Contacts of the helix formed by residues 1680 - 1690 (chain r) in PDB entry 6FF7
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 PRO1680 (chain r).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1678r ASP 3.3 5.0 - - - +
1679r TYR* 1.3 70.8 - - - +
1681r ILE* 1.3 65.4 + - - +
1682r TYR* 3.3 3.1 - - + +
1683r ASP* 3.0 29.2 + - + +
1684r VAL 3.3 3.8 + - - -
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Residues in contact with ILE1681 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1679r TYR 3.4 4.9 + - - -
1680r PRO* 1.3 70.3 - - - +
1682r TYR* 1.3 57.4 + - - +
1684r VAL* 3.1 10.7 + - - +
1685r LEU* 2.9 26.7 + - - +
1717r PHE* 6.3 2.5 - - + -
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Residues in contact with TYR1682 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1458r LEU* 6.1 7.0 - - + -
1680r PRO* 3.3 3.4 - - + +
1681r ILE* 1.3 75.3 - - - +
1683r ASP* 1.3 65.8 + - - +
1685r LEU* 3.3 8.6 + - - +
1686r GLN* 2.9 22.9 + - - +
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Residues in contact with ASP1683 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1651r CYS* 5.1 7.2 - - + +
1679r TYR* 5.0 6.1 - - + -
1680r PRO* 3.0 24.4 + - + +
1682r TYR* 1.3 78.2 - - - +
1684r VAL* 1.3 58.1 + - - +
1686r GLN* 2.8 25.2 + - - +
1687r MET* 2.9 14.4 + - - +
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Residues in contact with VAL1684 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1666r THR* 6.4 1.1 - - - -
1679r TYR* 5.1 11.6 - - + +
1680r PRO 3.3 4.9 + - - +
1681r ILE* 3.1 15.8 + - - +
1683r ASP* 1.3 79.2 - - - +
1685r LEU* 1.3 58.9 + - - +
1687r MET* 3.4 7.8 + - - +
1688r VAL* 2.9 28.1 + - - +
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Residues in contact with LEU1685 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1352r THR* 4.9 7.7 - - - -
1681r ILE 2.9 12.3 + - - +
1682r TYR* 3.6 11.7 - - - +
1683r ASP 3.2 0.4 - - - -
1684r VAL* 1.3 76.4 - - - +
1686r GLN* 1.3 58.2 + - - +
1688r VAL* 3.3 7.9 + - - +
1689r GLY* 2.9 24.8 + - - -
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Residues in contact with GLN1686 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1352r THR* 5.3 7.6 - - - -
1651r CYS* 5.1 16.5 - - + +
1652r TRP* 5.8 2.9 - - - +
1682r TYR 2.9 12.4 + - - +
1683r ASP* 2.8 13.7 + - - +
1685r LEU* 1.3 73.4 - - - +
1687r MET* 1.3 64.6 + - - +
1689r GLY* 3.0 4.9 + - - +
1690r HIS* 3.0 21.2 + - - +
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Residues in contact with MET1687 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1562r PHE* 5.1 15.0 - - + -
1651r CYS* 4.7 16.9 - - + +
1661r VAL* 4.1 11.6 - - + +
1663r ILE* 5.5 9.6 - - + -
1683r ASP 2.9 11.5 + - - +
1684r VAL* 3.6 11.0 - - - +
1686r GLN* 1.3 74.3 - - - +
1688r VAL* 1.3 63.2 + - - +
1690r HIS* 3.1 23.6 + - - +
1691r ALA 4.1 0.3 + - - -
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Residues in contact with VAL1688 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1661r VAL* 5.2 2.0 - - - -
1684r VAL 2.9 14.4 + - - +
1685r LEU* 3.5 12.1 - - - +
1687r MET* 1.3 77.2 - - - +
1689r GLY* 1.3 61.6 + - - +
1691r ALA* 3.0 22.9 + - - +
1702r CYS* 5.0 19.1 - - + +
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Residues in contact with GLY1689 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1352r THR* 3.9 26.9 - - - +
1353r GLY* 4.9 3.8 - - - -
1685r LEU 2.9 15.9 + - - -
1686r GLN 3.0 5.5 + - - -
1688r VAL* 1.3 75.7 - - - +
1690r HIS* 1.3 58.4 + - - +
1691r ALA 3.1 4.1 + - - +
1692r ASN* 3.8 18.4 - - - +
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Residues in contact with HIS1690 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1560r ILE* 5.8 6.3 - - + +
1651r CYS 5.7 4.3 - - - +
1656r VAL 5.7 2.0 - - - +
1657r ALA* 3.9 10.6 - - - +
1658r ALA* 3.2 25.3 + - - +
1661r VAL* 5.1 4.0 - - + -
1686r GLN 3.0 9.3 + - - +
1687r MET* 3.2 17.5 - - - +
1688r VAL 3.0 1.2 - - - -
1689r GLY* 1.3 78.5 - - - +
1691r ALA* 1.3 56.4 + - - +
1692r ASN 3.5 1.8 + - - -
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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