Contacts of the helix formed by residues 924 - 929 (chain F) in PDB entry 2X36
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 ALA 924 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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922F ASP 4.0 0.6 + - - -
923F LEU* 1.3 75.0 - - - +
925F ALA* 1.3 67.2 + - - +
926F PHE* 4.1 9.4 - - + +
927F ILE* 2.9 35.3 + - + +
928F THR* 3.2 8.8 + - - -
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Residues in contact with ALA 925 (chain F).
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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923F LEU 3.3 4.6 + - - -
924F ALA* 1.3 72.7 - - - +
926F PHE* 1.3 56.4 + - - +
928F THR* 4.5 4.9 - - - +
929F GLU* 2.8 37.7 + - + +
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Residues in contact with PHE 926 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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903F LYS* 3.8 8.9 + - - -
924F ALA* 3.0 9.3 - - + +
925F ALA* 1.3 78.9 - - - +
927F ILE* 1.3 72.1 + - + +
929F GLU* 3.9 8.7 + - - +
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Residues in contact with ILE 927 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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896F LYS* 4.7 14.8 - - + -
899F THR* 3.9 27.4 - - + +
900F ILE* 4.2 33.2 - - + -
903F LYS* 2.8 38.3 + - + +
923F LEU* 4.5 14.8 - - + -
924F ALA* 2.9 31.8 + - + +
926F PHE* 1.3 84.1 - - + +
928F THR* 1.3 62.4 + - - +
931F LEU* 4.6 0.7 - - - +
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Residues in contact with THR 928 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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920F PHE* 3.4 56.5 + - + -
921F TYR* 4.3 18.8 - - + -
923F LEU* 4.1 9.0 + - - +
924F ALA 3.2 12.9 + - - -
925F ALA* 4.2 4.5 - - - -
927F ILE* 1.3 76.8 - - - +
929F GLU* 1.3 66.8 + - - +
930F GLY 3.4 0.2 + - - -
931F LEU* 3.1 22.2 + - + +
933F VAL* 5.3 1.8 - - + -
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Residues in contact with GLU 929 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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903F LYS* 3.7 17.2 + - - -
925F ALA* 2.8 20.2 + - + +
926F PHE* 3.9 7.4 + - - +
927F ILE 3.3 0.8 - - - -
928F THR* 1.3 79.6 - - - +
930F GLY* 1.3 70.7 + - - +
931F LEU 3.4 2.3 + - - -
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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