Contacts of the helix formed by residues 236 - 253 (chain B) in PDB entry 3G33
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 236 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230B ALA* 4.3 1.3 - - - -
234B GLY 5.4 1.6 - - - +
235B THR* 1.3 78.8 + - - +
237B VAL* 1.3 65.6 + - - +
238B ASP* 3.2 23.4 - - - +
239B CYS* 3.4 22.3 + - - +
240B LEU* 3.1 23.6 + - - +
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Residues in contact with VAL 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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226B THR* 4.1 9.4 - - - +
227B GLU* 3.8 35.0 - - + +
230B ALA* 4.3 17.5 - - + -
235B THR 4.0 0.6 + - - +
236B GLU* 1.3 73.9 - - - +
238B ASP* 1.3 66.7 + - - +
240B LEU* 3.8 2.9 - - - +
241B ARG* 3.2 60.2 + - - +
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Residues in contact with ASP 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B GLU* 3.4 22.7 - - + +
237B VAL* 1.3 80.2 - - - +
239B CYS* 1.3 71.4 + - - +
241B ARG* 3.2 10.8 + - - +
242B ALA* 3.2 20.2 + - - +
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Residues in contact with CYS 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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202B MET* 4.2 27.8 - - + +
235B THR* 5.5 2.0 - - - -
236B GLU* 3.4 29.2 + - + +
238B ASP* 1.3 80.3 - - - +
240B LEU* 1.3 65.9 + - - +
241B ARG 3.1 0.7 + - - -
242B ALA* 3.1 5.8 + - - +
243B CYS* 2.8 27.0 + - - +
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Residues in contact with LEU 240 (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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202B MET* 4.6 6.5 - - + +
205B THR* 3.3 44.6 - - + +
206B GLY* 3.7 7.2 - - - -
226B THR* 3.2 34.8 - - - +
229B LEU* 3.7 14.6 - - + -
230B ALA* 3.6 19.7 - - + +
235B THR* 4.5 5.3 + - - +
236B GLU 3.1 14.2 + - - +
237B VAL* 3.8 5.4 - - - +
239B CYS* 1.3 77.8 - - - +
241B ARG* 1.3 53.6 + - - +
243B CYS* 3.5 3.8 - - + +
244B GLN* 2.7 45.9 + - - +
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Residues in contact with ARG 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222B GLY 5.8 0.2 - - - -
223B ASP* 3.2 48.6 + - - +
226B THR* 3.6 27.4 + - + +
227B GLU* 4.9 3.6 + - - +
237B VAL* 3.2 35.6 + - - +
238B ASP* 3.6 10.4 + - - +
239B CYS 3.2 0.6 - - - -
240B LEU* 1.3 75.9 - - - +
242B ALA* 1.3 60.2 + - - +
244B GLN* 3.2 7.0 + - - +
245B GLU* 2.8 47.7 + - - +
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Residues in contact with ALA 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B ASP 3.2 8.7 + - - +
239B CYS* 3.1 9.7 + - - +
241B ARG* 1.3 77.9 - - - +
243B CYS* 1.3 57.9 + - - +
245B GLU* 3.9 11.5 + - - +
246B GLN* 3.0 30.6 + - - +
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Residues in contact with CYS 243 (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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195B PHE* 4.8 1.5 - - - -
198B TYR* 4.1 21.8 - - + -
202B MET* 3.7 50.9 - - + -
203B ILE* 4.7 1.6 - - - -
206B GLY* 4.6 1.6 - - - -
239B CYS 2.8 17.3 + - - +
240B LEU* 3.5 4.7 - - + +
242B ALA* 1.3 74.9 - - - +
244B GLN* 1.3 67.4 + - - +
246B GLN* 3.1 7.0 + - - +
247B ILE* 3.0 41.6 + - - +
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Residues in contact with GLN 244 (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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206B GLY* 3.5 26.2 - - - +
209B GLY* 3.1 33.1 + - - -
210B ALA* 3.3 2.8 - - - +
213B GLN* 2.9 28.2 + - - -
226B THR* 3.5 25.4 - - - +
229B LEU* 5.1 1.4 - - - +
240B LEU* 2.7 26.4 + - + +
241B ARG* 3.7 4.2 - - - +
243B CYS* 1.3 74.1 - - - +
245B GLU* 1.3 63.5 + - + +
247B ILE* 3.4 4.2 + - - +
248B GLU* 3.2 45.8 + - - +
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Residues in contact with GLU 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B ARG* 2.8 33.4 + - - +
