Contacts of the helix formed by residues 806 - 810 (chain D) in PDB entry 1DQ8
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 GLY 806 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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765D GLY 4.9 0.3 - - - +
805D VAL* 1.3 81.3 - - - +
807D GLY* 1.3 63.6 + - - -
808D GLY 3.5 0.2 + - - -
809D THR* 2.8 31.3 + - - +
810D ASN* 3.4 20.5 + - - -
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Residues in contact with GLY 807 (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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558C THR 4.6 5.8 - - - -
525D ALA 5.6 2.5 - - - -
526D CYS* 3.8 15.9 - - - -
806D GLY* 1.3 71.3 - - - -
808D GLY* 1.3 57.6 + - - -
810D ASN* 3.0 31.3 + - - +
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Residues in contact with GLY 808 (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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558C THR* 3.7 37.3 + - - -
526D CYS* 4.4 0.7 - - - -
765D GLY* 3.7 15.9 + - - -
806D GLY 3.5 0.4 + - - -
807D GLY* 1.3 66.2 - - - -
809D THR* 1.3 56.3 + - - +
810D ASN 2.9 10.6 + - - -
811D LEU* 3.1 14.5 + - - +
814D GLN* 2.8 26.2 - - - +
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Residues in contact with THR 809 (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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764D CYS 3.5 9.4 + - - -
765D GLY* 3.5 8.2 + - - -
766D GLN* 3.5 12.1 + - - -
803D GLY 3.8 5.2 + - - -
804D THR 3.0 34.3 - - - +
805D VAL* 3.2 11.4 - - - +
806D GLY 2.8 18.2 - - - +
807D GLY 3.0 0.2 - - - -
808D GLY* 1.3 76.9 - - - +
810D ASN* 1.3 56.2 + - - +
811D LEU 3.4 0.7 - - - -
814D GLN* 4.8 1.6 - - - -
815D GLN* 3.0 27.8 + - - +
818D LEU* 3.5 21.8 - - + +
824D GLN* 4.9 1.2 + - - +
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Residues in contact with ASN 810 (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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521D LEU* 3.8 19.2 - - + +
525D ALA* 5.9 4.8 - - - +
526D CYS* 5.6 1.1 - - - -
805D VAL* 5.0 2.1 - - - +
806D GLY* 3.4 31.7 + - - -
807D GLY 3.0 16.8 + - - +
808D GLY 2.9 1.2 - - - -
809D THR* 1.3 79.2 - - - +
811D LEU* 1.3 66.2 + - + +
812D LEU* 4.0 1.7 + - - +
815D GLN* 3.5 16.6 + - - +
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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