Contacts of the helix formed by residues 236 - 253 (chain C) in PDB entry 4J1R
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 236 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173C HIS* 3.2 56.6 + - - +
176C GLY* 5.9 2.9 - - - -
177C ILE 4.6 2.5 - - - -
178C CYS* 3.6 20.2 - - - -
207C LEU* 4.0 4.9 - - - +
235C THR* 1.3 71.3 - - - +
237C SER* 1.3 56.8 + - - +
238C ILE 3.0 6.3 - - - -
239C ASP* 3.1 18.3 + - - +
240C VAL* 3.8 1.2 + - - +
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Residues in contact with SER 237 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226C GLU* 4.4 1.7 + - - -
235C THR* 2.7 24.1 + - - -
236C SER* 1.3 79.1 + - - +
238C ILE* 1.3 61.6 + - - +
239C ASP 3.2 0.4 - - - -
240C VAL* 3.4 18.2 + - - +
241C TRP 3.3 11.6 + - - -
325C PRO* 3.5 37.9 - - - +
328C ARG* 3.1 19.5 + - - -
329C LEU 6.0 0.4 - - - -
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Residues in contact with ILE 238 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178C CYS* 3.5 23.1 - - - -
180C ARG* 4.1 14.4 - - + -
217C ILE* 4.9 1.1 - - + -
218C CYS* 5.8 2.9 - - + -
224C ALA* 3.8 21.0 + - + +
226C GLU* 3.3 22.9 - - + +
227C LEU* 4.1 17.5 - - + -
234C TYR* 3.7 41.7 - - + -
235C THR 3.3 11.7 - - - +
236C SER 3.0 1.0 - - - -
237C SER* 1.3 75.5 - - - +
239C ASP* 1.3 72.7 + - - +
241C TRP* 3.1 5.5 + - - +
242C SER* 3.1 24.4 + - - +
328C ARG* 4.1 1.3 - - - +
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Residues in contact with ASP 239 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169C LEU* 4.2 9.9 - - + +
172C ILE* 4.6 0.5 - - - +
173C HIS* 3.1 24.1 - - + +
178C CYS* 3.3 13.3 - - - -
179C HIS* 2.7 28.6 + - - +
180C ARG* 3.0 24.2 + - - -
182C ILE* 3.8 24.3 + - + +
236C SER 3.1 9.0 + - - +
238C ILE* 1.3 84.5 - - - +
240C VAL* 1.3 56.6 + - - +
242C SER* 3.2 6.2 + - - -
243C ALA* 2.8 29.3 + - - +
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Residues in contact with VAL 240 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166C PHE* 5.1 5.2 - - + -
169C LEU* 5.0 4.0 - - + -
173C HIS* 4.7 2.9 - - + +
236C SER 4.2 3.6 - - - +
237C SER* 3.4 23.8 - - - +
238C ILE 3.2 0.4 - - - -
239C ASP* 1.3 74.2 - - - +
241C TRP* 1.3 62.9 + - - +
243C ALA* 3.4 7.6 + - - +
244C GLY* 3.0 19.6 + - - -
320C LEU* 3.7 29.8 - - + +
328C ARG* 4.1 14.4 - - + -
329C LEU 3.3 28.3 - - - +
331C PRO* 4.2 22.9 - - + -
334C ALA* 6.3 0.2 - - + -
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Residues in contact with TRP 241 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221C TYR 5.1 0.6 + - - -
222C TYR 3.6 7.4 - - - -
223C ARG 3.3 11.9 + - - -
224C ALA* 3.5 24.2 - - + -
225C PRO* 3.4 26.5 - - + -
237C SER 3.3 2.6 + - - -
238C ILE 3.1 9.7 + - - +
240C VAL* 1.3 79.0 - - - +
242C SER* 1.3 64.1 + - - +
244C GLY 3.0 10.9 + - - -
245C CYS* 3.0 24.4 + - - -
257C PHE* 3.5 24.8 - + - -
269C ILE* 3.5 21.8 - - + +
