Contacts of the helix formed by residues 210 - 234 (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 ALA 210 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B LEU* 4.0 12.6 - - + -
208B VAL* 2.8 15.7 + - + +
209B ASP* 1.3 70.1 - - - +
211B LYS* 1.3 65.2 + - - +
212B ILE 3.4 2.2 - - - -
213B HIS* 3.4 25.0 + - + +
214B ASP* 3.1 27.7 + - - +
260B VAL* 3.8 23.3 - - + -
243C ASN* 3.8 3.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 211 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B ASP* 2.7 36.1 + - - +
210B ALA* 1.3 71.6 - - - +
212B ILE* 1.3 64.6 + - - +
214B ASP* 3.4 6.6 + - - +
215B ARG* 3.0 29.6 + - + +
310B ARG* 5.6 0.2 + - - -
223C THR* 3.6 22.2 - - + +
226C GLU* 3.3 28.3 - - + +
227C ASP* 3.0 42.2 + - - +
230C LYS* 4.4 9.1 - - - +
240C VAL* 5.8 0.2 - - - +
243C ASN* 2.9 15.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 212 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B ALA 3.4 0.4 - - - -
211B LYS* 1.3 73.3 - - - +
213B HIS* 1.3 62.3 + - - +
215B ARG* 3.3 2.7 + - - -
216B PHE* 2.9 59.2 + - + +
255B LEU* 6.1 0.2 - - + -
219C GLY 4.0 2.2 - - - +
220C ILE* 3.8 25.4 - - + +
223C THR* 3.7 20.2 - - + +
243C ASN* 4.2 4.8 + - - +
246C TRP* 3.8 28.7 - - + +
247C ALA* 3.7 43.1 - - + +
250C GLN* 4.2 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 213 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B LEU* 3.7 22.0 - - + -
4B PHE* 5.0 0.9 - + - -
202B GLN 6.1 0.2 - - - +
210B ALA* 3.5 24.7 - - + +
211B LYS 3.3 0.4 - - - -
212B ILE* 1.3 77.6 - - - +
214B ASP* 1.3 58.4 + - - +
216B PHE* 3.9 4.5 - - - +
217B ALA* 2.9 32.1 + - - +
255B LEU 3.8 10.1 + - - -
256B ILE* 3.2 38.8 - - - +
258B ALA* 2.7 32.7 + - - +
260B VAL* 3.8 11.2 - - + -
246C TRP* 3.6 30.8 + + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 214 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-2B LYS* 5.3 2.9 + - - -
203B TYR* 3.4 10.8 - - - -
208B VAL 4.3 9.5 - - - +
210B ALA* 3.1 21.4 + - - +
211B LYS* 3.7 7.4 - - - +
213B HIS* 1.3 78.9 - - - +
215B ARG* 1.3 58.2 + - - +
217B ALA* 3.3 0.9 + - - +
218B GLU* 2.8 38.2 + - - +
303B LYS* 2.8 30.7 + - - -
306B GLN* 3.0 33.8 + - - +
310B ARG* 4.6 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 215 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B LYS* 3.0 20.8 + - + +
212B ILE* 3.8 3.6 - - - +
214B ASP* 1.3 75.8 - - - +
216B PHE* 1.3 60.2 + - + +
218B GLU* 3.4 7.5 + - - +
219B GLY* 2.8 27.0 + - - -
310B ARG* 3.3 51.0 - - - +
215C ARG* 4.8 4.7 - - - +
219C GLY* 3.7 31.9 - - - +
222C LEU* 3.7 38.0 - - - +
223C THR* 4.2 3.3 + - - +
226C GLU* 3.0 29.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 216 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B ILE* 2.9 47.7 + - + +
213B HIS* 3.9 2.2 - - - +
215B ARG* 1.3 77.4 - - + +
217B ALA* 1.3 66.7 + - - +
219B GLY 3.2 1.0 + - - -
220B ILE* 3.0 29.8 + - - +
255B LEU* 4.0 17.3 - - + -
256B ILE* 3.8 14.4 - - + -
216C PHE* 3.3 79.1 - + + -
219C GLY* 4.8 0.7 - - - -
220C ILE* 4.1 9.4 - - + -
250C GLN* 4.0 34.3 - - + -
255C LEU* 4.8 0.4 - - + -
256C ILE* 5.2 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 217 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B THR* 3.4 25.3 - - + +
203B TYR* 3.8 27.4 - - + -
