Contacts of the helix formed by residues 173 - 194 (chain B) in PDB entry 4O6M
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 THR 173 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171B SER 3.7 12.6 - - - +
172B VAL* 1.3 73.7 - - - +
174B PRO* 1.3 75.5 - - - +
175B ASN* 3.6 7.6 + - - +
176B GLN* 3.0 39.2 + - - +
177B ILE* 3.2 25.2 + - - +
226B MET* 3.9 17.9 - - + -
420B SO4 4.7 7.5 + - - +
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Residues in contact with PRO 174 (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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173B THR* 1.3 88.9 - - - +
175B ASN* 1.3 56.9 + - - +
177B ILE* 3.1 8.4 + - + -
178B THR* 2.9 30.1 + - - -
217B ASP* 3.4 22.4 - - - +
220B ILE* 4.1 4.9 - - + -
221B ALA* 3.6 31.9 - - + +
226B MET* 3.8 32.5 - - + +
422B C5P 3.2 22.2 + - + +
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Residues in contact with ASN 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B THR* 3.3 7.0 + - - +
174B PRO* 1.3 79.6 - - - +
176B GLN* 1.3 58.4 + - + +
178B THR* 3.3 3.8 + - - -
179B VAL* 3.0 34.3 + - - +
228B SER* 4.6 6.8 + - - -
230B TYR* 4.0 19.6 - - - -
231B GLY* 3.4 15.2 - - - -
234B LEU* 4.5 5.7 - - + +
407B MPG 4.2 21.8 - - + +
422B C5P 2.8 22.8 + - - -
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Residues in contact with GLN 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B SER 4.1 2.8 + - - +
172B VAL* 3.4 15.3 - - + +
173B THR* 3.0 41.0 + - - +
175B ASN* 1.3 78.2 - - + +
177B ILE* 1.3 56.8 + - - +
179B VAL* 3.3 5.7 + - - +
180B PHE* 2.9 30.3 + - - +
403B MPG 3.8 24.1 - - + +
420B SO4 3.1 39.5 + - - +
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Residues in contact with ILE 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B LEU* 4.2 11.0 - - + -
172B VAL* 3.6 21.3 - - + -
173B THR 3.2 15.7 + - - +
174B PRO 3.1 6.3 + - - +
176B GLN* 1.3 75.7 - - - +
178B THR* 1.3 53.9 + - - +
180B PHE* 3.7 5.9 - - - +
181B SER* 2.8 33.6 + - - -
213B ILE* 3.8 23.6 - - + +
216B CYS* 3.8 12.6 - - + +
217B ASP* 3.5 25.1 - - + +
220B ILE* 3.7 33.9 - - + -
403B MPG 4.5 11.2 - - + -
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Residues in contact with THR 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B PRO 2.9 4.3 + - - -
175B ASN* 3.5 9.2 - - - -
176B GLN 3.3 0.2 - - - -
177B ILE* 1.3 76.4 - - - +
179B VAL* 1.3 58.3 + - - +
181B SER* 3.7 4.6 - - - -
182B PHE* 3.0 26.5 + - - +
214B ASP* 5.2 1.0 - - - +
217B ASP* 2.7 22.8 + - - -
234B LEU* 4.2 7.9 - - + -
235B ASP* 3.7 34.5 - - - +
238B LEU* 4.1 19.4 - - + +
239B ASP* 5.9 0.2 - - - +
422B C5P 2.8 25.9 + - - +
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Residues in contact with VAL 179 (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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175B ASN 3.0 22.3 + - - +
176B GLN* 3.8 5.6 - - - +
178B THR* 1.3 72.7 - - - +
180B PHE* 1.3 66.7 + - - +
182B PHE* 3.2 7.9 + - - +
183B PHE* 2.9 22.9 + - + +
234B LEU* 4.5 7.0 - - + -
238B LEU* 4.6 3.6 - - + -
407B MPG 3.8 37.5 - - + -
413B MPG 4.4 22.4 - - + -
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Residues in contact with PHE 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B GLN 2.9 17.6 + - - +
177B ILE* 3.7 3.1 - - - +
