Contacts of the helix formed by residues 1658 - 1676 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1626C GLY* 3.7 8.6 - - - -
1630C HIS* 3.5 42.0 - - + +
1656C THR* 4.0 10.8 - - + +
1657C TYR* 1.3 77.6 - - - +
1659C LEU* 1.3 63.4 + - - +
1660C ASP* 3.3 13.9 + - - +
1661C SER* 3.1 35.6 + - - +
1662C ILE* 3.3 12.8 + - - +
1664C ARG* 4.5 2.1 + - - -
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Residues in contact with LEU1659 (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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1626C GLY 3.7 14.9 + - - +
1627C MET* 3.9 27.8 - - - -
1630C HIS* 4.8 2.4 + - - -
1632C THR* 5.8 7.9 - - + +
1658C THR* 1.3 74.1 - - - +
1660C ASP* 1.3 61.1 + - - +
1662C ILE* 3.1 13.0 + - + +
1663C LEU* 2.9 39.1 + - + +
1719C TYR* 4.4 6.3 - - + -
1720C ASN* 3.4 32.8 - - + +
1723C GLN* 3.7 35.7 - - + +
1724C LEU* 4.6 8.7 - - + -
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Residues in contact with ASP1660 (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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1658C THR* 3.2 11.3 + - - +
1659C LEU* 1.3 77.9 - - - +
1661C SER* 1.3 59.9 + - - +
1663C LEU* 3.8 17.5 - - - +
1664C ARG* 3.0 50.1 + - + +
1723C GLN* 5.1 4.9 + - - -
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Residues in contact with SER1661 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1622C MET* 3.3 24.8 - - - +
1656C THR 4.6 1.7 + - - -
1657C TYR* 3.9 12.3 - - - -
1658C THR* 3.1 33.5 + - - +
1660C ASP* 1.3 81.1 - - - +
1662C ILE* 1.3 60.8 + - - +
1664C ARG* 3.5 23.9 + - - +
1665C GLN* 3.1 18.0 + - - +
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Residues in contact with ILE1662 (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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1619C LEU* 4.5 6.5 - - + -
1622C MET* 3.9 39.0 - - + +
1623C ILE* 4.2 9.2 - - + -
1626C GLY* 4.0 11.7 - - - -
1627C MET* 4.0 30.7 - - + -
1658C THR 3.3 8.7 + - - +
1659C LEU* 3.1 10.3 + - + +
1661C SER* 1.3 74.1 - - - +
1663C LEU* 1.3 59.7 + - - +
1665C GLN* 3.2 3.4 + - - +
1666C LEU* 2.8 39.0 + - + +
1694C ILE* 3.9 28.3 - - + -
1724C LEU* 4.7 6.7 - - + -
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Residues in contact with LEU1663 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1659C LEU* 2.9 30.1 + - + +
1660C ASP* 3.8 18.6 - - - +
1661C SER 3.4 0.2 - - - -
1662C ILE* 1.3 76.6 - - - +
1664C ARG* 1.3 59.3 + - + +
1666C LEU* 3.3 6.6 + - + +
1667C ASN* 2.9 38.1 + - - +
1723C GLN* 4.0 32.5 - - + +
1724C LEU* 3.8 28.0 - - + -
1727C TRP* 4.1 29.8 + - + -
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Residues in contact with ARG1664 (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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1658C THR* 4.5 1.8 + - - -
1660C ASP* 3.0 31.2 + - + +
1661C SER* 3.7 33.9 + - - +
1663C LEU* 1.3 78.0 - - + +
1665C GLN* 1.3 57.3 + - - +
1667C ASN* 3.4 11.6 + - - +
1668C SER* 3.0 27.5 + - - -
5D ASP* 4.9 20.0 - - + -
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Residues in contact with GLN1665 (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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1618C ILE* 3.6 26.2 - - + +
1619C LEU* 4.1 9.9 - - + -
1622C MET* 4.2 13.6 - - + +
1661C SER 3.1 17.7 + - - +
1662C ILE* 3.5 6.3 - - - +
1664C ARG* 1.3 73.8 - - - +
1666C LEU* 1.3 60.9 + - - +
1668C SER* 3.3 13.1 + - - -
1669C PHE* 3.0 67.9 + - + -
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Residues in contact with LEU1666 (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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1619C LEU* 3.9 33.2 - - + -
1662C ILE* 2.8 25.7 + - + +
1663C LEU* 3.5 12.6 - - + +
1665C GLN* 1.3 73.9 - - - +
1667C ASN* 1.3 58.7 + - - +
1669C PHE* 3.4 6.0 + - + +
1670C HIS* 2.9 31.9 + - - +
1690C MET* 4.3 21.1 - - + +
1691C PHE* 4.0 18.4 - - + -
1694C ILE* 4.2 9.2 - - + -
1724C LEU* 3.9 28.5 - - + -
1727C TRP* 3.5 20.9 - - + -
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Residues in contact with ASN1667 (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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1663C LEU* 2.9 26.4 + - - +
1664C ARG* 3.5 14.3 - - - +
1666C LEU* 1.3 76.5 - - - +
1668C SER* 1.3 51.7 + - - +
1670C HIS* 3.7 1.8 - - - +
1671C SER* 2.8 38.9 + - - -
1727C TRP* 2.5 32.5 + - - +
1731C LYS* 3.3 21.6 + - - +
5D ASP* 5.6 8.3 - - - +
