Contacts of the helix formed by residues 1747 - 1756 (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 ASN1747 (chain r).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1745r ILE* 3.4 3.2 - - - +
1746r GLU* 1.3 81.6 + - + +
1748r LYS* 1.3 67.3 + - - +
1749r GLN* 3.1 5.2 - - + +
1750r ASP* 2.8 18.7 + - - +
1751r ALA* 3.3 8.0 + - - +
1808r MET* 3.6 8.7 - - + +
1809r ASP* 3.6 20.2 - - + -
1810r VAL* 3.9 9.2 - - - +
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Residues in contact with LYS1748 (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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1747r ASN* 1.3 72.6 - - - +
1749r GLN* 1.3 63.5 + - - +
1751r ALA* 2.9 25.6 + - - +
1752r VAL* 3.1 8.1 + - - +
1789r VAL* 4.8 7.3 - - + +
1807r GLU 5.0 6.1 - - - +
1808r MET* 3.1 18.8 + - + +
1810r VAL* 5.2 1.4 - - - +
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Residues in contact with GLN1749 (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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1747r ASN* 2.9 5.6 + - + +
1748r LYS* 1.3 76.6 - - - +
1750r ASP* 1.3 64.2 + - - +
1752r VAL* 2.9 18.6 + - - +
1753r ASP* 3.0 13.9 + - - +
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Residues in contact with ASP1750 (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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1744r THR 3.8 7.9 - - - +
1745r ILE* 3.7 10.4 - - - +
1746r GLU* 3.7 22.0 - - + +
1747r ASN* 2.8 17.0 + - + +
1749r GLN* 1.3 74.3 - - - +
1751r ALA* 1.3 57.0 + - - +
1753r ASP* 3.6 7.4 - - - +
1754r TYR* 2.8 29.5 + - - +
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Residues in contact with ALA1751 (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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1736r PHE* 6.4 1.6 - - + -
1745r ILE* 4.5 11.8 - - + +
1747r ASN 3.3 3.7 + - - +
1748r LYS* 2.9 21.6 + - - +
1750r ASP* 1.3 76.9 - - - +
1752r VAL* 1.3 58.6 + - - +
1754r TYR* 3.3 8.3 + - - +
1755r LEU* 3.0 25.3 + - - +
1789r VAL* 3.9 21.5 - - + +
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Residues in contact with VAL1752 (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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1748r LYS 3.1 8.3 + - - +
1749r GLN* 2.9 11.4 + - - +
1751r ALA* 1.3 72.1 - - - +
1753r ASP* 1.3 67.9 + - - +
1755r LEU* 3.0 19.1 + - - +
1756r THR* 3.0 12.0 + - - -
1785r LEU* 5.5 14.0 - - + +
1786r SER* 6.0 2.2 - - - +
1789r VAL* 4.8 6.8 - - + +
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Residues in contact with ASP1753 (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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1749r GLN 3.0 11.7 + - - +
1750r ASP* 3.6 12.6 - - - +
1752r VAL* 1.3 77.4 - - - +
1754r TYR* 1.3 63.1 + - - +
1756r THR* 2.8 23.5 + - - -
1757r TRP* 3.6 4.0 + - - +
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Residues in contact with TYR1754 (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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1744r THR 5.9 2.0 - - - +
1745r ILE* 5.8 4.0 - - + -
1750r ASP 2.8 21.6 + - - +
1751r ALA* 3.4 9.0 - - - +
1753r ASP* 1.3 71.0 - - - +
1755r LEU* 1.3 65.1 + - - +
1757r TRP* 3.0 21.4 + - - +
1758r THR* 4.2 2.4 + - - -
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Residues in contact with LEU1755 (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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1751r ALA 3.0 13.9 + - - +
1752r VAL* 3.2 15.0 - - - +
1754r TYR* 1.3 77.4 - - - +
1756r THR* 1.3 60.1 + - - +
1757r TRP 3.0 1.9 + - - -
1758r THR* 3.1 22.0 + - - -
1761r TYR* 3.5 9.2 + - - +
1785r LEU* 5.3 12.1 - - + -
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Residues in contact with THR1756 (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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1752r VAL 3.0 9.0 + - - -
1753r ASP* 2.8 21.7 + - - -
1755r LEU* 1.3 71.7 - - - +
1757r TRP* 1.3 56.4 + - - -
1758r THR 3.2 3.0 + - - +
1761r TYR* 4.0 16.1 - - - +
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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