179B VAL* 1.3 76.0 - - - +
181B SER* 1.3 65.5 + - - +
183B PHE* 3.2 19.4 + + + +
184B LEU* 3.0 55.5 + - + +
213B ILE* 4.1 12.8 - - + -
402B MPG 5.2 11.2 - - + -
403B MPG 3.8 61.0 - - + -
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Residues in contact with SER 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B ILE 2.8 21.4 + - - -
178B THR* 3.7 5.4 - - - -
180B PHE* 1.3 78.9 - - - +
182B PHE* 1.3 62.8 + - - +
184B LEU* 3.1 14.3 + - - +
185B SER 3.2 2.1 + - - -
210B HIS* 2.8 44.8 + - - -
213B ILE* 4.4 8.5 - - - -
214B ASP* 3.4 33.6 + - - +
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Residues in contact with PHE 182 (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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178B THR 3.0 15.3 + - - +
179B VAL 3.2 6.9 + - - +
181B SER* 1.3 75.8 - - - +
183B PHE* 1.3 63.2 + - - +
185B SER* 2.5 29.3 + - - -
186B LEU* 3.2 34.9 + - + +
210B HIS* 4.5 1.6 - - - -
238B LEU* 3.7 32.8 - - + -
241B TYR* 3.6 26.5 - - + -
242B SER* 3.2 23.3 - - - -
245B ILE* 4.4 2.0 - - + -
412B MPG 3.8 40.8 - - + -
413B MPG 3.8 22.7 - - + -
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Residues in contact with PHE 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B VAL* 2.9 14.5 + - + +
180B PHE* 3.2 26.2 + + - +
182B PHE* 1.3 79.1 - - - +
184B LEU* 1.3 66.3 + - + +
186B LEU* 3.0 21.1 + - + +
187B VAL* 3.0 33.9 + - + +
411B MPG 4.0 23.6 - - + -
413B MPG 4.3 27.6 - - + -
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Residues in contact with LEU 184 (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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180B PHE* 3.0 40.9 + - + +
181B SER* 3.1 9.8 + - - +
183B PHE* 1.3 78.3 - - + +
185B SER* 1.3 57.6 - - - +
187B VAL* 3.2 13.5 + - + +
188B GLY 3.0 23.9 + - - -
206B ILE* 3.3 24.6 - - + +
209B LEU* 4.6 8.7 - - + -
210B HIS* 4.2 22.9 - - + +
213B ILE* 3.4 34.3 - - + -
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Residues in contact with SER 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B SER 3.2 2.4 + - - -
182B PHE* 2.5 24.5 + - - -
184B LEU* 1.3 78.2 - - - +
186B LEU* 1.3 60.1 + - - +
188B GLY* 3.5 0.7 + - - -
189B SER* 3.0 31.6 + - - -
207B ILE* 4.1 12.1 - - - +
210B HIS* 3.8 21.5 + - - -
242B SER* 2.7 38.5 + - - -
245B ILE* 5.8 0.2 - - - -
246B ILE* 4.3 6.9 - - - +
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Residues in contact with LEU 186 (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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182B PHE* 3.6 39.3 - - + +
183B PHE* 3.0 11.5 + - + +
185B SER* 1.3 78.2 + - - +
187B VAL* 1.3 59.8 + - - +
189B SER* 3.3 4.6 + - - -
190B ALA* 2.9 30.5 + - - +
245B ILE* 3.7 38.6 - - + -
411B MPG 3.7 25.0 - - + +
412B MPG 4.3 10.3 - - + -
413B MPG 3.6 37.9 - - + -
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Residues in contact with VAL 187 (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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183B PHE* 3.0 42.5 + - + +
184B LEU* 3.2 17.0 + - + +
186B LEU* 1.3 76.7 - - - +
188B GLY* 1.3 62.2 + - - +
190B ALA* 3.3 4.8 + - - +
191B LEU* 3.0 28.9 + - + +
206B ILE* 4.0 22.9 - - + -
411B MPG 4.3 12.8 - - + -
