Contacts of the helix formed by residues 1658 - 1676 (chain A) in PDB entry 5JCY
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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1626A GLY* 3.6 9.8 - - - -
1630A HIS* 3.6 28.9 - - + +
1632A THR* 6.0 0.7 - - - -
1650A SER 5.1 0.2 + - - -
1652A ALA* 4.6 2.2 - - - -
1653A ASP* 3.6 27.6 - - + +
1656A THR 3.4 16.4 - - - +
1657A TYR* 1.3 75.5 - - - +
1659A LEU* 1.3 64.2 + - - +
1660A ASP* 3.0 22.4 + - - +
1661A SER* 3.0 27.4 + - - -
1662A ILE* 3.3 9.7 + - - +
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Residues in contact with LEU1659 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1626A GLY* 3.7 18.7 + - - +
1627A MET* 4.1 25.8 - - - -
1630A HIS* 4.9 2.0 + - - -
1632A THR* 6.0 6.1 - - + -
1658A THR* 1.3 75.0 - - - +
1660A ASP* 1.3 60.7 + - - +
1662A ILE* 3.1 13.0 + - + +
1663A LEU* 2.9 37.4 + - + +
1719A TYR* 4.7 4.0 - - + -
1720A ASN* 3.4 30.7 - - + +
1723A GLN* 3.5 35.2 - - + -
1724A LEU* 4.5 15.3 - - + -
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Residues in contact with ASP1660 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1649A SER* 4.2 24.6 + - - -
1650A SER* 4.2 20.3 + - - +
1658A THR* 3.0 11.6 + - - +
1659A LEU* 1.3 79.4 - - - +
1661A SER* 1.3 56.8 + - - +
1663A LEU* 3.4 18.7 + - - +
1664A ARG* 2.9 30.7 + - - +
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Residues in contact with SER1661 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1622A MET* 3.9 8.4 - - - +
1650A SER 4.8 0.6 + - - -
1651A ILE 3.0 27.6 + - - -
1652A ALA* 4.0 1.6 - - - -
1657A TYR* 3.5 25.1 - - - -
1658A THR* 3.0 30.7 + - - -
1660A ASP* 1.3 77.5 - - - +
1662A ILE* 1.3 62.9 + - - +
1664A ARG* 3.4 7.4 + - - +
1665A GLN* 3.1 23.2 + - - +
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Residues in contact with ILE1662 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1619A LEU* 4.5 8.9 - - + +
1622A MET* 3.8 39.0 - - + +
1623A ILE* 4.1 14.8 - - + -
1626A GLY* 4.0 16.4 - - - -
1627A MET* 4.1 19.3 - - + -
1658A THR 3.8 8.1 - - - +
1659A LEU* 3.1 11.7 + - + +
1661A SER* 1.3 77.5 - - - +
1663A LEU* 1.3 58.1 + - - +
1665A GLN* 3.1 4.9 + - - +
1666A LEU* 2.9 45.6 + - + +
1694A ILE* 4.1 19.5 - - + -
1724A LEU* 4.6 8.7 - - + -
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Residues in contact with LEU1663 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1659A LEU* 2.9 32.7 + - + +
1660A ASP* 3.8 20.4 - - - +
1662A ILE* 1.3 76.0 - - - +
1664A ARG* 1.3 56.6 + - - +
1666A LEU* 3.4 7.1 + - + +
1667A ASN* 2.9 38.0 + - - +
1723A GLN* 4.1 21.3 - - + +
1724A LEU* 4.1 23.8 - - + -
1727A TRP* 3.8 35.2 + - + -
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Residues in contact with ARG1664 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1649A SER* 3.4 36.8 + - - +
1650A SER* 3.9 2.0 + - - +
1651A ILE* 3.7 43.8 - - - +
1660A ASP 2.9 17.7 + - - +
1661A SER* 3.7 6.1 - - - +
1662A ILE 3.3 0.2 - - - -
1663A LEU* 1.3 75.5 - - - +
1665A GLN* 1.3 58.3 + - - +
1667A ASN* 3.3 12.4 + - + +
1668A SER* 3.0 28.4 + - - -
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Residues in contact with GLN1665 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1549A PHE* 4.9 3.6 - - - -
1618A ILE* 3.4 21.6 - - + +
1619A LEU* 3.9 14.6 - - + -
1622A MET* 3.6 19.5 - - + +
1661A SER 3.1 14.1 + - - +
1662A ILE 3.1 8.5 + - - +
1664A ARG* 1.3 79.6 - - - +
1666A LEU* 1.3 61.9 + - - +
1668A SER* 3.1 17.2 + - - -
1669A PHE* 3.0 67.4 + - + -
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Residues in contact with LEU1666 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1619A LEU* 4.4 17.7 - - + -
1662A ILE* 2.9 35.8 + - + +
1663A LEU* 3.7 8.5 - - + +
1665A GLN* 1.3 76.1 - - - +
1667A ASN* 1.3 56.3 + - - +
1669A PHE* 3.4 19.6 + - + +
1670A HIS* 2.9 31.4 + - - +
1687A VAL* 6.2 1.6 - - + -
1690A MET* 4.5 15.7 - - + -
1691A PHE* 4.1 24.9 - - + -
1694A ILE* 4.5 5.6 - - + -
1724A LEU* 4.1 12.3 - - + -
1727A TRP* 3.6 31.3 - - + -
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Residues in contact with ASN1667 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1663A LEU* 2.9 22.8 + - - +
