1553B SER* 4.0 2.0 - - - +
1668B SER* 3.1 25.1 + - - +
1669B PHE 3.7 4.5 - - - +
1670B HIS 3.3 0.2 - - - -
1671B SER* 1.3 75.7 - - - +
1673B MET* 1.3 64.9 + - - +
1675B GLN* 3.3 6.6 + - - +
1676B HIS* 3.1 49.6 + - + +
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Residues in contact with MET1673 (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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1549B PHE* 3.9 13.7 - - + -
1553B SER* 3.7 21.1 - - - +
1611B LEU* 4.5 2.0 - - - -
1669B PHE* 3.2 22.9 + - + +
1670B HIS* 3.8 12.3 - - - +
1672B VAL* 1.3 77.2 - - - +
1674B CYS* 1.3 63.2 + - - +
1676B HIS* 3.4 2.0 + - - +
1677B GLY 3.3 3.3 + - - -
1678B MET* 3.1 51.9 + - + +
1683B ILE* 3.9 35.6 - - + +
1686B VAL* 3.8 35.2 - - + -
1687B VAL* 4.7 6.3 - - + -
1690B MET* 5.3 1.1 - - + -
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Residues in contact with CYS1674 (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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1670B HIS* 3.0 55.4 + - - +
1671B SER* 3.7 7.0 - - - +
1673B MET* 1.3 75.3 - - - +
1675B GLN* 1.3 59.1 + - - +
1677B GLY* 3.0 19.9 + - - -
1683B ILE* 4.1 7.2 - - - -
129D ARG* 3.4 55.2 - - - +
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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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1501B ASN* 2.7 46.8 + - - +
1504B PRO* 4.9 5.0 - - - +
1671B SER* 3.0 18.2 + - - +
1672B VAL* 3.6 7.9 - - - +
1674B CYS* 1.3 77.2 - - - +
1676B HIS* 1.3 67.9 + - + +
1677B GLY* 3.3 0.9 + - - -
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Residues in contact with HIS1676 (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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1495B PRO* 4.3 15.0 + - + +
1501B ASN* 5.3 2.2 - - - -
1504B PRO* 3.5 16.2 - - - +
1505B GLY 4.5 3.5 + - - -
1550B GLU* 3.1 33.2 + - + +
1553B SER* 3.0 17.9 + - - +
1554B PHE* 3.3 34.5 + + + +
1557B SER* 3.8 25.0 - - - +
1558B ASN* 5.4 1.6 + - - -
1672B VAL* 3.1 32.0 + - + +
1673B MET 3.9 4.0 - - - +
1674B CYS 3.2 0.2 - - - -
1675B GLN* 1.3 88.0 - - + +
1677B GLY* 1.3 62.4 + - - +
1678B MET 3.5 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
------------------------------------------------------------
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