Contacts of the helix formed by residues 1747 - 1756 (chain D) in PDB entry 6AH0
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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1745D ILE 3.4 2.5 - - - -
1746D GLU* 1.3 78.0 + - - +
1748D LYS* 1.3 67.8 + - - +
1749D GLN 3.1 2.9 - - - -
1750D ASP* 2.8 16.0 + - - +
1751D ALA* 3.3 6.6 + - - -
1808D MET 3.8 10.3 - - - -
1809D ASP* 4.0 3.4 - - - +
1810D VAL* 3.9 6.5 - - - +
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Residues in contact with LYS1748 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1747D ASN* 1.3 68.6 - - - +
1749D GLN* 1.3 64.2 + - - +
1751D ALA* 2.9 13.6 + - - +
1752D VAL* 3.1 10.6 + - - -
1808D MET* 3.1 16.8 + - - +
1810D VAL 5.2 0.2 - - - +
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Residues in contact with GLN1749 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1747D ASN 2.9 1.6 + - - -
1748D LYS* 1.3 74.3 - - - +
1750D ASP* 1.3 62.1 + - - +
1752D VAL* 2.9 14.1 + - - +
1753D ASP* 3.0 11.4 + - - -
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Residues in contact with ASP1750 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1744D THR 4.9 5.8 - - - +
1745D ILE* 4.8 13.9 - - - +
1746D GLU 5.1 1.1 - - - +
1747D ASN 2.8 14.7 + - - +
1749D GLN* 1.3 70.4 - - - +
1751D ALA* 1.3 56.0 + - - +
1753D ASP* 3.8 1.7 - - - +
1754D TYR* 2.8 26.9 + - - -
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Residues in contact with ALA1751 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1745D ILE* 5.0 4.1 - - - +
1747D ASN 3.3 5.8 + - - -
1748D LYS* 2.9 11.5 + - - +
1750D ASP* 1.3 74.9 - - - +
1752D VAL* 1.3 58.5 + - - +
1754D TYR* 3.3 2.5 + - - +
1755D LEU* 3.0 23.2 + - - -
1789D VAL* 6.2 4.0 - - - +
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Residues in contact with VAL1752 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1748D LYS 3.1 7.6 + - - -
1749D GLN* 2.9 6.8 + - - +
1751D ALA* 1.3 71.5 - - - +
1753D ASP* 1.3 66.1 + - - +
1755D LEU* 3.0 12.3 + - - +
1756D THR* 3.0 10.2 + - - -
1785D LEU 5.9 4.9 - - - -
1789D VAL* 6.3 0.4 - - - +
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Residues in contact with ASP1753 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1749D GLN 3.0 12.3 + - - -
1750D ASP* 3.8 4.3 - - - +
1752D VAL* 1.3 75.3 - - - +
1754D TYR* 1.3 62.5 + - - +
1756D THR* 2.8 18.0 + - - +
1757D TRP 3.6 2.6 + - - -
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Residues in contact with TYR1754 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1750D ASP 2.8 20.3 + - - -
1751D ALA 3.7 2.7 - - - -
1752D VAL 3.3 0.2 - - - -
1753D ASP* 1.3 70.7 - - - +
1755D LEU* 1.3 62.3 + - - +
1757D TRP* 3.0 15.8 + - - +
1758D THR* 4.2 1.9 + - - -
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Residues in contact with LEU1755 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1751D ALA 3.0 14.1 + - - -
1752D VAL* 3.0 6.6 + - - +
1754D TYR* 1.3 76.2 - - - +
1756D THR* 1.3 61.3 + - - +
1757D TRP 3.0 1.6 + - - -
1758D THR* 3.1 14.4 + - - +
1761D TYR* 4.5 11.6 + - - -
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Residues in contact with THR1756 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1752D VAL 3.0 7.7 + - - -
1753D ASP* 2.8 18.7 + - - +
1755D LEU* 1.3 70.8 - - - +
1757D TRP* 1.3 55.8 + - - -
1758D THR 3.2 5.9 + - - +
1761D TYR* 5.4 6.4 - - - +
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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