1664A ARG* 3.4 13.0 - - - +
1666A LEU* 1.3 77.0 - - - +
1668A SER* 1.3 57.0 + - - +
1670A HIS* 3.9 4.9 - - - +
1671A SER* 2.9 31.7 + - - -
1727A TRP* 2.7 29.0 + - - +
1731A LYS* 3.1 22.2 + - - +
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Residues in contact with SER1668 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1549A PHE* 3.7 17.9 - - - -
1664A ARG* 3.0 13.8 + - - -
1665A GLN* 3.1 21.5 + - - -
1667A ASN* 1.3 72.2 - - - +
1669A PHE* 1.3 66.8 + - - +
1671A SER* 3.3 6.1 + - - -
1672A VAL* 3.1 29.2 + - - +
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Residues in contact with PHE1669 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1549A PHE* 4.0 19.8 - + - -
1615A LEU* 3.3 46.9 - - + -
1618A ILE* 3.9 26.5 - - + -
1619A LEU* 4.0 21.1 - - + -
1665A GLN* 3.0 53.4 + - + -
1666A LEU* 3.6 19.7 - - + +
1668A SER* 1.3 77.4 - - - +
1670A HIS* 1.3 63.7 + - - +
1672A VAL* 3.3 2.4 + - - +
1673A MET* 3.0 40.7 + - + +
1690A MET* 5.1 3.1 - - + -
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Residues in contact with HIS1670 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1666A LEU 2.9 17.8 + - - +
1667A ASN* 3.9 3.8 - - - +
1669A PHE* 1.3 77.4 - - - +
1671A SER* 1.3 66.5 + - - +
1673A MET* 3.3 12.5 + - + +
1674A CYS* 2.9 48.1 + - - -
1683A ILE* 4.0 19.6 - - + +
1687A VAL* 5.2 0.6 - - + +
1727A TRP* 4.1 12.3 - + + -
1731A LYS* 3.8 47.1 + - + +
1733A LEU* 4.1 16.9 - - + +
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Residues in contact with SER1671 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1496A ARG* 5.6 3.8 + - - -
1667A ASN 2.9 18.8 + - - -
1668A SER* 3.7 6.3 - - - -
1670A HIS* 1.3 81.7 - - - +
1672A VAL* 1.3 60.1 + - - +
1674A CYS* 3.5 4.7 + - - +
1675A GLN* 3.0 28.2 + - - +
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Residues in contact with VAL1672 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1496A ARG* 3.9 28.3 - - - +
1549A PHE* 3.7 30.3 - - + -
1550A GLU* 3.9 12.1 - - + +
1553A SER* 3.9 7.9 - - - +
1668A SER* 3.1 19.2 + - - +
1669A PHE 3.8 0.9 - - - +
1671A SER* 1.3 75.0 - - - +
1673A MET* 1.3 68.5 + - - +
1675A GLN* 3.2 7.9 + - - +
1676A HIS* 3.0 50.2 + - + +
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Residues in contact with MET1673 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1549A PHE* 6.4 1.1 - - + -
1553A SER* 3.8 15.3 - - - +
1611A LEU* 4.6 5.2 - - + -
1615A LEU* 5.3 1.6 - - + -
1669A PHE* 3.0 38.0 + - + +
1670A HIS* 3.8 10.5 - - + +
1672A VAL* 1.3 75.7 - - - +
1674A CYS* 1.3 60.7 + - - +
1676A HIS* 3.3 2.8 + - - +
1677A GLY 3.3 3.3 + - - -
1678A MET* 3.0 60.2 + - + +
1683A ILE* 4.1 29.8 - - + -
1686A VAL* 3.9 33.4 - - + -
1687A VAL* 4.7 8.1 - - + -
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Residues in contact with CYS1674 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1504A PRO* 5.3 1.6 - - - +
1670A HIS* 2.9 51.9 + - - +
1671A SER* 3.7 5.8 - - - +
1673A MET* 1.3 74.7 - - - +
1675A GLN* 1.3 66.4 + - - +
1677A GLY* 3.0 13.7 + - - +
1678A MET 5.0 0.7 - - - +
1683A ILE* 4.1 14.8 - - - -
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Residues in contact with GLN1675 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1496A ARG* 2.7 51.4 + - - +
1501A ASN* 3.6 41.9 + - + +
1504A PRO* 3.7 17.7 - - - +
1671A SER* 3.0 18.1 + - - +
1672A VAL* 3.2 7.0 + - - +
1674A CYS* 1.3 75.4 - - - +
1676A HIS* 1.3 65.3 + - + +
1677A GLY 3.3 1.2 + - - -
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Residues in contact with HIS1676 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1495A PRO* 3.0 21.3 + - + -
1496A ARG* 4.3 1.4 - - - -
1501A ASN* 3.6 15.0 - - - -
1504A PRO* 3.9 10.4 - - - +
1505A GLY* 4.1 10.2 + - - -
1550A GLU* 3.2 27.8 - - + -
1553A SER* 2.9 18.1 + - - +
1554A PHE* 3.3 31.0 + + + -
1557A SER* 3.6 28.7 - - - +
1558A ASN* 5.0 1.9 + - - -
1672A VAL* 3.0 31.7 + - + +
1673A MET 3.8 2.9 - - - +
1674A CYS 3.1 0.4 - - - -
1675A GLN* 1.3 85.2 + - - +
1677A GLY* 1.3 60.4 + - - +
1678A MET 3.6 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
------------------------------------------------------------
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