Contacts of the helix formed by residues 231 - 248 (chain B) in PDB entry 3OUY
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 SER 231 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168B ARG* 3.1 34.9 + - - +
229B ASN 3.3 3.1 + - - -
230B LEU* 1.3 74.0 - - - +
232B LEU* 1.3 65.5 - - - +
233B ASP* 3.7 7.1 + - - +
234B ASN* 3.0 30.5 + - - +
235B LEU* 2.9 20.0 + - - +
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Residues in contact with LEU 232 (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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349A PHE* 4.1 12.8 - - + -
371A ASN* 3.7 30.5 - - + +
372A GLY* 3.7 9.0 - - - +
197B ARG* 3.9 41.3 - - + +
230B LEU 3.8 1.8 + - - -
231B SER* 1.3 72.4 - - - +
233B ASP* 1.3 60.7 + - - +
235B LEU* 3.3 12.9 + - + +
236B ALA* 2.8 28.1 + - - +
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Residues in contact with ASP 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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369A ILE* 4.0 7.4 - - + +
370A GLU* 3.4 11.3 - - - +
371A ASN* 2.8 22.3 + - - +
372A GLY 2.7 32.6 + - - -
231B SER* 3.2 5.7 + - - +
232B LEU* 1.3 78.6 - - - +
234B ASN* 1.3 51.9 + - - +
236B ALA* 3.3 9.0 - - - +
237B ARG* 2.8 58.6 + - - +
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Residues in contact with ASN 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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160B ILE* 3.1 34.7 - - + +
167B VAL 3.2 20.1 - - - +
168B ARG* 3.6 12.5 - - - +
170B PHE* 4.5 2.8 - - - -
230B LEU* 4.1 8.3 - - + -
231B SER* 3.0 24.8 + - - +
233B ASP* 1.3 73.5 - - - +
235B LEU* 1.3 61.3 + - - +
236B ALA 3.2 1.3 - - - -
237B ARG* 3.3 28.3 + - - +
238B PHE* 2.9 27.5 + - - +
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Residues in contact with LEU 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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349A PHE* 4.2 16.4 - - + -
170B PHE* 4.9 2.2 - - + -
195B TRP* 4.1 17.3 - - + -
196B THR 4.2 10.8 - - - +
197B ARG* 4.2 6.1 - - - -
214B PHE* 3.7 60.6 - - + -
230B LEU* 3.8 18.4 - - + +
231B SER 2.9 11.4 + - - +
232B LEU* 3.5 15.7 - - + +
234B ASN* 1.3 76.9 - - - +
236B ALA* 1.3 61.0 + - - +
238B PHE* 3.3 4.1 + - - +
239B VAL* 3.2 33.7 + - + +
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Residues in contact with ALA 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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349A PHE* 3.6 38.1 - - + +
369A ILE* 3.6 27.6 - - + +
372A GLY* 4.4 1.3 - - - -
232B LEU 2.8 14.9 + - - +
233B ASP* 3.3 11.4 - - - +
235B LEU* 1.3 78.2 - - - +
237B ARG* 1.3 59.7 + - - +
239B VAL* 3.9 4.0 - - - +
240B HIS* 3.5 22.3 + - - +
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Residues in contact with ARG 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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368A PHE* 5.4 1.0 - - - +
369A ILE* 3.3 45.3 + - + +
160B ILE* 5.0 8.3 - - + -
231B SER* 5.2 0.2 + - - -
233B ASP* 2.8 43.2 + - - +
234B ASN* 3.5 30.6 + - - +
235B LEU 3.2 0.4 - - - -
236B ALA* 1.3 71.9 - - - +
238B PHE* 1.3 59.8 + - - +
240B HIS* 3.5 2.9 + - - +
241B LEU* 3.0 40.6 + - + +
317B ARG* 4.6 12.7 - - - +
431B GLU* 5.0 7.3 + - - -
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Residues in contact with PHE 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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151B LEU* 4.4 16.6 - - + -
154B PHE* 4.4 18.8 - + - -
155B LEU* 3.9 26.2 - - + -
160B ILE* 4.2 10.3 - - + -
170B PHE* 3.7 24.0 - + + -
178B LEU* 5.6 2.5 - - + -
188B THR* 5.1 7.4 - - + -
189B VAL* 5.3 2.2 - - + -
192B ALA* 3.5 15.3 - - + -
195B TRP* 3.4 39.9 - + - -
234B ASN 2.9 16.6 + - - +
235B LEU* 3.3 4.9 + - + +
237B ARG* 1.3 77.4 - - - +
239B VAL* 1.3 59.6 + - + +
240B HIS 3.1 0.2 - - - -
241B LEU* 3.1 4.7 + - + +
242B CYS* 2.9 52.4 + - - -
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Residues in contact with VAL 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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349A PHE* 3.5 42.2 - - + +
192B ALA 3.3 27.6 - - - +
193B ARG* 3.9 9.8 - - - +
195B TRP* 4.0 29.4 - - + +
235B LEU* 3.2 16.4 + - + +
236B ALA 3.9 4.3 - - - +
238B PHE* 1.3 77.3 - - + +
240B HIS* 1.3 61.8 + - + +
242B CYS* 3.9 7.9 - - - +
243B ARG* 3.3 32.1 + - - +
