Contacts of the helix formed by residues 239 - 257 (chain B) in PDB entry 3OP5
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 239 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174B VAL* 3.5 16.3 - - - +
204B TYR* 4.6 2.7 - - - -
210B HIS* 3.9 17.3 - - - -
231B ASP* 4.2 2.8 + - - +
237B ALA 3.7 0.6 + - - -
238B PRO* 1.3 75.3 - - - +
240B ARG* 1.3 65.8 + - - +
241B ARG* 3.4 11.8 - - - +
242B GLY* 3.3 13.5 + - - +
243B ASP* 3.5 8.3 + - - +
311B TYR* 2.8 51.1 + - - -
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Residues in contact with ARG 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B HIS* 3.4 32.9 - - + +
170B GLU* 4.4 8.3 + - - -
174B VAL* 3.6 2.4 - - + +
204B TYR* 3.3 39.7 + - + -
205B CYS* 5.8 1.8 - - - -
210B HIS* 3.9 12.7 + - - -
239B SER* 1.3 75.5 - - - +
241B ARG* 1.4 62.3 + - - +
243B ASP* 3.2 15.1 + - - +
244B LEU* 3.4 16.6 + - - +
311B TYR 4.8 1.3 + - - +
312B THR 3.0 27.3 + - - -
313B GLU 3.8 7.0 + - - +
314B LYS* 3.5 39.8 - - - +
315B PRO* 3.7 13.7 - - + -
317B TYR* 3.6 15.9 + - - -
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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
----------------------------------------------------------
213B TYR* 4.2 8.3 + - - -
231B ASP* 2.8 39.1 + - - +
239B SER* 3.8 8.5 + - - +
240B ARG* 1.4 76.7 - - - +
242B GLY* 1.3 60.2 + - - +
244B LEU* 3.3 5.0 + - - +
245B GLU* 3.0 28.5 + - - +
279B ARG* 4.5 4.6 - - - +
306B VAL* 3.7 8.2 - - + +
309B LEU* 3.0 60.0 + - + +
310B ASP* 3.5 14.4 + - - +
311B TYR* 3.4 28.9 + - - +
313B GLU 5.3 2.3 + - - +
367B EDO 3.4 28.0 + - - -
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Residues in contact with GLY 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B SER* 3.6 23.7 - - - -
231B ASP* 4.8 2.7 - - - -
238B PRO* 6.1 2.0 - - - -
239B SER* 3.3 11.4 + - - -
240B ARG 3.2 0.8 - - - -
241B ARG* 1.3 83.0 - - - +
243B ASP* 1.4 56.0 + - - +
245B GLU* 3.2 4.6 + - - +
246B ILE* 2.9 39.2 + - - +
367B EDO 4.5 3.6 - - - -
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Residues in contact with ASP 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B LEU* 3.6 12.8 - - + +
169B HIS* 2.7 30.3 + - + +
174B VAL* 3.4 10.9 - - - +
175B HIS 2.9 21.7 + - - -
176B GLY* 2.8 31.0 + - - -
178B ILE* 3.6 25.0 - - + +
238B PRO* 5.5 0.9 - - - +
239B SER 3.5 3.3 + - - +
240B ARG 3.2 10.4 + - - +
242B GLY* 1.4 74.4 - - - +
244B LEU* 1.3 56.8 + - - +
246B ILE* 3.6 2.3 + - - -
247B LEU* 3.2 24.6 + - - +
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Residues in contact with LEU 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B LEU* 3.7 29.8 - - + -
165B LEU* 4.0 15.3 - - + -
169B HIS* 4.9 2.2 - - + -
240B ARG 3.6 9.2 - - - +
241B ARG 3.3 6.5 + - - +
242B GLY 3.3 0.4 - - - -
243B ASP* 1.3 74.5 - - - +
245B GLU* 1.3 60.9 + - - +
247B LEU* 3.5 1.5 + - - -
248B GLY 3.1 14.7 + - - -
302B TYR* 2.6 29.7 + - - +
306B VAL* 3.8 12.6 - - + -
309B LEU* 3.7 13.5 - - + -
315B PRO* 3.6 37.7 - - + -
317B TYR* 4.6 9.9 - - + -
320B LEU* 3.7 16.8 - - + -
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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
----------------------------------------------------------
