Contacts of the helix formed by residues 196 - 214 (chain B) in PDB entry 4O6M
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 196 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B LEU* 4.3 4.3 + - - +
195B ASN* 1.3 78.4 - - - +
197B TYR* 1.3 65.9 + - - +
198B LEU* 3.8 5.7 + - - +
199B THR* 2.9 30.5 + - - +
200B THR* 2.9 27.2 + - - -
315B ASN* 4.8 1.1 - - - -
421B SO4 3.9 19.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 197 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B SER* 1.3 71.2 - - - +
198B LEU* 1.3 56.8 + - - +
200B THR 3.1 0.5 + - - -
201B LEU* 2.8 60.0 + - + +
312B SER 4.0 6.5 - - - -
313B VAL* 2.6 30.5 + - - +
314B VAL* 4.5 0.7 - - - -
315B ASN* 3.5 45.0 + - + +
421B SO4 3.0 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 198 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B SER* 3.3 7.0 + - - +
197B TYR* 1.3 85.0 - - + +
199B THR* 1.3 62.9 + - + +
201B LEU* 3.4 13.9 + - + +
202B LEU* 3.0 52.5 + - + +
421B SO4 4.1 3.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 199 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B LEU* 3.4 35.8 + - + +
194B LEU* 3.5 27.6 - - + +
195B ASN 4.0 0.2 + - - -
196B SER* 2.9 28.6 + - - +
197B TYR 3.3 0.2 - - - -
198B LEU* 1.3 83.2 - - + +
200B THR* 1.3 56.6 + - - +
202B LEU* 3.7 9.6 - - + -
203B ALA* 2.8 33.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 200 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B LEU 5.0 0.4 - - - -
192B PHE* 4.2 22.3 + - + -
195B ASN* 5.0 1.2 - - - -
196B SER 2.9 28.0 + - - -
197B TYR 3.5 3.4 - - - +
199B THR* 1.3 75.3 + - - +
201B LEU* 1.3 59.5 + - - +
203B ALA* 3.3 7.9 + - - +
204B GLY 3.0 23.0 + - - -
312B SER* 3.5 34.4 + - - +
315B ASN* 3.9 16.8 + - - +
317B PRO* 4.3 15.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 201 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B TYR* 2.8 48.2 + - + +
198B LEU* 3.5 14.6 - - + +
200B THR* 1.3 74.1 - - - +
202B LEU* 1.3 66.2 + - + +
204B GLY* 3.3 2.4 + - - -
205B VAL* 3.1 36.5 + - + +
312B SER 4.2 8.0 + - - -
313B VAL* 3.5 33.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 202 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B LEU* 4.1 21.1 - - + -
198B LEU* 3.0 42.3 + - + +
199B THR* 3.7 13.0 - - + +
200B THR 3.3 0.2 - - - -
201B LEU* 1.3 80.0 - - + +
203B ALA* 1.3 57.1 + - - +
205B VAL* 3.3 11.1 + - + +
206B ILE* 2.9 38.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 203 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B GLY* 3.3 25.8 - - - +
191B LEU* 3.7 11.8 - - + +
192B PHE* 3.7 24.9 - - + +
199B THR 2.8 21.0 + - - +
200B THR 3.5 6.1 - - - +
201B LEU 3.2 0.2 - - - -
202B LEU* 1.3 74.6 - - - +
204B GLY* 1.3 56.9 + - - +
206B ILE* 3.3 2.8 + - - +
207B ILE* 2.9 35.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 204 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B PHE* 4.7 0.9 - - - -
200B THR 3.0 10.5 + - - -
201B LEU 3.3 3.1 + - - -
202B LEU 3.3 0.2 - - - -
203B ALA* 1.3 76.9 - - - +
205B VAL* 1.3 60.9 + - - +
207B ILE* 3.2 7.3 + - - +
208B GLN 3.1 18.4 + - - -
308B ILE 4.7 0.4 - - - -
309B PHE* 3.3 25.3 - - - +
312B SER* 3.8 24.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 205 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B LEU* 3.1 28.2 + - + +
202B LEU* 3.6 15.0 - - + +
204B GLY* 1.3 73.9 - - - +
206B ILE* 1.3 62.2 + - + +
208B GLN* 3.2 4.5 + - - +
209B LEU* 2.9 39.5 + - + +
309B PHE* 3.8 22.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 206 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B LEU* 3.3 41.7 - - + +
