Contacts of the helix formed by residues 806 - 812 (chain N) in PDB entry 2JA7
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 THR 806 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31N TRP* 5.8 0.9 - - + -
754N SER* 3.3 20.3 + - - +
756N ILE 4.0 14.6 + - - -
757N PRO* 4.8 0.9 - - - +
805N THR* 1.3 82.0 + - - +
807N ARG* 1.3 56.5 + - + +
808N ALA* 2.6 34.1 + - + +
809N MET* 2.5 44.7 + - - +
810N GLU 3.9 1.0 + - - -
815N ARG* 4.8 2.5 + - - -
1043N ASP* 4.6 0.2 - - - -
1044N ALA 4.5 0.9 + - - -
1045N SER* 3.1 17.2 + - - +
1046N PRO* 3.8 17.1 - - + +
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Residues in contact with ARG 807 (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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28N GLU* 3.3 28.4 + - - -
31N TRP* 3.3 70.1 - - + +
806N THR* 1.3 70.4 - - - +
808N ALA* 1.3 57.7 + - - +
809N MET 3.3 0.7 + - - -
810N GLU* 3.4 28.3 + - - +
811N TYR* 3.0 26.8 + - - -
815N ARG* 5.4 4.6 - - - +
1043N ASP* 3.6 23.7 + - - +
1045N SER* 2.6 30.7 + - - +
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Residues in contact with ALA 808 (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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31N TRP* 4.5 10.2 - - + -
541N LEU* 4.3 12.4 - - + +
746N SER* 5.5 6.1 - - - +
747N MET* 5.6 2.7 - - - -
754N SER* 3.8 25.1 - - - +
806N THR* 2.6 22.7 + - + +
807N ARG* 1.3 77.8 - - - +
809N MET* 1.3 62.2 + - - +
810N GLU 3.3 0.3 + - - -
811N TYR* 3.3 20.2 + - - +
812N LEU* 3.6 14.3 + - - +
1046N PRO* 6.0 0.4 - - + -
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Residues in contact with MET 809 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
754N SER 4.2 4.9 - - - +
755N ILE* 3.7 25.4 - - + +
802N PRO* 4.3 2.2 - - + -
804N GLY 3.9 0.9 - - - +
805N THR* 3.4 29.4 - - - -
806N THR* 2.5 49.4 + - - +
808N ALA* 1.3 73.2 - - - +
810N GLU* 1.3 55.9 + - - +
812N LEU* 2.7 33.0 + - + -
813N LYS 3.1 8.3 + - - -
814N PHE* 3.5 36.5 + - + -
815N ARG* 4.4 10.8 - - + +
983N ARG* 3.6 21.3 - - - +
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Residues in contact with GLU 810 (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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35N SER* 3.4 18.9 + - - -
39N ARG* 5.5 1.7 + - - -
665N GLU* 5.3 2.8 - - - +
807N ARG* 3.4 29.1 + - - +
808N ALA 3.2 0.2 - - - -
809N MET* 1.3 78.0 - - - +
811N TYR* 1.3 78.9 + - + +
813N LYS* 3.9 19.1 + - - +
815N ARG* 3.0 38.1 + - - +
816N GLU* 4.9 1.9 - - - +
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Residues in contact with TYR 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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31N TRP* 4.0 25.5 + + - +
34N ILE* 4.1 5.8 - - + -
35N SER* 3.0 50.7 + - - -
38N PHE* 3.0 50.6 - + + +
43N LEU* 3.1 23.1 - - + +
541N LEU* 6.3 1.1 - - + -
807N ARG* 3.0 24.7 + - - -
808N ALA* 3.4 17.7 - - - +
809N MET 3.0 0.4 - - - -
810N GLU* 1.3 93.9 + - + +
812N LEU* 1.3 58.4 + - + +
813N LYS* 3.1 24.4 + - - +
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Residues in contact with LEU 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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43N LEU* 3.5 15.0 - - + -
488N TYR* 3.7 15.5 - - - -
489N SER* 5.8 3.7 - - - -
492N LEU* 3.5 24.2 - - + +
541N LEU* 4.3 18.4 - - + -
751N VAL* 3.7 27.4 - - + +
754N SER* 3.7 30.1 - - - -
755N ILE* 4.7 11.4 - - + -
808N ALA 3.8 12.8 - - - +
809N MET* 2.7 11.9 + - - +
811N TYR* 1.3 76.8 - - + +
813N LYS* 1.3 73.8 + - - +
814N PHE* 3.1 11.2 + - + +
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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