Contacts of the helix formed by residues 239 - 257 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174D VAL* 3.5 17.5 - - - +
204D TYR* 4.6 3.4 - - - -
210D HIS* 3.9 17.5 - - - -
231D ASP* 4.2 2.6 + - - -
237D ALA 3.6 1.0 + - - -
238D PRO* 1.3 74.5 - - - +
240D ARG* 1.3 66.3 + - - +
241D ARG* 3.4 11.9 - - - +
242D GLY* 3.3 12.7 + - - +
243D ASP* 3.5 8.1 + - - +
311D TYR* 2.7 50.7 + - - -
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Residues in contact with ARG 240 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169D HIS* 3.4 32.1 - - + +
170D GLU* 4.5 8.3 + - - -
174D VAL* 3.7 2.2 - - + +
204D TYR* 3.2 38.9 + - + -
205D CYS* 5.8 0.6 - - - -
210D HIS* 3.8 12.7 + - - -
239D SER* 1.3 75.5 - - - +
241D ARG* 1.4 62.6 + - - +
243D ASP* 3.2 14.9 + - - +
244D LEU* 3.4 17.2 + - - +
311D TYR 4.8 0.6 + - - +
312D THR 3.0 26.5 + - - -
313D GLU 3.7 6.9 + - - +
314D LYS* 3.5 39.6 - - - +
315D PRO* 3.7 14.6 - - + -
317D TYR* 3.5 16.2 - - - -
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Residues in contact with ARG 241 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B ARG* 5.9 1.6 - - - +
213D TYR* 4.2 8.7 - - - -
231D ASP* 2.8 40.7 + - - +
239D SER* 3.8 9.1 + - - +
240D ARG* 1.4 76.1 - - - +
242D GLY* 1.3 59.8 + - - +
244D LEU* 3.3 5.6 + - - +
245D GLU* 2.9 31.6 + - - +
279D ARG* 4.4 13.5 - - - +
306D VAL* 3.7 8.2 - - + +
309D LEU* 3.0 58.2 + - + +
310D ASP* 3.5 15.3 + - - +
311D TYR* 3.4 27.5 + - - +
313D GLU 5.3 1.8 + - - +
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Residues in contact with GLY 242 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229D SER* 3.7 23.4 - - - -
231D ASP* 4.8 4.5 - - - -
238D PRO* 6.0 2.0 - - - -
239D SER* 3.3 11.4 + - - -
240D ARG 3.2 1.2 - - - -
241D ARG* 1.3 84.1 - - - +
243D ASP* 1.4 55.0 + - - +
245D GLU* 3.2 6.2 + - - +
246D ILE* 2.9 39.3 + - - +
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Residues in contact with ASP 243 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165D LEU* 3.6 12.5 - - + +
169D HIS* 2.7 31.3 + - + +
174D VAL* 3.5 10.0 - - - +
175D HIS 3.0 21.5 + - - -
176D GLY* 2.8 31.1 + - - -
178D ILE* 3.6 25.2 - - + +
238D PRO* 5.5 0.9 - - - +
239D SER 3.5 3.4 + - - +
240D ARG 3.2 10.6 + - - +
242D GLY* 1.4 73.6 - - - +
244D LEU* 1.3 58.1 + - - +
246D ILE* 3.6 1.9 + - - -
247D LEU* 3.2 24.1 + - - +
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Residues in contact with LEU 244 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162D LEU* 3.7 30.5 - - + -
165D LEU* 4.0 15.0 - - + -
169D HIS* 4.9 1.6 - - + -
240D ARG 3.6 9.2 - - - +
241D ARG 3.3 6.9 + - - +
243D ASP* 1.3 74.3 - - - +
245D GLU* 1.4 59.7 + - - +
247D LEU* 3.5 1.6 + - - -
248D GLY 3.1 15.6 + - - -
302D TYR* 2.6 30.1 + - - +
306D VAL* 3.8 12.8 - - + -
309D LEU* 3.7 14.1 - - + -
315D PRO* 3.6 38.8 - - + -
317D TYR* 4.7 10.5 - - + -
320D LEU* 3.7 14.4 - - + -
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Residues in contact with GLU 245 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229D SER* 3.6 8.4 - - - -
