Contacts of the helix formed by residues 810 - 821 (chain N) 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 SER 810 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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807N CYS* 4.7 2.6 - - - +
808N PRO 2.6 16.5 + - - +
809N ASN* 1.3 75.5 - - - +
811N GLY* 1.3 65.3 + - - +
812N ILE 3.5 2.2 - - - -
813N LEU* 4.0 9.0 + - - +
814N TRP* 4.1 6.6 + - - -
837N CYS* 5.9 0.3 - - - -
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Residues in contact with GLY 811 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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809N ASN 3.5 3.4 + - - -
810N SER* 1.3 72.8 - - - +
812N ILE* 1.3 66.1 + - - +
813N LEU 3.6 0.2 + - - -
814N TRP* 3.7 7.3 + - - -
815N SER* 3.8 5.4 + - - -
837N CYS* 6.1 3.1 - - - -
842N HIS 6.0 0.5 - - - -
843N VAL* 5.5 5.9 + - - -
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Residues in contact with ILE 812 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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810N SER 3.5 0.2 - - - -
811N GLY* 1.3 76.3 - - - +
813N LEU* 1.3 54.7 + - - +
815N SER* 2.7 30.2 + - - +
816N GLU 3.5 3.5 + - - -
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Residues in contact with LEU 813 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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800N MET* 6.1 1.6 - - - -
810N SER* 4.0 6.8 + - - +
811N GLY 3.4 0.8 - - - -
812N ILE* 1.3 75.7 - - - +
814N TRP* 1.3 59.3 + - - +
816N GLU* 3.3 3.8 + - - +
817N ALA* 3.1 17.8 + - - -
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Residues in contact with TRP 814 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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810N SER 4.1 6.4 + - - -
811N GLY 3.7 6.7 + - - -
812N ILE 3.0 1.2 + - - -
813N LEU* 1.3 73.9 - - - +
815N SER* 1.3 59.0 + - - +
817N ALA* 3.3 4.1 + - - +
818N ILE* 2.9 24.9 + - - -
833N ALA* 6.0 6.1 - - - +
843N VAL* 6.2 2.0 - - - -
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Residues in contact with SER 815 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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811N GLY 3.8 5.5 + - - -
812N ILE 2.7 17.8 + - - -
814N TRP* 1.3 72.3 - - - +
816N GLU* 1.3 54.2 + - - +
818N ILE* 3.2 2.3 + - - +
819N PHE* 2.9 24.8 + - - -
842N HIS 5.3 9.4 - - - -
843N VAL* 5.7 5.3 - - - +
846N ALA* 6.3 2.2 - - - +
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Residues in contact with GLU 816 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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812N ILE 3.5 4.8 + - - -
813N LEU* 3.3 6.6 + - - +
814N TRP 3.2 0.2 - - - -
815N SER* 1.3 74.6 - - - +
817N ALA* 1.3 64.5 + - - +
818N ILE 3.1 1.3 - - - -
819N PHE* 4.1 2.4 - - - +
820N LEU* 3.2 18.5 + - - -
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Residues in contact with ALA 817 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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800N MET* 6.5 0.9 - - - +
813N LEU 3.1 13.3 + - - -
814N TRP* 3.3 6.0 + - - +
816N GLU* 1.3 76.6 - - - +
818N ILE* 1.3 60.4 + - - +
820N LEU* 3.8 5.4 + - - +
821N GLU 4.1 6.2 + - - -
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Residues in contact with ILE 818 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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814N TRP 2.9 14.1 + - - -
815N SER* 3.6 3.4 - - - +
816N GLU 3.1 0.2 - - - -
817N ALA* 1.3 72.4 - - - +
819N PHE* 1.3 62.8 + - - +
820N LEU 2.8 6.4 + - - -
821N GLU 3.0 24.9 + - - +
846N ALA 6.5 1.1 - - - -
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Residues in contact with PHE 819 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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815N SER 2.9 18.7 + - - -
816N GLU* 3.6 3.3 + - - +
818N ILE* 1.3 70.9 - - - +
820N LEU* 1.3 63.1 + - - +
821N GLU 4.5 0.2 - - - -
822N ALA* 4.0 8.8 + - - +
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Residues in contact with LEU 820 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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816N GLU 3.2 14.7 + - - -
817N ALA* 4.1 3.4 - - - +
818N ILE 2.8 2.8 + - - -
819N PHE* 1.3 80.6 - - - +
821N GLU* 1.3 56.8 + - - +
822N ALA 3.2 5.0 + - - -
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Residues in contact with GLU 821 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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817N ALA 4.1 4.9 + - - -
818N ILE 3.0 20.7 + - - +
820N LEU* 1.3 69.3 - - - +
822N ALA* 1.3 65.6 + - - +
823N ARG 3.2 15.2 + - - -
824N PRO* 4.3 5.1 - - - +
850N LEU* 5.8 0.9 - - - -
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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