242B ALA* 3.9 11.3 + - - +
244B GLN* 1.3 71.9 - - + +
246B GLN* 1.3 59.8 + - - +
248B GLU* 3.4 15.6 + - - +
249B ALA* 2.9 29.1 + - - +
252B ARG* 5.1 1.4 + - - -
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Residues in contact with GLN 246 (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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194B THR* 4.9 13.4 + - - +
195B PHE* 4.0 17.4 - - + -
198B TYR* 2.7 33.6 + - - -
242B ALA 3.0 19.2 + - - +
243B CYS* 3.1 6.1 + - - +
245B GLU* 1.3 74.4 - - - +
247B ILE* 1.3 61.0 + - - +
249B ALA* 3.3 7.9 + - + +
250B ALA* 2.8 28.6 + - + +
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Residues in contact with ILE 247 (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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185B PHE* 3.6 33.9 - - + -
188B LEU* 3.6 13.6 - - + +
189B CYS* 3.8 22.0 - - - -
195B PHE* 3.7 24.0 - - + -
203B ILE* 4.2 4.5 - - - +
206B GLY 3.8 6.5 - - - +
207B SER* 3.6 28.9 - - - +
210B ALA* 5.0 1.6 - - + -
243B CYS* 3.0 25.7 + - - +
244B GLN 3.7 6.1 - - - +
246B GLN* 1.3 73.5 - - - +
248B GLU* 1.3 59.9 + - + +
250B ALA* 3.1 1.3 + - - -
251B LEU* 3.0 25.3 + - - +
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Residues in contact with GLU 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B PHE* 4.8 6.7 - - + -
210B ALA* 3.7 22.4 - - + +
213B GLN* 4.9 4.3 - - - +
244B GLN* 3.2 47.4 + - - +
245B GLU* 3.7 12.1 - - - +
247B ILE* 1.3 77.1 - - - +
249B ALA* 1.3 59.0 + - - +
251B LEU* 3.5 8.2 + - - +
252B ARG* 2.9 55.4 + - - +
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Residues in contact with ALA 249 (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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245B GLU 2.9 18.2 + - - +
246B GLN* 3.5 9.2 - - + +
247B ILE 3.1 0.2 - - - -
248B GLU* 1.3 76.3 - - - +
250B ALA* 1.3 64.2 + - - +
252B ARG* 3.5 13.0 + - - +
253B GLU* 3.4 34.5 + - - +
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Residues in contact with ALA 250 (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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188B LEU* 3.9 10.8 - - + +
192B ASP* 3.8 22.4 - - - +
195B PHE* 3.9 17.7 - - + -
246B GLN* 2.8 18.6 + - + +
247B ILE 3.1 5.4 + - - +
249B ALA* 1.3 74.5 - - - +
251B LEU* 1.3 63.5 + - - +
253B GLU* 3.7 4.6 - - - +
254B SER* 3.1 25.8 + - - -
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Residues in contact with LEU 251 (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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184B THR* 5.0 10.5 - - - +
185B PHE* 3.5 32.3 - - + -
188B LEU* 3.5 26.0 - - + +
247B ILE 3.0 16.3 + - - +
248B GLU* 3.6 9.0 - - - +
249B ALA 3.2 0.2 - - - -
250B ALA* 1.3 77.6 - - - +
252B ARG* 1.3 59.3 + - + +
254B SER* 2.8 23.3 + - - -
177D LEU* 5.4 3.6 - - + -
181D HIS* 4.7 18.2 - - + +
214D GLY* 3.6 11.9 - - - +
215D LEU* 3.0 42.2 - - + +
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Residues in contact with ARG 252 (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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245B GLU 5.1 1.4 + - - -
248B GLU* 2.9 49.1 + - - +
249B ALA* 3.5 11.4 + - - +
251B LEU* 1.3 77.6 - - + +
253B GLU* 1.3 61.6 + - + +
213D GLN 5.3 2.5 - - - +
214D GLY* 3.4 21.1 - - - +
215D LEU* 3.4 3.4 - - - +
216D GLY* 2.9 28.4 + - - +
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Residues in contact with GLU 253 (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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249B ALA* 3.4 23.1 + - - +
250B ALA* 3.7 5.1 - - - +
251B LEU 3.1 0.6 - - - -
252B ARG* 1.3 81.9 - - + +
254B SER* 1.3 64.5 + - - +
174D ARG* 5.2 2.1 + - - -
215D LEU 4.1 0.2 - - - -
216D GLY* 5.2 0.9 - - - -
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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