230D ILE* 3.2 43.9 + - - +
231D ASP* 4.8 3.1 + - - +
241D ARG* 2.9 14.4 + - - +
242D GLY* 3.2 11.2 + - - +
244D LEU* 1.4 73.6 - - - +
246D ILE* 1.4 64.4 + - - +
248D GLY* 3.0 12.5 + - - -
249D TYR* 2.6 53.2 + - + +
279D ARG* 5.5 5.2 + - - -
302D TYR* 5.4 0.4 - - - -
303D MET* 5.0 6.1 - - + +
306D VAL* 3.8 14.4 - - + +
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Residues in contact with ILE 246 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176D GLY* 3.5 37.7 - - - +
177D ASP* 4.2 1.3 - - - +
178D ILE* 3.1 41.7 - - + +
227D PHE* 3.2 30.7 + - + +
228D THR* 4.1 4.3 - - - +
229D SER* 3.8 19.3 - - - +
242D GLY 2.9 26.0 + - - +
243D ASP* 3.7 7.9 - - - +
245D GLU* 1.4 74.4 - - - +
247D LEU* 1.4 61.1 + - - +
249D TYR* 3.2 6.1 + - - +
250D CYS* 3.0 21.7 + - - -
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Residues in contact with LEU 247 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158D SER* 3.9 27.1 - - - +
161D ILE* 3.8 45.8 - - + -
162D LEU* 3.9 22.0 - - + -
165D LEU* 4.5 6.1 - - + -
178D ILE* 4.8 6.0 - - + +
243D ASP 3.2 14.0 + - - +
244D LEU* 3.6 8.1 - - - +
245D GLU 3.3 0.2 - - - -
246D ILE* 1.4 74.3 - - - +
248D GLY* 1.3 57.5 + - - +
250D CYS* 3.1 8.3 + - + +
251D MET* 2.9 39.6 + - + +
254D TRP* 4.5 9.0 - - + -
302D TYR* 3.6 18.2 - - + +
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Residues in contact with GLY 248 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244D LEU 3.1 7.7 + - - -
245D GLU 3.0 8.7 + - - -
247D LEU* 1.3 75.6 - - - +
249D TYR* 1.4 59.6 + - - +
251D MET* 3.3 12.1 + - - +
252D ILE* 3.3 24.9 + - - +
299D ILE* 5.3 0.2 - - - +
302D TYR* 3.7 20.3 - - - -
303D MET* 3.8 20.0 - - - +
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Residues in contact with TYR 249 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227D PHE* 3.3 38.1 - - + -
228D THR 3.5 14.1 - - - -
230D ILE* 4.1 4.0 - - - +
245D GLU* 2.6 48.5 + - + +
246D ILE 3.2 4.7 + - - +
248D GLY* 1.4 70.3 - - - +
250D CYS* 1.4 59.0 + - - +
252D ILE* 3.5 5.6 + - + +
253D GLN* 3.1 28.6 + - - +
259D LEU* 3.5 17.6 - - + +
261D TRP* 3.7 24.9 - + - -
275D LYS* 3.6 32.2 + - + +
278D TYR* 6.4 0.9 - - + -
279D ARG* 5.5 2.1 - - - +
285D LEU* 5.2 3.6 - - + -
303D MET* 3.8 23.1 - - + -
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Residues in contact with CYS 250 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178D ILE* 3.4 32.3 - - - -
179D LYS* 3.9 15.3 - - - -
227D PHE* 4.2 15.0 - - - -
246D ILE 3.0 16.9 + - - +
247D LEU* 3.1 11.9 + - - +
249D TYR* 1.4 74.0 - - - +
251D MET* 1.4 52.7 + - - +
253D GLN* 3.3 6.0 + - - +
254D TRP* 2.9 68.5 + - + +
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Residues in contact with MET 251 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154D VAL* 3.8 18.1 - - + +
155D LEU* 5.9 0.4 - - - -
158D SER* 3.3 35.4 - - - +
247D LEU* 2.9 20.5 + - + +
248D GLY* 3.3 13.2 + - - +
250D CYS* 1.4 74.0 - - - +
252D ILE* 1.4 56.4 + - + +
254D TRP* 3.4 5.4 + - + +
