Contacts of the helix formed by residues 845 - 854 (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 GLY 845 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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843D GLU 3.9 0.8 + - - -
844D LEU* 1.3 76.5 - - - +
846D ALA* 1.3 67.9 + - - +
847D LEU 3.3 2.7 - - - -
848D ASP* 3.5 12.2 + - - +
849D ILE* 3.6 8.7 + - - -
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Residues in contact with ALA 846 (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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845D GLY* 1.3 73.5 - - - +
847D LEU* 1.3 58.5 + - - +
848D ASP 3.2 0.3 + - - -
849D ILE* 3.4 0.9 + - - -
850D LEU* 3.0 26.2 + - - -
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Residues in contact with LEU 847 (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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845D GLY 3.3 0.6 - - - -
846D ALA* 1.3 75.7 - - - +
848D ASP* 1.3 56.9 + - - +
850D LEU* 4.5 2.0 - - - +
851D GLN* 2.9 26.4 + - - +
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Residues in contact with ASP 848 (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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813D ALA* 6.1 0.3 - - - -
845D GLY* 3.5 10.8 + - - +
846D ALA 3.2 1.2 - - - -
847D LEU* 1.3 74.5 - - - +
849D ILE* 1.3 64.5 + - - +
851D GLN* 3.9 0.7 - - - -
852D MET* 3.0 19.8 + - - -
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Residues in contact with ILE 849 (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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844D LEU 5.8 0.2 - - - -
845D GLY 3.6 7.7 + - - -
846D ALA 3.4 4.7 + - - -
848D ASP* 1.3 72.4 - - - +
850D LEU* 1.3 66.1 + - - +
852D MET* 2.9 2.1 + - - +
853D LEU* 2.8 26.2 + - - -
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Residues in contact with LEU 850 (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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505D THR* 5.7 3.3 - - - -
846D ALA 3.0 17.2 + - - -
847D LEU* 4.0 1.8 - - - +
849D ILE* 1.3 72.3 - - - +
851D GLN* 1.3 56.5 + - - +
853D LEU* 4.0 0.7 - - - +
854D GLY* 3.1 25.5 + - - -
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Residues in contact with GLN 851 (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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816D ALA* 5.2 11.0 - - - +
847D LEU 2.9 19.1 + - - -
848D ASP 3.9 0.9 - - - -
850D LEU* 1.3 77.0 - - - +
852D MET* 1.3 60.1 + - - +
854D GLY* 3.4 10.1 + - - -
855D ARG* 3.5 8.7 + - - -
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Residues in contact with MET 852 (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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813D ALA* 6.4 1.6 - - - +
816D ALA* 5.2 11.0 - - - +
826D VAL* 6.0 1.9 - - - -
848D ASP 3.0 11.6 + - - -
849D ILE* 2.9 9.4 + - - +
851D GLN* 1.3 73.6 - - - +
853D LEU* 1.3 58.2 + - - +
854D GLY 3.3 0.2 - - - -
855D ARG* 3.6 11.8 + - - +
856D ALA 4.6 0.2 + - - -
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Residues in contact with LEU 853 (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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849D ILE 2.8 13.0 + - - -
850D LEU* 4.0 0.7 - - - +
852D MET* 1.3 73.4 - - - +
854D GLY* 1.3 56.3 + - - +
855D ARG 3.0 7.5 + - - -
856D ALA* 3.4 14.6 + - - +
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Residues in contact with GLY 854 (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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505D THR* 4.8 23.2 - - - +
506D GLY* 4.9 4.7 + - - -
850D LEU 3.1 20.0 + - - -
851D GLN 3.4 5.4 + - - -
852D MET 3.3 0.6 - - - -
853D LEU* 1.3 76.4 - - - +
855D ARG* 1.3 55.8 + - - +
856D ALA 3.3 5.5 - - - +
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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