Contacts of the helix formed by residues 230 - 239 (chain B) in PDB entry 4G84
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 LYS 230 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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226B VAL* 4.2 6.3 - - + -
227B SER* 3.0 33.5 + - - +
229B SER* 1.3 82.2 + - - +
231B PHE* 1.3 63.2 + - - +
232B ARG 3.5 1.8 - - - -
233B THR* 3.6 12.4 + - - +
234B ILE* 3.0 31.9 + - + +
257B LYS 4.2 15.0 - - - +
258B GLY 3.4 22.0 + - - -
259B LEU* 4.2 19.2 - - + +
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Residues in contact with PHE 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B ARG* 3.8 29.4 - - + -
217B LEU* 3.9 9.4 - - + -
218B ASP* 3.0 44.0 - - - -
221B PHE* 3.4 31.8 - + + -
226B VAL* 4.7 0.4 - - - -
227B SER 3.7 3.4 + - - +
228B ASP* 3.3 20.8 + - - +
229B SER 3.3 1.2 - - - -
230B LYS* 1.3 78.6 - - - +
232B ARG* 1.3 78.5 + - + +
235B CYS* 2.9 49.8 + - - -
328B LEU* 4.0 13.0 - - + -
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Residues in contact with ARG 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B ARG* 4.5 6.2 - - - +
229B SER 5.0 2.5 + - - +
230B LYS 3.5 0.6 - - - -
231B PHE* 1.3 100.9 - - + +
233B THR* 1.3 61.6 + - + +
235B CYS* 3.1 7.2 + - - +
236B SER* 2.8 32.7 + - - +
327B GLY* 5.6 0.6 - - - +
328B LEU* 3.4 42.7 + - - +
329B ASP* 2.7 39.4 + - - +
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Residues in contact with THR 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229B SER 5.4 0.2 + - - -
230B LYS* 3.6 20.1 + - - +
232B ARG* 1.3 81.1 - - + +
234B ILE* 1.3 67.6 + - - +
236B SER* 3.1 11.7 + - - +
237B SER* 3.1 25.1 + - - -
257B LYS* 5.5 8.1 - - - +
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Residues in contact with ILE 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221B PHE* 3.7 22.7 - - + -
226B VAL* 4.2 13.2 - - + -
230B LYS* 3.0 26.8 + - + +
231B PHE 3.8 2.7 - - - +
232B ARG 3.3 0.6 - - - -
233B THR* 1.3 75.3 + - - +
235B CYS* 1.3 61.0 + - - +
237B SER* 3.2 4.4 + - - +
238B VAL* 2.9 28.5 + - + +
253B MET* 4.0 16.2 - - + -
257B LYS* 4.3 25.4 - - + +
259B LEU* 3.9 26.7 - - + -
267B ILE* 3.9 22.0 - - + -
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Residues in contact with CYS 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217B LEU* 4.8 4.5 - - - -
221B PHE* 3.4 21.8 - - - -
231B PHE* 2.9 39.6 + - - -
232B ARG 3.2 11.9 - - - +
234B ILE* 1.3 76.3 - - - +
236B SER* 1.3 54.3 + - - +
238B VAL* 3.2 4.1 + - - +
239B ASP* 2.9 32.8 + - - +
325B ALA* 3.9 13.0 - - + +
328B LEU* 3.3 35.4 - - + -
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Residues in contact with SER 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232B ARG* 2.8 22.5 + - - +
233B THR* 3.1 15.6 + - - +
235B CYS* 1.3 73.7 - - - +
237B SER* 1.3 61.5 + - - +
239B ASP* 3.5 11.0 + - - +
240B LYS* 3.5 28.8 - - - +
252B GLU* 5.8 0.4 - - - -
325B ALA 5.4 0.9 - - - -
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Residues in contact with SER 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233B THR 3.1 14.0 + - - -
234B ILE* 3.5 7.9 - - - -
235B CYS 3.2 0.2 - - - -
236B SER* 1.3 74.1 - - - +
238B VAL* 1.3 65.9 + - - +
240B LYS* 3.1 20.9 + - - +
249B VAL* 3.7 17.2 - - - +
252B GLU* 3.2 32.2 + - - +
253B MET* 3.7 29.0 - - - +
257B LYS* 5.0 4.5 - - - +
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Residues in contact with VAL 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217B LEU* 4.8 4.0 - - + -
221B PHE* 4.2 11.7 - - + -
234B ILE* 2.9 22.7 + - + +
235B CYS* 3.8 5.4 - - - +
237B SER* 1.3 74.8 - - - +
239B ASP* 1.3 63.2 + - - +
240B LYS 3.2 0.9 + - - -
241B LEU* 3.2 27.6 + - + +
246B TRP* 5.3 0.2 - - + -
249B VAL* 4.4 1.3 - - + +
253B MET* 4.6 7.0 - - - -
267B ILE* 4.1 16.6 - - + -
271B VAL* 3.4 36.3 - - + -
322B LEU 4.2 2.7 - - - +
323B SER* 3.3 23.4 - - - +
325B ALA* 4.4 9.2 - - + -
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Residues in contact with ASP 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235B CYS 2.9 17.4 + - - +
236B SER* 3.5 11.2 - - - +
237B SER 3.1 0.2 - - - -
238B VAL* 1.3 78.4 - - - +
240B LYS* 1.3 56.6 + - + +
241B LEU 3.2 2.4 + - - -
242B ASP* 3.0 18.2 + - - +
243B LYS* 5.1 2.0 + - - -
323B SER 3.6 8.1 - - - +
325B ALA 3.1 32.3 + - - +
326B ARG* 2.7 52.3 + - - +
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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