Contacts of the helix formed by residues 237 - 252 (chain C) in PDB entry 1OJ7
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 ASN 237 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234C GLU* 2.8 46.8 + - + +
235C PRO 3.4 0.6 - - - -
236C GLU* 1.3 74.6 - - - +
238C TYR* 1.3 63.5 + - - +
239C ASP* 3.2 13.2 + - - +
240C VAL* 3.2 32.5 + - + +
241C ARG* 3.0 24.4 + - - +
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Residues in contact with TYR 238 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0B GLY* 5.6 1.3 - - - -
1B LEU* 4.3 22.7 + - + -
2B ASN 5.8 0.2 - - - -
3B ASN* 4.1 4.0 + - - -
14C PHE* 4.2 4.3 - - - -
15C GLY* 3.2 12.1 - - - -
16C LYS* 3.0 43.3 + - + -
177C PRO* 3.7 31.3 - - + +
178C VAL* 4.1 8.1 - - + -
181C TYR* 3.2 24.2 - - - +
236C GLU 3.2 6.2 + - - +
237C ASN* 1.3 71.1 + - - +
239C ASP* 1.3 68.5 + - - +
241C ARG* 3.3 1.9 + - - +
242C ALA* 2.8 45.5 + - + +
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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
----------------------------------------------------------
-2B LYS 4.2 14.6 - - - +
-1B ALA 4.2 2.6 - - - +
0B GLY* 3.4 27.1 - - - -
1B LEU 4.5 1.2 + - - -
209B ASP* 3.6 31.6 - - + +
237C ASN* 3.2 8.4 + - - +
238C TYR* 1.3 86.8 - - - +
240C VAL* 1.3 57.8 + - + +
242C ALA* 3.7 5.5 - - - +
243C ASN* 2.9 36.3 + - - -
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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
----------------------------------------------------------
209B ASP* 5.4 2.7 - - - +
211B LYS* 5.8 0.2 - - - +
227C ASP* 3.5 27.8 - - + +
230C LYS* 3.7 27.1 - - + +
231C ALA* 3.4 36.3 - - + +
234C GLU* 4.7 1.8 - - - +
237C ASN* 3.2 33.7 + - + +
239C ASP* 1.3 76.2 - - + +
241C ARG* 1.3 66.8 + - - +
243C ASN* 3.3 3.5 + - - +
244C VAL* 3.1 23.7 + - - +
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Residues in contact with ARG 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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177C PRO* 4.2 7.7 - - + +
180C THR* 3.2 54.2 + - - +
181C TYR* 3.7 18.6 + - + +
183C LEU* 4.2 3.0 + - - +
188C VAL* 3.4 29.8 - - - +
231C ALA* 3.8 31.9 + - - +
234C GLU 4.3 1.1 - - - -
235C PRO* 2.8 55.9 + - - +
237C ASN 3.0 20.5 + - - +
238C TYR 3.9 2.9 - - - +
240C VAL* 1.3 75.5 - - - +
242C ALA* 1.3 56.1 + - - +
244C VAL* 4.0 6.1 - - - +
245C MET* 3.0 29.8 + - - +
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Residues in contact with ALA 242 (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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1B LEU* 4.5 12.1 - - + -
14C PHE* 4.0 15.9 - - + -
177C PRO* 3.9 22.8 - - + +
238C TYR* 2.8 32.5 + - + +
239C ASP* 3.7 6.3 - - - +
241C ARG* 1.3 71.0 - - - +
243C ASN* 1.3 59.5 + - - +
245C MET* 3.4 1.6 + - - +
246C TRP* 2.9 33.5 + - - +
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Residues in contact with ASN 243 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B LEU* 5.7 2.6 - - - +
209B ASP* 3.2 34.4 + - - +
210B ALA* 3.8 2.3 - - - -
211B LYS* 2.9 33.9 + - - +
212B ILE* 4.2 4.6 + - - +
223C THR* 4.0 13.8 - - + +
227C ASP* 2.9 30.3 + - - +
239C ASP 2.9 20.3 + - - +
240C VAL 3.7 1.6 - - - +
242C ALA* 1.3 76.6 - - - +
244C VAL* 1.3 56.9 + - - +
246C TRP* 4.0 3.2 - - - +
247C ALA* 2.9 31.4 + - - +
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Residues in contact with VAL 244 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188C VAL* 5.8 2.5 - - + -
191C GLY 6.0 1.1 - - - -
192C VAL* 4.0 23.6 - - + +
223C THR* 5.4 0.9 - - - +
224C LEU* 4.4 12.1 - - + +
227C ASP* 3.7 33.0 - - + +
228C GLY* 3.9 7.2 - - - +
231C ALA* 4.2 11.9 - - + -
240C VAL 3.1 17.2 + - - +
241C ARG* 4.0 7.6 - - - +
243C ASN* 1.3 76.2 - - - +
245C MET* 1.3 63.8 + - - +
247C ALA* 3.7 5.9 - - - +
248C ALA* 3.0 25.3 + - + +
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Residues in contact with MET 245 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C PHE* 4.0 9.0 - - + -
137C LEU* 5.4 12.6 - - + +
