Contacts of the helix formed by residues 237 - 252 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B GLU* 2.8 46.3 + - + +
235B PRO 3.5 0.4 - - - -
236B GLU* 1.3 74.7 - - - +
238B TYR* 1.3 63.6 + - - +
239B ASP* 3.2 20.3 + - - +
240B VAL* 3.2 23.3 + - + +
241B ARG* 3.0 24.6 + - - +
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Residues in contact with TYR 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B PHE* 4.1 4.5 - - - -
15B GLY* 3.2 12.6 - - - -
16B LYS* 3.1 40.4 + - + -
177B PRO* 3.6 31.8 - - + +
178B VAL* 4.2 8.7 - - + -
181B TYR* 3.3 23.6 - - - +
236B GLU 3.2 6.6 + - - +
237B ASN* 1.3 72.6 + - - +
239B ASP* 1.3 72.8 + - - +
241B ARG* 3.7 0.9 - - - +
242B ALA* 2.8 35.2 + - + +
0C GLY* 5.6 1.1 - - - -
1C LEU* 4.3 22.3 + - + -
3C ASN* 4.1 4.6 + - - -
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Residues in contact with ASP 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237B ASN* 3.2 9.9 + - - +
238B TYR* 1.3 86.7 - - - +
240B VAL* 1.3 59.9 + - + +
242B ALA* 3.4 5.0 + - - +
243B ASN* 3.0 36.5 + - - -
-2C LYS 4.4 7.1 - - - +
-1C ALA 4.2 8.7 - - - +
0C GLY* 3.6 24.2 - - - -
1C LEU 4.5 1.2 + - - -
209C ASP* 3.6 31.1 - - + +
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Residues in contact with VAL 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B ASP* 3.3 42.0 - - + +
230B LYS* 3.6 25.1 - - + +
231B ALA* 3.4 26.5 - - + +
234B GLU* 4.8 1.8 - - - +
237B ASN* 3.2 34.1 + - + +
239B ASP* 1.3 78.1 - - + +
241B ARG* 1.3 63.9 + - - +
243B ASN* 3.3 3.1 + - - +
244B VAL* 3.0 23.2 + - - +
209C ASP* 5.4 2.9 - - - +
211C LYS* 5.7 0.2 - - - +
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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
----------------------------------------------------------
140B PRO* 5.3 5.0 - - - +
177B PRO* 4.2 7.5 - - + +
180B THR* 2.9 53.8 + - - +
181B TYR* 3.7 20.0 + - + +
183B LEU* 3.9 5.1 + - - +
188B VAL* 3.6 29.0 - - - +
231B ALA* 3.7 32.9 + - - +
234B GLU 4.2 2.2 - - - -
235B PRO* 2.8 58.1 + - - +
237B ASN 3.0 19.2 + - - +
238B TYR 3.9 3.1 - - - +
240B VAL* 1.3 76.0 - - - +
242B ALA* 1.3 56.8 + - - +
244B VAL* 3.9 6.8 - - - +
245B MET* 3.0 30.0 + - - +
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Residues in contact with ALA 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B PHE* 3.9 15.6 - - + -
177B PRO* 3.9 23.9 - - + +
238B TYR* 2.8 27.1 + - + +
239B ASP* 3.7 7.0 - - - +
241B ARG* 1.3 74.8 - - - +
243B ASN* 1.3 60.4 + - - +
245B MET* 3.4 1.7 + - - +
246B TRP* 2.9 33.1 + - - +
1C LEU* 4.5 11.4 - - + -
209C ASP 6.2 0.2 - - - +
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Residues in contact with ASN 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223B THR* 4.2 14.5 - - + +
227B ASP* 3.0 29.3 + - + +
239B ASP 3.0 21.2 + - - +
240B VAL 3.3 1.1 + - - +
242B ALA* 1.3 77.4 - - - +
244B VAL* 1.3 58.0 + - - +
246B TRP* 3.9 3.4 - - - +
247B ALA* 3.0 31.4 + - - +
1C LEU* 5.6 2.8 - - - +
209C ASP* 3.2 33.5 + - - +
210C ALA* 3.7 2.6 - - - -
211C LYS* 3.0 32.6 + - - +
212C ILE* 4.3 5.1 + - - +
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Residues in contact with VAL 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B PRO* 4.4 19.3 - - + +
188B VAL* 5.6 3.6 - - + +
191B GLY 5.9 0.4 - - - -
192B VAL* 4.3 19.1 - - + +
223B THR* 5.6 0.9 - - - +
224B LEU* 4.6 10.7 - - + +
227B ASP* 3.8 31.6 - - + +
228B GLY* 3.9 9.2 - - - +
231B ALA* 4.2 12.8 - - + -
240B VAL 3.0 20.2 + - - +
241B ARG* 4.0 8.3 - - - +
243B ASN* 1.3 74.7 - - - +
245B MET* 1.3 64.5 + - - +
247B ALA* 3.3 6.8 + - - +
248B ALA* 3.1 22.5 + - + +
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Residues in contact with MET 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B PHE* 4.5 4.5 - - + -
137B LEU* 3.8 36.3 - - + +
140B PRO* 3.7 21.6 - - + +
145B GLU* 4.6 0.3 - - - +
175B LEU* 3.9 29.2 - - + +
176B ASP 3.9 11.9 - - - +
177B PRO* 3.7 28.0 - - - -
