Contacts of the helix formed by residues 1683 - 1696 (chain A) in PDB entry 6J8H
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 THR1683 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1213A ASP* 3.8 15.0 - - - +
1215A TYR* 3.4 38.6 - - + -
1663A MET* 4.2 5.6 - - - -
1682A GLU* 1.3 86.5 - - + +
1684A PHE* 1.3 60.2 + - - +
1685A GLY* 3.5 9.4 + - - -
1686A ASN* 3.2 22.6 + - - +
1687A SER* 3.0 27.7 + - - -
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Residues in contact with PHE1684 (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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1210A ALA* 3.7 34.1 - - + +
1213A ASP* 4.2 3.6 + - - +
1652A PHE* 6.0 0.9 - + - -
1656A PHE* 3.6 39.3 - + - -
1659A ALA* 4.1 21.1 - - + -
1660A ILE* 4.0 18.8 - - + -
1663A MET* 3.8 16.0 - - - -
1683A THR* 1.3 70.9 - - - +
1685A GLY* 1.3 70.0 + - - +
1687A SER* 3.9 1.3 - - - -
1688A MET* 3.2 44.6 + - + +
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Residues in contact with GLY1685 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A LYS* 6.0 0.9 - - - -
1683A THR* 3.3 5.8 + - - -
1684A PHE* 1.3 85.5 - - - +
1686A ASN* 1.3 62.0 + - - +
1688A MET* 3.5 6.2 + - - +
1689A ILE* 3.4 26.2 + - - +
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Residues in contact with ASN1686 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A LYS* 3.2 34.3 + - - +
1678A MET* 4.7 1.6 - - - +
1679A PHE* 4.6 7.7 + - - +
1680A ASN* 2.5 49.7 + - - +
1682A GLU* 4.4 2.0 + - - +
1683A THR* 3.2 29.8 + - - +
1685A GLY* 1.3 73.9 - - - +
1687A SER* 1.3 64.3 + - - +
1689A ILE* 3.2 17.5 + - - +
1690A CYS* 3.3 13.3 + - - -
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Residues in contact with SER1687 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1659A ALA* 3.9 28.4 + - - -
1663A MET* 3.9 7.8 - - - +
1680A ASN 3.7 4.0 + - - -
1681A PHE* 2.8 39.6 - - - +
1683A THR 3.0 14.7 + - - -
1684A PHE* 3.9 5.2 - - - -
1685A GLY 3.4 0.2 - - - -
1686A ASN* 1.3 76.2 - - - +
1688A MET* 1.3 62.7 + - - +
1690A CYS* 3.4 4.4 + - - +
1691A LEU* 3.1 28.2 + - - +
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Residues in contact with MET1688 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A MET* 5.5 1.7 - - - +
1652A PHE* 3.7 33.4 - - + -
1655A MET* 4.4 26.1 - - + +
1656A PHE* 4.6 10.5 - - + -
1659A ALA* 4.0 20.2 - - - -
1684A PHE* 3.2 40.4 + - + +
1685A GLY* 3.6 11.0 - - - +
1686A ASN 3.2 0.4 - - - -
1687A SER* 1.3 80.9 - - - +
1689A ILE* 1.3 61.9 + - + +
1691A LEU* 3.5 2.3 + - - +
1692A PHE* 3.1 24.4 + - - +
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Residues in contact with ILE1689 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A TYR* 2.9 37.0 + - + +
371A LEU* 4.3 8.3 - - + -
376A LYS* 3.5 46.0 - - + +
379A MET* 4.3 17.0 - - + -
1679A PHE* 3.5 33.9 - - + +
1685A GLY 3.4 14.3 + - - +
1686A ASN* 3.2 11.1 + - - +
1688A MET* 1.3 79.5 - - + +
1690A CYS* 1.3 61.2 + - - +
1692A PHE* 3.6 3.2 + - - +
1693A GLN* 3.3 15.3 + - - +
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Residues in contact with CYS1690 (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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1679A PHE* 3.4 43.7 - - - -
1680A ASN* 3.7 8.5 - - - -
1681A PHE* 4.6 15.0 - - + -
1686A ASN 3.3 8.6 + - - -
1687A SER* 3.7 7.2 - - - +
1688A MET 3.3 0.2 - - - -
1689A ILE* 1.3 78.0 - - - +
1691A LEU* 1.3 67.3 + - - +
1693A GLN* 3.0 22.1 + - - +
1694A ILE* 3.0 17.4 + - - +
1703A LEU* 4.5 23.1 - - + -
