Contacts of the helix formed by residues 808 - 818 (chain N) in PDB entry 5X22
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 808 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63L HIS* 5.6 2.9 - - + +
806N PHE* 4.2 3.5 - - - +
807N ALA* 1.3 86.4 - - + +
809N PRO* 1.3 70.1 - - + +
810N GLU* 3.2 30.0 - - - +
811N GLU* 3.2 36.0 + - - +
812N ALA 3.5 3.6 + - - -
829N VAL* 3.6 6.0 - - - +
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Residues in contact with PRO 809 (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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63L HIS* 5.6 1.6 - - + -
65L PHE* 3.6 49.4 - - + -
807N ALA 4.5 1.1 - - - +
808N THR* 1.3 89.5 - - + +
810N GLU* 1.3 63.0 + - - +
812N ALA* 3.0 4.9 + - + +
813N LEU* 2.9 33.4 + - - +
829N VAL* 3.5 20.4 - - + -
839N LEU* 4.1 18.8 - - + -
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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
----------------------------------------------------------
63L HIS* 3.4 53.1 + - - +
65L PHE* 3.8 11.5 - - + -
808N THR* 3.2 32.1 - - - +
809N PRO* 1.3 77.9 - - - +
811N GLU* 1.3 56.8 + - + +
813N LEU* 3.6 13.4 - - + +
814N ALA* 2.9 30.5 + - - +
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Residues in contact with GLU 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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806N PHE* 4.1 12.9 - - + -
807N ALA* 3.4 34.2 + - - +
808N THR* 3.2 23.1 + - - +
809N PRO 3.2 0.2 - - - -
810N GLU* 1.3 80.6 - - + +
812N ALA* 1.3 56.1 + - - +
814N ALA* 3.4 6.2 + - - +
815N ALA* 2.9 29.1 + - - +
818N ARG* 5.0 1.4 + - - -
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Residues in contact with ALA 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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806N PHE* 3.9 29.7 - - + -
808N THR 3.5 2.5 + - - +
809N PRO* 3.0 11.3 + - + +
811N GLU* 1.3 80.7 - - - +
813N LEU* 1.3 56.0 + - + +
815N ALA* 3.3 2.8 + - - +
816N HIS* 2.9 29.7 + - - +
821N VAL* 5.3 0.9 - - - +
827N ILE* 4.4 10.8 - - + -
829N VAL* 4.2 18.2 - - + -
836N VAL* 4.6 6.7 - - + +
839N LEU* 4.4 7.6 - - + -
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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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64L GLU* 5.9 1.3 - - - +
65L PHE* 4.4 19.3 - - + -
154L GLU* 5.8 3.4 - - - +
809N PRO 2.9 18.8 + - - +
810N GLU* 3.6 12.3 - - + +
812N ALA* 1.3 78.1 - - - +
814N ALA* 1.3 55.9 + - - +
816N HIS* 3.2 10.6 + - - +
817N GLU* 2.9 27.2 + - - +
836N VAL* 4.5 7.4 - - + -
839N LEU* 3.7 32.3 - - + -
840N LYS* 4.0 29.4 - - + +
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Residues in contact with ALA 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 GLU 2.9 17.5 + - - +
811N GLU* 3.8 6.3 - - - +
813N LEU* 1.3 76.9 - - - +
815N ALA* 1.3 57.5 + - - +
817N GLU* 3.2 9.3 + - - +
818N ARG* 3.0 44.9 + - - +
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Residues in contact with ALA 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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806N PHE* 3.8 24.9 - - + -
811N GLU 2.9 18.0 + - - +
812N ALA 3.5 5.6 - - - +
814N ALA* 1.3 77.5 - - - +
816N HIS* 1.3 58.1 + - - +
818N ARG* 3.5 29.1 + - - +
820N GLU* 3.1 32.0 + - - +
821N VAL* 3.7 9.4 + - + -
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Residues in contact with HIS 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 ALA 2.9 13.0 + - - +
813N LEU* 3.5 10.5 - - - +
815N ALA* 1.3 74.7 - - - +
817N GLU* 1.3 70.0 + - - +
819N GLY* 3.1 14.2 + - - -
821N VAL* 2.9 31.4 + - - +
822N ALA* 4.2 1.0 - - - -
823N LEU* 4.1 33.9 + - + +
836N VAL* 3.7 28.0 - - + +
840N LYS* 4.0 25.4 - - + +
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Residues in contact with GLU 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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154L GLU* 5.9 1.4 - - - +
813N LEU 2.9 12.3 + - - +
814N ALA* 3.2 13.4 + - - +
816N HIS* 1.3 79.5 - - - +
818N ARG* 1.3 61.1 + - + +
819N GLY* 3.0 5.7 + - - -
840N LYS* 4.5 14.6 + - - -
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Residues in contact with ARG 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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811N GLU 5.0 1.2 + - - -
814N ALA* 3.0 35.0 + - + +
815N ALA* 3.6 26.1 - - - +
816N HIS 3.3 0.6 - - - -
817N GLU* 1.3 76.0 - - + +
819N GLY* 1.3 59.9 + - - +
820N GLU* 3.0 42.9 + - - +
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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