180B THR* 3.5 25.8 - - + -
241B ARG 3.0 18.8 + - - +
242B ALA* 3.7 5.4 - - - +
244B VAL* 1.3 77.5 - - - +
246B TRP* 1.3 63.1 + - - +
248B ALA* 3.3 5.2 + - - +
249B THR* 3.2 23.3 + - - -
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Residues in contact with TRP 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B ILE* 3.9 26.9 - - + -
14B PHE* 4.1 20.6 - + + -
175B LEU* 4.1 2.0 - - + -
242B ALA 2.9 17.5 + - - +
243B ASN* 4.2 3.8 - - - +
245B MET* 1.3 73.3 - - - +
247B ALA* 1.3 66.5 + - - +
249B THR* 3.2 23.9 + - + -
250B GLN* 3.0 53.9 + - - +
1C LEU* 5.6 3.4 - - + -
4C PHE* 3.9 25.6 - + - -
6C LEU* 4.0 17.5 - - + -
212C ILE* 3.8 28.0 - - + +
213C HIS* 3.6 29.6 + + - -
255C LEU* 3.6 22.8 + - + +
258C ALA* 5.2 0.9 - - + -
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Residues in contact with ALA 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B ALA* 5.0 0.4 - - - -
220B ILE* 3.8 10.0 - - + +
223B THR* 4.5 5.2 - - + -
224B LEU* 3.8 25.4 - - + -
243B ASN 3.0 19.7 + - - +
244B VAL 3.6 4.7 - - - +
245B MET 3.3 0.2 - - - -
246B TRP* 1.3 77.6 - - - +
248B ALA* 1.3 56.4 + - - +
250B GLN* 3.3 3.0 + - - +
251B ALA* 3.0 29.6 + - - +
212C ILE* 3.8 26.3 - - + +
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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
----------------------------------------------------------
140B PRO* 4.0 9.4 - - + -
141B ALA* 3.8 27.8 - - - +
142B THR 4.6 0.9 - - - -
143B GLY* 3.6 15.5 + - - +
145B GLU* 4.4 3.1 - - - +
191B GLY 5.2 0.2 - - - +
195B ALA* 3.9 24.7 - - + -
198B HIS* 5.5 0.2 + - - -
244B VAL* 3.1 16.8 + - + +
245B MET 3.7 4.7 - - - +
246B TRP 3.3 0.2 - - - -
247B ALA* 1.3 75.8 - - - +
249B THR* 1.3 63.5 + - - +
251B ALA* 3.5 12.5 + - - +
252B LEU 4.0 0.9 + - - -
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Residues in contact with THR 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B ILE* 4.7 4.0 - - + -
143B GLY* 4.5 2.5 - - - -
145B GLU* 2.6 27.9 + - + +
146B SER* 3.4 22.9 + - - +
175B LEU* 3.6 15.9 - - + +
245B MET* 3.2 14.4 + - - +
246B TRP* 3.5 32.7 - - + -
247B ALA 3.2 0.2 - - - -
248B ALA* 1.3 78.9 - - - +
250B GLN* 1.3 67.0 + - - +
251B ALA 3.4 0.9 + - - -
252B LEU 3.6 5.5 + - - +
253B ASN* 3.5 20.0 + - + +
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Residues in contact with GLN 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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220B ILE* 3.7 13.5 - - + +
246B TRP* 3.0 48.1 + - - +
247B ALA 3.9 3.6 - - - +
249B THR* 1.3 79.5 - - - +
251B ALA* 1.3 63.6 + - - +
252B LEU 3.2 1.0 + - - -
253B ASN* 3.6 31.0 + - - +
255B LEU* 4.3 6.3 - - - +
256B ILE* 4.1 12.3 - - - +
212C ILE* 4.1 20.0 - - + -
216C PHE* 3.9 18.8 - - + -
255C LEU* 3.7 33.7 - - - +
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Residues in contact with ALA 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B ALA* 3.5 20.6 - - + +
198B HIS* 4.0 10.2 - - + +
199B THR* 3.5 19.3 - - - +
202B GLN* 2.7 31.5 + - - -
220B ILE* 3.9 11.0 - - + +
247B ALA 3.0 16.1 + - - +
248B ALA 3.6 9.2 - - - +
249B THR 3.2 1.2 - - - -
250B GLN* 1.3 78.7 - - - +
252B LEU* 1.3 52.9 + - + +
256B ILE* 3.6 6.3 - - - +
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Residues in contact with LEU 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B THR 3.6 7.9 - - - +
143B GLY* 3.7 4.9 - - - +
147B ASN* 3.0 29.4 + - + +
164B HIS* 6.5 0.7 - - + -
198B HIS* 3.5 40.4 - - + +
202B GLN* 3.6 26.0 - - - +
248B ALA 4.0 1.4 + - - -
249B THR 3.6 4.6 + - - -
250B GLN 3.2 0.2 - - - -
251B ALA* 1.3 79.8 - - + +
253B ASN* 1.3 59.9 + - - +
254B GLY 3.5 4.3 - - - +
256B ILE* 5.7 0.7 - - - -
264B TRP* 3.7 24.5 - - + -
1388B NZQ 3.5 23.6 - - + +
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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
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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