187B VAL* 4.0 11.9 - - + -
188B GLY* 3.8 11.2 - - - +
191B LEU* 3.2 32.1 - - + -
202B LEU* 2.9 20.7 + - + +
203B ALA 3.8 2.7 - - - +
205B VAL* 1.3 78.9 - - + +
207B ILE* 1.3 57.8 + - - +
209B LEU* 3.3 16.2 + - + +
210B HIS* 2.8 27.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 207 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B SER* 4.1 13.7 - - - +
188B GLY* 3.8 24.0 - - - -
192B PHE* 4.2 14.4 - - + -
203B ALA 2.9 22.1 + - - +
204B GLY* 3.2 7.2 + - - +
206B ILE* 1.3 77.3 - - - +
208B GLN* 1.3 56.2 + - - +
210B HIS* 3.3 7.6 + - + +
211B SER* 2.9 25.5 + - - -
246B ILE* 3.8 28.7 - - + -
305B LEU* 3.8 40.8 - - + +
308B ILE* 4.2 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 208 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B ILE* 5.2 1.2 - - - +
155B ILE* 4.6 6.7 - - - +
156B ASN* 2.9 32.3 + - - +
204B GLY 3.1 12.6 + - - +
205B VAL 3.7 6.7 - - - +
207B ILE* 1.3 74.0 - - - +
209B LEU* 1.3 65.4 + - - +
211B SER* 3.2 9.3 + - - -
212B ILE* 3.0 36.6 + - + +
302B ASP 5.0 0.5 - - - +
305B LEU 4.0 1.2 - - - -
306B LEU* 3.6 41.0 + - + +
309B PHE* 3.9 26.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 209 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B ILE* 5.9 3.6 - - + -
184B LEU* 4.8 7.6 - - + -
205B VAL* 2.9 27.0 + - + +
206B ILE* 3.4 21.1 - - + +
208B GLN* 1.3 77.7 - - - +
210B HIS* 1.3 56.7 + - - +
212B ILE* 3.1 16.9 + - + +
213B ILE* 2.8 57.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 210 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B SER* 2.8 46.8 + - - -
182B PHE* 4.4 0.9 - - - -
184B LEU* 4.2 19.9 - - + +
185B SER* 3.8 25.3 - - - +
206B ILE 2.8 14.0 + - - +
207B ILE* 3.3 12.3 - - - +
208B GLN 3.3 0.2 - - - -
209B LEU* 1.3 75.9 - - - +
211B SER* 1.3 58.6 + - - +
213B ILE* 4.6 0.4 - - - +
214B ASP* 2.9 38.3 + - + +
239B ASP* 4.8 2.5 - - - -
242B SER* 4.0 7.0 - - - -
246B ILE* 4.8 7.2 - - + -
301B ARG* 3.0 38.2 + - - -
305B LEU* 3.9 11.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 211 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B ASN* 3.3 23.6 + - - +
207B ILE 2.9 10.2 + - - -
208B GLN* 3.2 18.3 + - - -
210B HIS* 1.3 78.3 - - - +
212B ILE* 1.3 63.6 + - - +
214B ASP* 3.6 12.3 + - - +
215B GLY* 3.9 3.5 + - - -
301B ARG* 5.2 0.7 - - - +
302B ASP* 4.3 8.5 + - - -
305B LEU* 3.4 38.2 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
155B ILE* 6.0 2.0 - - + -
156B ASN* 3.9 31.2 - - + +
159B VAL* 3.7 43.1 - - + -
160B SER* 3.4 27.3 + - - +
163B ILE* 4.4 7.0 - - + -
208B GLN* 3.0 33.0 + - + +
209B LEU* 3.5 17.0 - - + +
211B SER* 1.3 74.6 - - - +
213B ILE* 1.3 62.8 + - + +
215B GLY* 3.0 17.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 213 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B ILE* 4.4 19.5 - - + -
177B ILE* 3.8 17.6 - - + +
180B PHE* 4.1 28.3 - - + -
181B SER* 4.4 8.1 - - - +
184B LEU* 3.4 28.5 - - + -
209B LEU* 2.8 36.2 + - + +
210B HIS* 4.1 2.5 - - - +
212B ILE* 1.3 73.9 - - + +
214B ASP* 1.3 57.4 + - - +
215B GLY 3.0 0.2 - - - -
216B CYS* 2.8 33.1 + - - +
403B MPG 4.5 16.8 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
178B THR* 5.2 2.3 - - - +
181B SER* 3.4 21.3 + - - +
210B HIS* 2.9 20.3 + - + +
211B SER 3.8 7.6 - - - +
212B ILE 3.2 0.2 - - - -
213B ILE* 1.3 75.9 - - - +
215B GLY* 1.3 53.1 + - - +
217B ASP* 2.3 13.6 - - - +
235B ASP* 3.1 10.7 - - - +
239B ASP* 3.0 31.6 - - - +
301B ARG* 3.6 13.9 + - - +
401B CA 2.3 44.7 - - - -
422B C5P 3.1 3.3 + - - -
----------------------------------------------------------
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