229B SER* 3.6 5.0 - - - -
230B ILE* 3.2 30.5 + - - +
241B ARG 3.0 12.6 + - - +
242B GLY 3.2 8.7 + - - +
244B LEU* 1.3 73.9 - - - +
246B ILE* 1.4 63.3 + - - +
248B GLY* 3.0 12.9 + - - -
249B TYR* 2.6 51.3 + - + +
279B ARG* 5.8 1.6 - - - -
302B TYR* 5.4 0.4 - - - -
303B MET* 5.0 6.6 - - + +
306B VAL* 3.9 13.9 - - + +
367B EDO 2.6 37.9 + - - -
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Residues in contact with ILE 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B GLY* 3.5 38.1 - - - +
177B ASP* 4.8 0.7 - - - -
178B ILE* 3.2 41.1 - - + +
227B PHE* 3.3 31.1 - - + +
228B THR* 4.0 4.0 - - - +
229B SER* 3.8 18.8 - - - +
238B PRO* 6.4 0.4 - - + -
242B GLY 2.9 26.9 + - - +
243B ASP* 3.7 7.9 - - - +
245B GLU* 1.4 73.9 - - - +
247B LEU* 1.4 61.7 + - - +
249B TYR* 3.2 6.3 + - - +
250B CYS* 3.0 21.1 + - - -
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Residues in contact with LEU 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B SER* 3.9 27.6 - - - +
161B ILE* 3.8 45.8 - - + -
162B LEU* 3.9 22.0 - - + -
165B LEU* 4.5 6.3 - - + -
178B ILE* 4.9 6.0 - - + +
243B ASP 3.2 13.8 + - - +
244B LEU* 3.6 2.0 - - - +
245B GLU 3.3 0.4 - - - -
246B ILE* 1.4 74.5 - - - +
248B GLY* 1.3 57.2 + - - +
250B CYS* 3.2 8.7 + - + +
251B MET* 2.9 39.1 + - + +
254B TRP* 4.5 9.2 - - + -
302B TYR* 3.6 25.1 - - + +
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Residues in contact with GLY 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B LEU 3.1 7.3 + - - -
245B GLU 3.0 9.5 + - - -
247B LEU* 1.3 75.0 - - - +
249B TYR* 1.3 60.2 + - - +
251B MET* 3.3 22.8 + - - +
252B ILE* 3.3 24.8 + - - +
299B ILE* 5.3 0.3 - - - +
302B TYR* 3.8 5.1 - - - -
303B MET* 3.8 23.2 - - - +
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Residues in contact with TYR 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B PHE* 3.3 35.4 - - + -
228B THR 3.5 15.5 - - - -
230B ILE* 4.1 4.0 - - - +
245B GLU* 2.6 49.0 + - + +
246B ILE 3.2 4.4 + - - +
248B GLY* 1.3 71.1 - - - +
250B CYS* 1.4 59.8 + - - +
252B ILE* 3.4 6.5 + - + +
253B GLN* 3.1 28.8 + - - +
259B LEU* 3.5 18.1 - - + +
261B TRP* 3.7 25.4 - + - -
275B LYS* 3.5 33.2 + - + +
278B TYR* 6.3 1.3 - - + -
279B ARG* 5.5 1.6 - - - +
285B LEU* 5.2 3.1 - - + -
303B MET* 3.8 23.5 - - + +
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Residues in contact with CYS 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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178B ILE* 3.4 31.9 - - - -
179B LYS* 3.9 15.0 - - - -
227B PHE* 4.2 15.2 - - - -
246B ILE 3.0 15.9 + - - +
247B LEU* 3.3 12.3 - - + +
249B TYR* 1.4 74.2 - - - +
251B MET* 1.4 52.7 + - - +
253B GLN* 3.3 6.7 + - - +
254B TRP* 2.9 68.1 + - + +
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Residues in contact with MET 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B VAL* 3.8 17.2 - - + +
155B LEU* 5.9 0.4 - - - -
158B SER* 3.3 35.2 - - - +
247B LEU* 2.9 20.0 + - + +
248B GLY* 3.3 14.1 + - - +
250B CYS* 1.4 75.2 - - - +
252B ILE* 1.3 56.3 + - + +
254B TRP* 3.4 5.4 + - + +
255B LEU* 3.0 36.9 + - - +
299B ILE* 3.9 31.9 - - + -
302B TYR* 3.5 44.9 - - + -
303B MET* 5.4 0.2 - - - -
324B LEU* 4.2 10.8 - - + -