139C LEU 5.6 3.6 - - - +
140C PRO* 6.3 1.8 - - + -
141C ALA* 5.4 2.9 - - + +
175C LEU* 3.9 31.0 - - + -
176C ASP 4.0 12.8 - - - +
177C PRO* 3.7 26.9 - - + -
180C THR* 3.4 33.9 - - + -
241C ARG 3.0 18.9 + - - +
242C ALA* 3.7 4.0 - - - +
244C VAL* 1.3 78.3 - - - +
246C TRP* 1.3 61.8 + - - +
248C ALA* 3.3 6.4 + - - +
249C THR* 3.1 25.9 + - - +
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Residues in contact with TRP 246 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B LEU* 5.4 4.3 - - + -
4B PHE* 3.7 33.7 - + - -
6B LEU* 4.0 15.5 - - + -
212B ILE* 3.8 31.0 - - + +
213B HIS* 3.6 30.9 + + - -
255B LEU* 3.7 22.4 + - + +
258B ALA* 5.0 0.9 - - + -
12C ILE* 4.0 22.4 - - + -
14C PHE* 3.9 22.0 - + + -
175C LEU* 4.4 0.7 - - + -
242C ALA 2.9 17.5 + - - +
243C ASN* 4.1 3.8 - - - +
245C MET* 1.3 73.6 - - - +
247C ALA* 1.3 66.6 + - - +
249C THR* 3.3 27.7 + - + -
250C GLN* 3.1 46.2 + - - +
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Residues in contact with ALA 247 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B ILE* 3.7 28.1 - - + +
220C ILE* 3.8 9.9 - - + +
223C THR* 4.3 7.0 - - + -
224C LEU* 3.8 24.7 - - + -
243C ASN 2.9 19.9 + - - +
244C VAL 3.7 3.8 - - - +
246C TRP* 1.3 78.0 - - - +
248C ALA* 1.3 56.2 + - - +
250C GLN* 3.3 4.5 + - - +
251C ALA* 3.0 27.5 + - - +
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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
----------------------------------------------------------
140C PRO* 6.3 1.1 - - + -
141C ALA* 4.4 21.5 - - + +
191C GLY 5.2 2.7 - - - +
195C ALA* 3.9 27.1 - - + +
224C LEU* 5.6 0.2 - - + -
244C VAL* 3.0 19.2 + - + +
245C MET* 3.7 6.7 - - - +
246C TRP 3.3 0.2 - - - -
247C ALA* 1.3 72.5 - - - +
249C THR* 1.3 62.3 + - - +
251C ALA* 3.3 5.6 + - - +
252C LEU* 2.8 29.9 - - + +
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Residues in contact with THR 249 (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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12C ILE* 4.9 11.0 - - + -
141C ALA* 4.7 8.5 - - - +
145C GLU* 5.1 8.3 + - + +
146C SER* 6.1 4.0 - - - -
175C LEU* 3.4 25.0 - - + +
245C MET* 3.1 14.9 + - - +
246C TRP* 3.3 34.1 + - + -
248C ALA* 1.3 75.2 - - - +
250C GLN* 1.3 68.5 + - - +
252C LEU* 3.4 10.0 + - - +
253C ASN* 3.3 29.1 + - - +
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Residues in contact with GLN 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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212B ILE* 4.2 10.5 - - + -
216B PHE* 4.0 21.2 - - + -
255B LEU* 3.7 32.5 - - - +
220C ILE* 3.8 21.4 - - + +
246C TRP* 3.1 43.8 + - - +
247C ALA* 3.7 4.7 - - - +
248C ALA 3.3 0.2 - - - -
249C THR* 1.3 80.9 - - - +
251C ALA* 1.3 65.8 + - - +
252C LEU 3.3 0.7 + - - -
253C ASN* 3.6 25.8 + - - +
255C LEU* 4.2 10.8 - - - +
256C ILE* 4.3 13.8 + - + +
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Residues in contact with ALA 251 (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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195C ALA* 3.6 18.2 - - - +
198C HIS* 4.3 8.0 - - + +
199C THR* 3.2 25.8 - - - +
202C GLN* 3.1 24.9 + - - +
220C ILE* 3.8 8.3 - - + +
247C ALA 3.0 12.6 + - - +
248C ALA* 3.3 15.4 + - - +
250C GLN* 1.3 77.6 - - - +
252C LEU* 1.3 59.4 + - + +
253C ASN 3.7 0.2 - - - -
256C ILE* 4.0 6.1 - - - +
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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
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141C ALA* 3.9 14.4 - - + +
142C THR* 3.6 16.2 - - - +
143C GLY* 3.6 29.2 - - - +
145C GLU* 3.8 11.0 - - - +
146C SER* 3.8 10.9 + - - +
147C ASN* 5.9 1.9 - - - +
194C ASP* 5.4 0.9 - - - +
195C ALA* 5.4 4.9 - - + -
198C HIS* 3.3 46.4 - - + +
202C GLN* 5.2 1.1 - - - -
248C ALA* 2.8 27.6 - - + +
249C THR* 3.4 6.5 + - - +
250C GLN 3.2 0.4 - - - -
251C ALA* 1.3 80.5 - - + +
253C ASN* 1.3 61.9 + - - +
254C GLY 3.5 2.6 + - - -
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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