255D LEU* 3.0 36.0 + - - +
299D ILE* 3.9 31.0 - - + -
302D TYR* 3.5 45.3 - - + -
303D MET* 5.4 0.2 - - - -
324D LEU* 4.2 11.2 - - + -
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Residues in contact with ILE 252 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248D GLY 3.3 14.6 + - - +
249D TYR* 3.8 11.9 - - + +
250D CYS 3.4 0.2 - - - -
251D MET* 1.4 71.0 - - - +
253D GLN* 1.3 55.4 + - - +
255D LEU* 3.3 6.9 + - - -
256D THR* 2.7 44.4 + - + +
258D HIS 3.9 5.6 - - - +
259D LEU* 3.8 13.9 - - + -
285D LEU* 3.8 31.6 - - + -
286D MET* 4.2 9.9 - - + -
289D CYS* 3.6 32.5 - - + -
290D PHE* 4.7 7.6 - - + -
299D ILE* 4.0 19.3 - - + -
303D MET* 4.1 12.1 - - + -
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Residues in contact with GLN 253 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142D TYR* 2.8 46.1 + - + +
147D LYS* 5.5 2.2 - - - +
226D GLU* 5.6 0.9 - - - +
227D PHE* 3.8 27.1 - - + -
249D TYR 3.1 18.6 + - - +
250D CYS 3.5 4.5 - - - +
252D ILE* 1.3 75.1 - - - +
254D TRP* 1.3 63.4 + - + +
257D GLY* 2.8 40.2 + - - -
258D HIS* 3.6 15.9 + - - +
259D LEU* 3.5 24.0 + - + +
262D GLU* 4.3 6.3 + - - +
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Residues in contact with TRP 254 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138D LEU* 5.0 1.8 - - + -
142D TYR* 3.7 20.0 - + - -
147D LYS 4.4 0.2 - - - +
148D ARG* 3.5 7.1 - - - -
149D PHE* 2.9 46.7 + + + -
154D VAL* 3.7 21.8 - - + -
157D LEU* 4.1 26.0 - - + -
158D SER* 4.5 9.2 - - - -
161D ILE* 3.8 17.7 - - + -
178D ILE* 5.5 0.4 - - + -
180D ALA* 3.8 26.8 - - + +
183D LEU* 3.7 31.0 - - + -
227D PHE* 5.8 2.6 - - - -
247D LEU* 4.5 4.0 - - + -
250D CYS* 2.9 53.0 + - + +
251D MET* 3.8 6.5 - - - +
253D GLN* 1.3 86.1 - - + +
255D LEU* 1.3 60.8 + - - +
256D THR 3.8 0.2 + - - -
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Residues in contact with LEU 255 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148D ARG* 3.7 12.7 + - - +
149D PHE 3.9 7.9 - - - +
151D ARG* 3.7 39.9 - - + +
154D VAL* 3.8 18.4 - - + -
251D MET 3.0 22.0 + - - +
252D ILE 3.3 3.3 + - - +
254D TRP* 1.3 77.7 - - - +
256D THR* 1.3 63.7 + - + +
290D PHE* 4.4 11.8 - - + -
296D PRO* 4.2 13.9 - - + -
298D GLU* 5.9 0.2 - - - +
299D ILE* 3.8 35.4 - - + -
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Residues in contact with THR 256 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148D ARG* 3.1 23.4 + - - +
252D ILE* 2.7 27.9 + - - +
255D LEU* 1.3 72.4 - - - +
257D GLY* 1.3 57.1 + - - +
258D HIS* 2.9 38.9 + - - +
289D CYS* 3.3 32.7 - - + +
290D PHE* 3.5 32.3 - - + -
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Residues in contact with GLY 257 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142D TYR* 3.2 3.2 + - - -
147D LYS* 3.2 33.2 + - - +
148D ARG* 3.4 7.1 + - - -
253D GLN* 2.8 31.3 + - - -
255D LEU 3.8 1.0 - - - -
256D THR* 1.3 75.3 - - - +
258D HIS* 1.4 72.9 + - - +
262D GLU* 4.1 1.7 - - - +
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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