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Residues in contact with ILE 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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248B GLY 3.3 15.7 + - - +
249B TYR* 3.8 10.8 - - + +
250B CYS 3.4 0.2 - - - -
251B MET* 1.3 74.5 - - - +
253B GLN* 1.3 55.0 + - - +
255B LEU* 3.3 4.3 + - - -
256B THR* 2.8 41.6 + - + +
258B HIS 3.9 5.4 - - - +
259B LEU* 3.8 14.4 - - + -
285B LEU* 3.8 32.1 - - + -
286B MET* 4.2 9.6 - - + -
289B CYS* 3.6 32.1 - - + -
290B PHE* 4.4 8.7 - - + -
299B ILE* 4.0 18.6 - - + -
303B MET* 4.1 11.2 - - + -
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Residues in contact with GLN 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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142B TYR* 2.7 51.3 + - + +
147B LYS* 4.2 9.3 - - - +
226B GLU* 5.4 1.9 - - - +
227B PHE* 3.8 28.5 - - + -
249B TYR 3.1 17.4 + - - +
250B CYS 3.5 4.7 - - - +
252B ILE* 1.3 75.9 - - - +
254B TRP* 1.3 62.6 + - + +
257B GLY* 2.8 35.6 + - - -
258B HIS* 3.6 16.2 - - - +
259B LEU* 3.5 24.7 + - + +
262B GLU* 4.3 6.0 + - - +
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Residues in contact with TRP 254 (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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138B LEU* 5.0 2.0 - - + -
142B TYR* 3.7 22.2 - + - -
148B ARG* 3.5 6.6 - - - -
149B PHE* 2.9 45.6 + + + -
154B VAL* 3.7 21.5 - - + -
157B LEU* 4.1 26.2 - - + -
158B SER* 4.5 9.2 - - - -
161B ILE* 3.8 18.2 - - + -
178B ILE* 5.5 0.7 - - + -
180B ALA* 3.8 31.2 - - + +
183B LEU* 3.7 31.2 - - + -
227B PHE* 5.8 2.6 - - - -
247B LEU* 4.5 3.4 - - + -
250B CYS* 2.9 48.5 + - + +
251B MET* 3.8 6.7 - - - +
253B GLN* 1.3 84.8 - - + +
255B LEU* 1.3 61.2 + - - +
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Residues in contact with LEU 255 (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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148B ARG* 3.7 13.1 + - - -
149B PHE 3.9 7.5 - - - +
151B ARG* 3.7 39.7 - - + +
154B VAL* 3.8 18.4 - - + -
251B MET 3.0 21.6 + - - +
252B ILE 3.3 3.1 + - - +
254B TRP* 1.3 79.9 - - - +
256B THR* 1.3 57.6 + - - +
290B PHE* 4.1 23.3 - - + -
296B PRO* 4.2 8.5 - - + -
298B GLU* 5.9 0.2 - - - +
299B ILE* 3.8 34.8 - - + -
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Residues in contact with THR 256 (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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148B ARG* 3.1 23.5 + - - +
252B ILE* 2.8 27.8 + - + +
255B LEU* 1.3 72.6 - - - +
257B GLY* 1.3 57.7 + - - +
258B HIS* 2.9 38.2 + - - +
289B CYS* 3.3 33.6 - - + +
290B PHE* 3.5 31.0 - - + -
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Residues in contact with GLY 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B TYR* 3.2 2.1 + - - -
147B LYS* 3.2 37.6 + - - +
148B ARG* 3.4 6.4 + - - -
253B GLN* 2.8 35.2 + - - -
255B LEU 3.8 1.0 - - - -
256B THR* 1.3 70.3 - - - +
258B HIS* 1.4 72.5 + - - +
262B GLU* 4.1 1.9 - - - +
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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
------------------------------------------------------------
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