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Residues in contact with HIS 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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349A PHE* 6.0 1.8 - - + +
355A VAL* 4.3 14.8 - - + +
356A LYS* 4.8 8.7 + - - +
359A LEU* 4.1 18.2 - - + +
366A ARG* 5.0 5.8 - - - -
369A ILE* 4.9 0.6 - - + +
374A TRP* 3.7 41.5 - + + +
236B ALA 3.5 15.4 + - - +
237B ARG* 3.5 5.5 + - - +
238B PHE 3.1 0.8 - - - -
239B VAL* 1.3 80.7 - - + +
241B LEU* 1.3 67.9 + - - +
242B CYS 3.2 1.3 - - - -
243B ARG* 3.4 20.9 + - + +
244B GLU* 3.0 53.3 + - + +
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Residues in contact with LEU 241 (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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154B PHE* 4.7 10.5 - - + -
158B ASN* 3.9 36.6 - - + +
160B ILE* 5.8 4.0 - - + -
237B ARG* 3.0 28.4 + - + +
238B PHE* 3.1 7.6 + - + +
240B HIS* 1.3 80.3 + - - +
242B CYS* 1.3 53.8 + - - +
244B GLU* 3.1 16.8 + - - +
245B PHE* 2.7 36.3 + - - +
253B PHE* 3.5 35.9 - - + -
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Residues in contact with CYS 242 (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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154B PHE* 4.5 4.0 - - - -
189B VAL* 3.6 37.0 - - + +
192B ALA* 3.7 13.5 - - + -
193B ARG* 3.8 9.0 - - + -
238B PHE* 2.9 52.5 + - - +
239B VAL 3.9 4.7 - - - +
241B LEU* 1.3 74.0 - - - +
243B ARG* 1.3 65.1 + - - +
245B PHE* 3.3 3.6 + - - +
246B MET* 3.0 30.5 + - - +
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Residues in contact with ARG 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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349A PHE 3.2 22.6 + - - -
350A GLU* 3.3 26.7 + - - +
351A ASP 4.4 0.8 - - - -
352A GLU* 3.4 53.6 + - - +
355A VAL* 4.9 6.5 - - - +
356A LYS* 4.1 21.6 + - - +
193B ARG* 3.4 45.0 + - + +
195B TRP 5.4 1.0 + - - -
239B VAL* 3.3 22.1 + - - +
240B HIS* 3.7 22.3 - - + +
241B LEU 3.4 0.4 - - - -
242B CYS* 1.3 77.9 - - - +
244B GLU* 1.3 60.5 + - - +
246B MET* 3.8 1.9 + - - +
247B GLU* 3.5 26.3 + - - +
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Residues in contact with GLU 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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356A LYS* 4.6 9.4 - - - +
359A LEU* 5.8 2.8 - - - +
366A ARG* 5.0 9.3 + - - -
240B HIS* 3.0 42.4 + - + +
241B LEU* 3.1 22.3 + - - +
243B ARG* 1.3 76.8 - - - +
245B PHE* 1.3 65.4 + - - +
247B GLU* 3.3 4.8 + - - +
248B ALA* 3.2 21.8 + - - +
253B PHE* 4.5 12.6 - - + -
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Residues in contact with PHE 245 (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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3B VAL* 4.5 6.1 - - + -
6B ILE* 4.4 9.0 - - + -
7B LEU* 4.7 10.3 - - + -
154B PHE* 3.9 14.8 - + + -
185B PHE* 4.6 13.9 - + - -
189B VAL* 4.5 8.5 - - + -
241B LEU 2.7 19.6 + - - +
242B CYS* 3.8 4.7 - - - +
244B GLU* 1.3 71.8 - - - +
246B MET* 1.3 89.6 + - + +
248B ALA 3.2 1.1 - - - -
249B PRO* 3.0 42.7 - - + +
250B SER 3.8 24.5 - - - -
253B PHE* 3.5 42.1 - + + -
254B PHE* 4.2 18.4 - + - -
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Residues in contact with MET 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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3B VAL* 4.2 20.5 - - + +
186B LEU* 4.9 13.7 - - + +
189B VAL* 3.8 16.4 - - + -
190B LYS* 4.2 24.0 - - - -
193B ARG* 3.3 34.5 - - - +
242B CYS 3.0 20.1 + - - +
243B ARG 4.1 3.4 - - - +
244B GLU 3.3 0.2 - - - -
245B PHE* 1.3 104.8 - - + +
247B GLU* 1.3 62.4 + - + +
249B PRO* 3.8 10.3 - - + +
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Residues in contact with GLU 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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356A LYS* 3.8 24.2 + - - +
193B ARG* 6.0 1.8 - - - +
243B ARG 3.5 14.4 + - - +
244B GLU* 3.3 5.4 + - - +
245B PHE 3.3 0.4 - - - -
246B MET* 1.3 80.1 - - + +
248B ALA* 1.3 59.4 + - + +
249B PRO* 3.9 3.6 - - - +
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Residues in contact with ALA 248 (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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244B GLU 3.2 11.7 + - - +
245B PHE 3.2 4.7 - - - +
247B GLU* 1.3 79.6 - - + +
249B PRO* 1.4 67.4 - - - +
250B SER* 3.5 4.9 + - - -
253B PHE* 4.0 15.2 - - - -
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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