213B HIS 2.9 17.7 + - - +
214B ASP 3.6 3.6 - - - +
216B PHE* 1.3 76.5 - - - +
218B GLU* 1.3 62.2 + - - +
220B ILE* 3.2 5.3 + - - -
221B LEU* 3.1 27.4 + - - +
256B ILE* 4.3 10.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 218 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B TYR* 2.7 34.8 + - + +
214B ASP 2.8 22.9 + - - +
215B ARG* 3.7 13.8 + - - +
217B ALA* 1.3 73.2 - - - +
219B GLY* 1.3 56.5 + - - +
221B LEU* 3.3 3.8 + - - +
222B LEU* 2.9 42.0 + - + +
306B GLN* 2.7 26.5 + - - +
310B ARG* 3.0 43.4 + - + -
311B VAL* 4.2 14.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 219 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B ARG 2.8 18.3 + - - -
216B PHE* 3.2 2.7 + - - -
218B GLU* 1.3 74.7 - - - +
220B ILE* 1.3 57.6 + - - +
222B LEU* 3.6 1.4 + - - +
223B THR* 2.8 34.4 + - - -
212C ILE* 4.5 2.5 - - - -
215C ARG* 3.6 33.7 - - - +
216C PHE* 5.1 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 220 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B THR* 3.5 18.6 - - - +
216B PHE 3.0 20.9 + - - +
217B ALA* 3.6 4.9 - - - +
219B GLY* 1.3 75.1 - - - +
221B LEU* 1.3 58.8 + - - +
223B THR* 3.3 3.5 + - - -
224B LEU* 2.9 43.3 + - + +
247B ALA* 3.8 19.3 - - + +
250B GLN* 3.7 35.2 - - + +
251B ALA* 3.9 7.2 - - + -
256B ILE* 4.1 22.0 - - + -
212C ILE* 3.8 19.1 - - + -
216C PHE* 4.1 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 221 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B PHE* 3.6 52.2 - - + +
199B THR* 3.7 14.4 - - + +
200B VAL* 3.9 10.3 - - + -
203B TYR* 4.1 15.0 - - + -
217B ALA 3.1 14.2 + - - +
218B GLU 3.6 5.8 - - - +
220B ILE* 1.3 78.3 - - - +
222B LEU* 1.3 56.6 + - - +
224B LEU* 3.3 5.7 + - + +
225B ILE* 3.0 35.6 + - - +
307B TYR* 3.9 24.2 - - + -
311B VAL* 3.9 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 222 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B GLU* 2.9 29.5 + - + +
219B GLY* 3.9 3.6 - - - +
221B LEU* 1.3 75.4 - - - +
223B THR* 1.3 62.4 + - - +
225B ILE* 3.4 7.5 + - + +
226B GLU* 3.1 24.4 + - - +
310B ARG 3.7 20.4 - - - +
311B VAL* 3.5 27.8 - - - +
215C ARG* 3.7 44.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 223 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B GLY 2.8 21.4 + - - -
220B ILE 3.5 4.5 - - - -
222B LEU* 1.3 76.0 - - - +
224B LEU* 1.3 60.0 + - - +
226B GLU* 3.4 1.3 + - - +
227B ASP* 2.9 29.6 + - - +
243B ASN* 4.2 24.2 - - + +
244B VAL* 5.6 0.6 - - + +
247B ALA* 4.5 2.9 - - + -
211C LYS* 3.6 43.8 + - + +
212C ILE* 3.6 24.4 - - + +
215C ARG* 4.1 4.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 224 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B VAL* 3.9 23.1 - - + +
195B ALA* 3.8 17.7 - - + -
196B PHE* 3.4 46.0 - - + +
220B ILE* 2.9 29.9 + - + +
221B LEU* 3.7 4.5 - - - +
223B THR* 1.3 73.8 - - - +
225B ILE* 1.3 61.6 + - - +
228B GLY* 2.9 30.0 + - - +
229B PRO* 3.5 2.3 - - - +
244B VAL* 4.6 18.8 - - + +
247B ALA* 3.8 22.9 - - + -
248B ALA* 5.8 0.2 - - + -
333B PHE* 3.6 6.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 225 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B PHE* 3.8 18.2 - - + -
221B LEU 3.0 22.9 + - - +
222B LEU* 3.8 7.6 - - + +
223B THR 3.3 0.2 - - - -
224B LEU* 1.3 78.1 - - - +
226B GLU* 1.3 59.0 + - - +
229B PRO* 3.2 22.7 - - - +