273C LEU* 3.8 21.3 - - + -
320C LEU 4.4 4.7 - - - -
321C LEU* 3.3 44.5 - - + +
322C GLU 3.5 27.4 - - - -
328C ARG* 3.8 18.8 - - - +
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Residues in contact with SER 242 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182C ILE* 3.5 35.1 - - - +
218C CYS* 3.5 14.0 - - - -
222C TYR* 2.5 32.1 + - - -
238C ILE* 3.1 11.0 + - - +
239C ASP* 3.2 6.3 + - - -
241C TRP* 1.3 78.3 - - - +
243C ALA* 1.3 57.7 - - - +
245C CYS* 3.1 6.9 + - - +
246C VAL* 3.0 28.8 + - - +
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Residues in contact with ALA 243 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162C MET* 3.3 13.1 - - - +
165C LEU* 3.9 23.8 - - + -
166C PHE* 3.8 25.4 - - + -
169C LEU* 4.3 7.2 - - + -
182C ILE* 4.0 4.6 - - + +
239C ASP 2.8 16.8 + - - +
240C VAL* 3.5 7.4 - - - +
241C TRP 3.2 0.2 - - - -
242C SER* 1.3 76.3 - - - +
244C GLY* 1.3 56.3 + - - +
246C VAL* 3.2 3.4 + - - +
247C LEU 3.0 23.6 + - - -
320C LEU* 4.5 0.7 - - - -
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Residues in contact with GLY 244 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240C VAL 3.0 8.4 + - - -
241C TRP 3.0 8.2 + - - -
243C ALA* 1.3 76.7 - - - +
245C CYS* 1.3 57.4 + - - +
247C LEU* 3.7 3.5 - - - +
248C ALA* 3.0 30.0 + - - +
317C CYS* 4.4 3.1 - - - -
320C LEU* 3.5 24.8 - - - +
321C LEU* 3.9 18.3 - - - +
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Residues in contact with CYS 245 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221C TYR 3.7 16.8 - - - +
222C TYR* 3.5 21.2 - - + -
241C TRP* 3.0 43.9 + - - -
242C SER 3.2 10.5 - - - +
244C GLY* 1.3 77.9 - - - +
246C VAL* 1.3 58.5 + - - +
248C ALA* 4.0 1.7 - - - +
249C GLU* 3.2 26.2 + - - +
255C PRO* 5.6 0.2 - - - +
256C ILE* 4.3 14.9 + - + +
257C PHE* 4.0 16.4 - - - -
321C LEU* 4.0 5.8 - - - -
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Residues in contact with VAL 246 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139C VAL* 5.0 2.9 - - + -
162C MET* 4.0 15.5 - - + -
165C LEU* 4.8 0.9 - - + -
182C ILE* 4.3 15.9 - - + -
183C LYS 4.5 0.4 - - - -
184C PRO* 3.9 33.4 - - + +
187C LEU* 4.2 20.4 - - + -
222C TYR* 4.3 7.0 - - + -
242C SER 3.0 21.0 + - - +
243C ALA* 3.2 8.7 + - - +
245C CYS* 1.3 73.9 - - - +
247C LEU* 1.3 67.7 + - - +
249C GLU* 3.2 6.0 + - - +
250C LEU* 3.0 37.9 + - + +
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Residues in contact with LEU 247 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158C VAL* 3.7 26.9 - - + -
162C MET* 3.8 23.8 - - + -
243C ALA 3.0 15.8 + - - +
244C GLY* 3.7 5.4 - - - +
246C VAL* 1.3 77.9 - - - +
248C ALA* 1.3 62.5 + - - +
250C LEU* 3.1 13.2 + - - +
251C LEU* 3.1 22.4 + - + +
313C ALA* 4.4 4.7 - - + +
316C LEU* 3.7 35.4 - - + -
317C CYS* 3.7 22.4 - - - -
320C LEU* 4.2 9.6 - - + -
339C PHE* 4.3 9.9 - - + -