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Residues in contact with SER1668 (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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1549C PHE* 5.9 0.2 - - - -
1664C ARG 3.0 14.4 + - - -
1665C GLN* 3.5 22.5 + - - -
1666C LEU 3.3 0.2 - - - -
1667C ASN* 1.3 73.8 - - - +
1669C PHE* 1.3 66.3 + - - +
1671C SER* 3.9 4.2 - - - -
1672C VAL* 3.1 36.6 + - - +
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Residues in contact with PHE1669 (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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1549C PHE* 3.6 49.2 - + + -
1615C LEU* 3.8 23.1 - - + -
1618C ILE* 3.8 20.6 - - + -
1619C LEU* 3.9 18.8 - - + -
1665C GLN* 3.0 55.7 + - + +
1666C LEU* 3.6 5.4 - - - +
1668C SER* 1.3 78.6 - - - +
1670C HIS* 1.3 62.4 + - - +
1672C VAL 3.4 0.2 + - - -
1673C MET* 3.2 31.1 + - + +
1690C MET* 3.5 31.6 - - + -
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Residues in contact with HIS1670 (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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129A ARG* 5.1 3.7 + - - -
1666C LEU 2.9 17.3 + - - +
1667C ASN* 3.9 2.9 + - - +
1669C PHE* 1.3 74.4 - - - +
1671C SER* 1.3 69.7 + - - +
1673C MET* 3.5 9.7 + - + +
1674C CYS* 3.1 52.0 + - - -
1683C ILE* 3.9 23.7 - - + +
1687C VAL* 4.5 4.5 - - + -
1690C MET* 5.5 0.6 - - + +
1727C TRP* 3.9 16.2 - + + -
1731C LYS* 3.9 37.1 + - + +
1733C LEU* 3.9 26.3 - - + +
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Residues in contact with SER1671 (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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1667C ASN 2.8 23.9 + - - -
1668C SER* 3.9 5.6 - - - -
1670C HIS* 1.3 77.0 + - - +
1672C VAL* 1.3 59.4 + - - +
1674C CYS* 3.6 5.7 + - - +
1675C GLN* 3.1 28.8 + - - +
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Residues in contact with VAL1672 (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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1549C PHE* 3.9 18.2 - - + -
1550C GLU* 3.9 33.9 - - + +
1553C SER* 3.9 7.2 - - - +
1668C SER* 3.1 28.3 + - - +
1669C PHE 3.8 3.8 - - - +
1671C SER* 1.3 76.3 - - - +
1673C MET* 1.3 65.5 + - - +
1675C GLN* 3.3 6.4 + - - +
1676C HIS* 3.0 50.6 + - + +
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Residues in contact with MET1673 (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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1549C PHE* 4.0 14.6 - - + -
1553C SER* 3.8 13.2 - - - +
1611C LEU* 4.5 1.3 - - - -
1669C PHE* 3.2 25.6 + - + +
1670C HIS* 3.9 14.4 - - + +
1671C SER 3.5 0.2 - - - -
1672C VAL* 1.3 76.0 - - - +
1674C CYS* 1.3 60.3 - - - +
1676C HIS* 3.4 1.7 + - - +
1677C GLY 3.3 3.3 + - - -
1678C MET* 3.1 58.5 + - + +
1683C ILE* 3.9 31.4 - - + +
1686C VAL* 3.7 38.1 - - + -
1687C VAL* 4.7 7.0 - - + -
1690C MET* 5.1 1.3 - - + -
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Residues in contact with CYS1674 (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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129A ARG* 3.4 55.4 - - - +
1670C HIS* 3.1 56.0 + - - +
1671C SER* 3.8 6.3 - - - +
1673C MET* 1.3 74.8 - - - +
1675C GLN* 1.3 60.9 + - - +
1677C GLY* 3.0 19.0 + - - -
1683C ILE* 4.1 7.0 - - - -
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Residues in contact with GLN1675 (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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1501C ASN* 2.8 45.0 + - - +
1504C PRO* 5.1 4.7 - - - +
1671C SER* 3.1 19.9 + - - +
1672C VAL* 3.7 6.5 - - - +
1674C CYS* 1.3 76.8 - - - +
1676C HIS* 1.3 67.1 + - + +
1677C GLY 3.1 1.1 + - - -
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Residues in contact with HIS1676 (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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1495C PRO* 4.2 14.8 + - + +
1501C ASN* 5.3 2.5 - - - -
1504C PRO* 3.7 14.5 - - - +
1505C GLY 4.6 3.5 + - - -
1550C GLU* 3.1 34.2 + - + +
1553C SER* 2.9 18.3 + - - +
1554C PHE* 3.2 35.7 + + + +
1557C SER* 3.7 25.5 - - - +
1558C ASN* 5.4 1.7 + - - -
1672C VAL* 3.0 35.1 + - + +
1673C MET 3.8 3.8 - - - +
1674C CYS 3.2 0.2 - - - -
1675C GLN* 1.3 86.1 - - + +
1677C GLY* 1.3 63.6 + - - +
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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) + - + + + + + -
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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