311B VAL* 3.4 36.6 - - + +
312B TRP* 3.6 41.5 - - + -
333B PHE* 3.7 14.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 226 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222B LEU 3.1 16.8 + - - +
223B THR* 4.0 3.4 - - - +
225B ILE* 1.3 81.0 - - - +
227B ASP* 1.3 73.1 + - - +
229B PRO* 3.8 5.9 - - - +
230B LYS* 3.1 42.1 + - - +
211C LYS* 4.0 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 227 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223B THR* 2.9 16.9 + - + +
226B GLU* 1.3 72.5 - - - +
228B GLY* 1.3 65.5 + - - +
229B PRO 3.5 0.7 - - - -
230B LYS* 3.0 32.7 + - - +
231B ALA* 2.9 20.4 + - - +
240B VAL* 3.3 29.8 - - + +
243B ASN* 3.0 24.2 + - + +
244B VAL* 3.8 11.2 - - + +
209C ASP* 4.5 0.2 - - - +
211C LYS* 2.8 33.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 228 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B VAL* 3.8 26.3 - - - +
223B THR 4.1 0.2 + - - -
224B LEU* 2.9 17.1 + - - -
227B ASP* 1.3 75.6 - - - +
229B PRO* 1.3 66.2 - - - +
231B ALA* 3.1 17.5 + - - +
232B LEU* 3.7 9.7 + - - +
244B VAL* 3.9 8.5 - - - +
337B LEU* 4.1 6.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 229 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B LEU 3.5 4.0 - - - +
225B ILE 3.2 24.9 - - - +
226B GLU 3.8 4.5 - - - +
227B ASP 3.7 2.0 - - - -
228B GLY* 1.3 89.6 - - - +
230B LYS* 1.3 60.3 + - + +
232B LEU* 3.3 18.0 + - + +
233B LYS* 3.4 33.1 + - - +
333B PHE* 4.0 19.5 - - + -
337B LEU* 3.9 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 230 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B GLU* 3.1 40.4 + - - +
227B ASP* 3.0 33.6 + - - +
229B PRO* 1.3 75.1 - - + +
231B ALA* 1.3 57.2 + - - +
233B LYS* 4.4 8.1 - - - +
234B GLU* 2.7 55.1 + - - +
240B VAL* 3.6 23.0 - - + +
211C LYS* 4.2 7.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 231 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B VAL* 3.9 19.3 - - + +
227B ASP 2.9 12.2 + - - +
228B GLY* 3.1 11.6 + - - +
230B LYS* 1.3 75.6 - - - +
232B LEU* 1.3 60.5 + - - +
234B GLU 4.1 1.6 - - - -
235B PRO* 3.5 22.0 - - - +
240B VAL* 3.4 9.6 - - + +
241B ARG* 3.7 32.6 + - - +
244B VAL* 4.2 11.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 232 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B PRO* 3.3 43.6 - - + +
188B VAL* 3.7 19.3 - - + -
189B ALA* 4.0 4.9 - - + +
192B VAL* 6.3 0.2 - - + -
228B GLY 3.9 8.7 - - - +
229B PRO* 3.5 9.6 - - + +
230B LYS 3.2 0.6 - - - -
231B ALA* 1.3 78.1 - - - +
233B LYS* 1.3 62.4 + - + +
235B PRO* 4.3 9.7 - - - +
336B GLN 4.7 3.8 - - - +
337B LEU* 3.6 46.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 233 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B PRO* 3.4 29.9 + - - +
230B LYS* 3.2 9.3 + - - +
232B LEU* 1.3 80.6 - - + +
234B GLU* 1.3 68.1 + - + +
235B PRO* 3.5 8.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 234 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B LYS* 2.7 42.5 + - + +
231B ALA* 3.9 2.5 - - - +
233B LYS* 1.3 83.0 - - + +
235B PRO* 1.3 67.6 - - - +
236B GLU 3.2 3.3 + - - -
237B ASN* 2.8 48.7 + - + +
240B VAL* 4.8 1.1 - - + +
241B ARG* 4.2 5.7 - - - -
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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