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Residues in contact with LEU1691 (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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1655A MET* 3.8 24.5 - - + +
1658A TYR* 3.8 18.6 - - + -
1659A ALA* 4.7 5.4 - - - +
1681A PHE* 3.9 18.4 - - + -
1687A SER 3.1 18.7 + - - +
1688A MET* 4.0 5.6 - - - +
1689A ILE 3.4 0.2 - - - -
1690A CYS* 1.3 80.1 - - - +
1692A PHE* 1.3 61.5 + - - +
1694A ILE* 3.4 7.1 + - + -
1695A THR* 2.9 26.0 + - - -
1739A TYR* 3.9 20.2 - - + +
1740A PHE* 6.2 0.7 - - + -
1743A TYR* 3.2 53.3 + - + +
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Residues in contact with PHE1692 (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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363A TRP* 3.9 23.2 - + - -
367A TYR* 4.1 23.6 - + - -
379A MET* 5.0 4.7 - - + -
382A PHE 4.1 5.8 - - - -
383A VAL* 3.6 54.3 - - + -
386A ILE* 4.2 19.5 - - + -
387A PHE* 4.9 17.9 - + - -
391A PHE* 6.5 0.2 - + - -
1655A MET* 4.3 16.9 - - + -
1688A MET 3.1 17.2 + - - +
1689A ILE* 3.8 4.3 - - - +
1691A LEU* 1.3 76.5 - - - +
1693A GLN* 1.3 64.5 + - - +
1695A THR* 3.3 23.1 + - + -
1696A THR* 4.3 3.8 + - + +
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Residues in contact with GLN1693 (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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363A TRP* 3.8 14.8 - - + -
364A GLU* 3.8 28.7 + - + +
367A TYR* 3.9 22.1 - - + -
368A GLN* 3.5 23.6 + - - +
1679A PHE* 4.8 5.7 - - - +
1689A ILE 3.3 9.6 + - - +
1690A CYS* 3.0 16.7 + - - +
1692A PHE* 1.3 80.5 - - - +
1694A ILE* 1.3 60.7 + - + +
1696A THR* 3.3 22.7 + - - -
1698A ALA 3.4 24.3 + - - +
1699A GLY* 4.1 11.7 + - - -
1703A LEU* 4.8 9.7 - - - +
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Residues in contact with ILE1694 (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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1690A CYS 3.0 12.2 + - - +
1691A LEU* 3.8 9.0 - - + +
1692A PHE 3.3 0.2 - - - -
1693A GLN* 1.3 74.4 - - + +
1695A THR* 1.3 58.5 + - - +
1696A THR 3.0 2.9 - - - -
1697A SER* 2.6 23.9 + - - +
1698A ALA 4.0 9.0 - - - +
1699A GLY 4.4 0.2 - - - -
1700A TRP* 3.8 24.7 - - + -
1703A LEU* 2.3 44.6 - - + -
1740A PHE* 3.9 17.9 - - + -
1743A TYR* 3.9 16.6 - - + -
1744A ILE* 3.4 30.9 - - + +
1747A SER* 4.7 1.0 + - - -
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Residues in contact with THR1695 (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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387A PHE* 5.8 2.9 - - + -
391A PHE* 5.2 6.7 - - + -
1651A LEU* 4.7 22.4 - - + -
1655A MET* 4.1 7.6 - - + +
1691A LEU 2.9 19.3 + - - -
1692A PHE* 3.4 19.6 + - + -
1693A GLN 3.2 0.8 - - - -
1694A ILE* 1.3 77.6 - - - +
1696A THR* 1.3 63.4 + - + +
1697A SER* 3.4 2.3 + - - -
1743A TYR* 3.3 17.6 + - - -
1747A SER* 3.3 28.9 + - - -
1748A PHE* 5.9 0.2 - - - -
1751A VAL* 5.0 16.9 - - + +
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Residues in contact with THR1696 (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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360A GLN* 3.8 19.8 - - - +
363A TRP* 3.0 31.4 + - + +
386A ILE* 4.4 13.2 - - + -
391A PHE* 3.5 33.2 - - + -
1406A LYS* 4.8 4.5 + - - -
1692A PHE* 5.0 3.4 - - + +
1693A GLN 3.3 10.7 + - - +
1695A THR* 1.3 79.2 - - - +
1697A SER* 1.3 72.2 + - - +
1698A ALA* 3.3 4.0 + - - +
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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