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Residues in contact with ALA 248 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244C GLY 3.0 17.7 + - - +
245C CYS 4.0 0.2 - - - +
247C LEU* 1.3 76.2 - - - +
249C GLU* 1.3 57.4 + - - +
251C LEU* 3.1 3.8 + - - +
252C LEU* 2.9 35.5 + - - +
256C ILE* 3.9 38.8 - - + -
305C PHE* 4.2 16.6 - - + -
317C CYS* 4.2 10.3 - - - -
321C LEU* 4.8 2.0 - - + -
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Residues in contact with GLU 249 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140C TYR* 4.8 12.5 - - - -
143C ALA* 5.4 10.9 - - + +
184C PRO* 4.2 13.2 - - + +
222C TYR* 2.7 38.7 + - - -
245C CYS 3.2 12.6 + - - +
246C VAL* 3.2 6.3 + - - +
248C ALA* 1.3 78.5 - - - +
250C LEU* 1.3 62.5 + - + +
253C GLY* 2.9 27.1 + - - -
254C GLN* 3.4 26.2 - - - +
255C PRO* 3.8 27.1 - - + +
256C ILE 5.0 0.6 - - - +
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Residues in contact with LEU 250 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139C VAL* 3.9 27.6 - - + -
143C ALA* 4.0 22.0 - - + -
152C THR* 3.5 12.1 + - - +
153C LEU* 4.5 24.3 + - + +
158C VAL* 4.1 40.9 - - + +
161C TYR* 5.1 7.6 - - + -
162C MET* 4.3 11.9 - - + -
184C PRO* 6.1 2.2 - - + -
246C VAL* 3.0 29.3 + - + +
247C LEU* 3.1 7.2 + - - +
249C GLU* 1.3 80.7 - - + +
251C LEU* 1.3 61.3 + - - +
252C LEU 3.4 0.2 - - - -
253C GLY* 4.4 1.3 + - - -
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Residues in contact with LEU 251 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152C THR* 3.3 15.1 + - - +
155C VAL* 5.7 5.6 - - + -
158C VAL* 4.5 18.8 - - + -
247C LEU* 3.4 23.6 - - + +
248C ALA 3.1 6.6 + - - +
250C LEU* 1.3 79.5 - - - +
252C LEU* 1.3 60.8 + - - +
305C PHE* 4.0 27.4 - - + -
306C ARG* 4.0 15.9 + - - +
309C THR* 4.3 20.4 + - + -
310C PRO* 5.0 7.0 - - + -
313C ALA* 3.7 33.4 - - + -
314C ILE 4.8 0.2 - - - +
317C CYS* 4.2 11.0 - - - -
339C PHE* 5.4 1.6 - - + -
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Residues in contact with LEU 252 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152C THR* 4.5 1.3 - - - -
248C ALA 2.9 18.2 + - - +
251C LEU* 1.3 80.9 - - - +
253C GLY* 1.3 58.4 + - - +
254C GLN* 3.2 30.8 + - + +
255C PRO 5.0 0.7 - - - +
256C ILE* 4.0 33.7 - - + -
304C VAL* 3.6 28.3 - - + +
305C PHE* 3.7 30.5 - - + -
306C ARG* 3.7 28.9 + - + +
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Residues in contact with GLY 253 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143C ALA* 5.7 4.3 - - - -
147C SER* 3.1 35.0 + - - -
151C GLN 5.5 3.6 - - - -
152C THR* 4.4 6.9 + - - -
249C GLU* 2.9 13.9 + - - -
250C LEU 4.4 2.1 - - - -
251C LEU 3.7 1.2 - - - -
252C LEU* 1.3 76.4 - - - +
254C GLN* 1.3 62.5 + - - +
306C ARG* 5.2 3.4 - - - -
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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
------------------------------------------------------------
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