Contacts of the helix formed by residues 232 - 240 (chain R) in PDB entry 5GJQ
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 GLU 232 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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372Q LYS* 6.0 0.2 + - - -
230R ALA 4.3 1.3 + - - +
231R LEU* 1.3 75.5 - - - +
233R ARG* 1.3 56.2 + - - +
234R PRO* 3.1 18.2 - - + +
235R ASP* 3.9 21.5 - - + +
236R LEU* 2.6 38.2 + - - +
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Residues in contact with ARG 233 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367Q GLN* 2.4 37.9 + - - +
370Q LEU* 2.6 60.2 - - + +
371Q ASP* 3.4 11.8 + - - +
231R LEU 4.0 0.2 + - - -
232R GLU* 1.3 72.3 - - - +
234R PRO* 1.4 65.2 - - + +
236R LEU* 3.6 10.2 - - + +
237R ARG* 3.2 21.7 + - - +
264R TYR* 2.7 60.8 + - + +
266R CYS* 5.1 1.8 - - - -
306R GLN* 3.8 15.5 + - - +
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Residues in contact with PRO 234 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370Q LEU 5.9 0.7 - - - +
371Q ASP* 4.4 30.2 - - + +
372Q LYS* 5.6 7.6 - - + -
232R GLU* 3.1 19.7 - - + +
233R ARG* 1.4 95.1 - - + +
235R ASP* 1.3 77.1 + - - +
237R ARG* 2.7 35.7 + - + +
238R GLU* 3.0 13.3 + - - +
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Residues in contact with ASP 235 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231R LEU* 4.3 5.5 - - + +
232R GLU* 3.5 25.0 - - + +
234R PRO* 1.3 94.0 - - + +
236R LEU* 1.3 59.6 + - - +
238R GLU* 3.7 20.4 - - - +
239R LYS* 3.0 56.1 + - - +
240R VAL 4.2 0.2 + - - -
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Residues in contact with LEU 236 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227R SER 4.4 0.7 - - - +
228R MET* 4.1 30.7 - - - +
231R LEU* 4.1 20.4 - - + +
232R GLU 2.6 24.0 + - - +
233R ARG* 3.6 9.9 - - + +
235R ASP* 1.3 74.2 - - - +
237R ARG* 1.3 64.8 + - - +
240R VAL* 2.9 41.6 + - + -
241R ILE* 2.9 16.3 + - + -
260R LEU* 3.6 28.7 - - + -
263R LEU* 4.7 10.8 - - + -
264R TYR* 4.9 10.8 - - + -
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Residues in contact with ARG 237 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371Q ASP* 5.6 7.2 + - - +
233R ARG 3.2 2.2 + - - +
234R PRO* 2.7 39.0 + - + +
236R LEU* 1.3 80.3 - - - +
238R GLU* 1.3 83.1 + - - +
241R ILE* 3.7 12.6 - - - +
242R LYS* 3.1 61.7 + - - +
264R TYR* 2.6 41.0 - - + +
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Residues in contact with GLU 238 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234R PRO* 3.0 17.4 + - - +
235R ASP* 3.8 20.5 - - - +
236R LEU 3.2 0.2 - - - -
237R ARG* 1.3 110.4 + - - +
239R LYS* 1.3 70.8 + - + +
242R LYS* 3.8 18.9 - - - +
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Residues in contact with LYS 239 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199R GLU* 5.3 10.5 + - - +
202R LEU* 3.6 38.4 - - + +
231R LEU* 4.0 16.1 - - - +
235R ASP* 3.0 36.0 + - + +
238R GLU* 1.3 88.6 - - + +
240R VAL* 1.3 65.1 + - - +
242R LYS 4.8 0.9 - - - -
243R GLY* 4.4 10.5 - - - -
246R ILE* 5.4 1.0 - - - +
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Residues in contact with VAL 240 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202R LEU* 3.8 12.1 - - + -
223R THR 6.0 0.2 - - - -
224R VAL* 4.2 25.6 - - + -
227R SER* 3.5 23.6 - - - +
231R LEU* 3.4 30.3 - - + -
236R LEU* 2.9 21.5 + - + +
238R GLU 3.6 0.6 - - - -
239R LYS* 1.3 84.5 - - - +
241R ILE* 1.3 68.6 + - - +
242R LYS 2.9 1.1 - - - -
243R GLY* 2.9 14.8 + - - +
246R ILE* 4.1 14.4 - - + +
247R LEU* 5.7 0.2 - - - +
250R LEU* 5.6 3.0 - - + +
260R LEU* 4.5 8.0 - - + +
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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