Contacts of the helix formed by residues 236 - 241 (chain S) in PDB entry 4HOK
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 PRO 236 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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233S MET 5.2 1.8 - - - +
234S SER 2.7 18.4 - - - +
235S THR* 1.3 83.8 - - - +
237S ILE* 1.3 64.8 + - - +
238S GLU* 3.4 5.8 - - + +
239S VAL* 3.1 34.9 + - + +
240S LEU 3.1 16.3 + - - -
256S ARG* 5.6 0.7 - - - +
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Residues in contact with ILE 237 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235S THR 3.5 0.8 + - - +
236S PRO* 1.3 68.9 - - - +
238S GLU* 1.3 69.6 + - - +
239S VAL 2.9 4.9 - - - -
240S LEU* 3.0 13.5 + - + +
241S CYS* 2.9 25.1 + - - -
249S SER* 3.7 30.7 - - - -
252S LEU* 3.2 34.5 - - + -
253S ASN* 3.8 20.0 - - - +
256S ARG* 2.7 57.3 - - - +
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Residues in contact with GLU 238 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236S PRO* 3.4 4.9 - - + +
237S ILE* 1.3 81.6 + - - +
239S VAL* 1.3 62.6 + - + +
241S CYS* 3.8 7.0 - - - +
242S LYS* 3.4 21.5 + - - +
249S SER* 4.5 13.0 - - - +
253S ASN* 3.4 26.3 + - - +
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Residues in contact with VAL 239 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235S THR* 4.5 7.9 - - + -
236S PRO* 3.2 44.4 - - + +
238S GLU* 1.3 78.4 - - + +
240S LEU* 1.3 66.3 + - - +
242S LYS* 2.9 27.9 - - + +
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Residues in contact with LEU 240 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201S TYR* 4.4 18.4 - - + -
204S MET* 3.8 33.0 - - + +
208S LEU* 4.2 14.2 - - + +
211S LEU* 4.5 5.6 - - + -
212S PRO* 3.3 42.0 - - + -
213S TRP* 3.9 26.2 - - + -
235S THR* 3.8 13.5 - - + +
236S PRO 3.1 3.0 + - - +
237S ILE* 3.0 14.8 + - + +
239S VAL* 1.3 81.8 - - - +
241S CYS* 1.3 57.7 + - - +
242S LYS* 3.3 4.3 + - - +
252S LEU* 4.8 9.6 - - + -
256S ARG* 6.1 0.7 - - - +
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Residues in contact with CYS 241 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204S MET* 3.9 25.1 - - - -
237S ILE* 2.9 19.2 + - - +
238S GLU* 3.8 5.7 - - - +
240S LEU* 1.3 78.5 - - - +
242S LYS* 1.3 63.8 + - - +
243S GLY 3.0 3.8 + - - -
244S TYR* 3.2 20.8 + - + +
245S PRO 5.1 0.2 - - - +
248S PHE* 3.6 33.0 - - + -
249S SER* 4.0 18.4 - - - +
252S LEU* 3.8 15.0 - - - -
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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