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Residues in contact with GLY 188 (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 LEU 3.0 12.2 + - - -
187B VAL* 1.3 76.5 - - - +
189B SER* 1.3 60.3 + - - +
191B LEU* 3.1 15.3 + - - -
192B PHE* 3.2 15.2 + - - -
203B ALA* 3.3 16.7 - - - +
206B ILE* 3.8 11.4 - - - +
207B ILE* 3.8 20.9 - - - -
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Residues in contact with SER 189 (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 SER 3.0 19.3 + - - -
186B LEU 3.6 4.9 - - - -
187B VAL 3.3 0.2 - - - -
188B GLY* 1.3 75.6 - - - +
190B ALA* 1.3 61.7 + - - +
192B PHE* 3.2 26.0 + - - +
193B LEU* 3.4 5.9 + - - +
207B ILE* 4.4 0.8 - - - +
245B ILE* 3.5 16.1 - - - +
246B ILE* 3.3 30.0 + - - +
249B SER* 3.4 26.3 + - - -
411B MPG 4.1 4.3 - - - -
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Residues in contact with ALA 190 (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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186B LEU 2.9 17.6 + - - +
187B VAL* 3.3 6.5 + - - +
189B SER* 1.3 75.6 - - - +
191B LEU* 1.3 63.5 + - + +
193B LEU* 3.1 29.3 + - - +
194B LEU* 3.6 10.2 + - - +
411B MPG 3.8 26.2 - - + +
414B MPG 4.2 19.0 - - + +
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Residues in contact with LEU 191 (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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187B VAL* 3.0 24.6 + - + +
188B GLY 3.1 6.9 + - - +
190B ALA* 1.3 75.1 - - + +
192B PHE* 1.3 64.9 + - - +
194B LEU* 3.2 29.9 + - + +
199B THR* 3.4 46.7 + - + +
200B THR 4.5 0.2 + - - -
202B LEU* 4.1 13.0 - - + -
203B ALA* 3.7 15.3 - - + +
206B ILE* 3.2 34.8 - - + -
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Residues in contact with PHE 192 (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 GLY 3.2 21.1 + - - -
189B SER* 3.2 16.1 + - - +
191B LEU* 1.3 76.1 - - - +
193B LEU* 1.3 60.8 + - - +
195B ASN* 3.1 14.4 + - - -
200B THR* 4.1 25.2 + - + -
203B ALA* 3.7 23.5 - - + +
204B GLY 4.3 3.8 - - - -
207B ILE* 4.2 16.6 - - + -
246B ILE* 4.2 9.9 - - + -
249B SER* 4.2 12.1 - - - -
250B ILE* 3.8 40.2 - - + -
253B VAL* 3.4 13.8 - - + +
308B ILE* 4.0 7.2 - - + -
312B SER* 3.4 26.5 - - - -
317B PRO* 4.3 8.5 - - + -
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Residues in contact with LEU 193 (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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189B SER 3.4 8.7 + - - +
190B ALA* 3.1 16.7 + - - +
192B PHE* 1.3 77.4 - - - +
194B LEU* 1.3 60.5 + - - +
195B ASN* 3.1 7.5 + - - +
249B SER* 4.1 22.0 - - - +
252B TYR* 3.9 28.7 - - + -
253B VAL* 3.7 9.3 - - + +
411B MPG 4.1 23.6 - - + -
414B MPG 4.1 24.7 - - + +
415B MPG 3.6 39.1 - - + +
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Residues in contact with LEU 194 (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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190B ALA 3.9 8.7 - - - +
191B LEU* 3.2 28.5 + - + +
192B PHE 3.1 1.4 + - - -
193B LEU* 1.3 73.9 - - - +
195B ASN* 1.3 72.3 + - - +
196B SER* 3.5 4.5 + - - +
199B THR* 3.5 30.7 - - + +
414B MPG 4.0 35.4 - - + -
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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
------------------------------------------------------------
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