Contacts of the helix formed by residues 196 - 214 (chain B) in PDB entry 3A4Y
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 PRO 196 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B GLU* 3.5 16.6 - - - +
194B HIS 3.4 5.5 - - - +
195B ARG* 1.3 87.1 - - + +
197B TYR* 1.3 57.3 + - - +
198B ARG* 4.6 5.6 - - + +
199B GLU* 3.2 32.3 - - + +
200B THR* 2.5 30.7 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
165B ASN* 5.6 1.3 - - - +
167B GLU* 3.2 45.5 + - + +
168B LYS* 3.1 40.4 - - + -
169B ASP* 4.0 26.4 + - - +
170B VAL* 5.9 0.3 - - - +
195B ARG 3.4 2.5 + - - -
196B PRO* 1.3 70.5 - - - +
198B ARG* 1.3 73.1 + - + +
200B THR* 3.1 7.0 + - - -
201B VAL* 3.0 39.9 + - + +
230B GLU* 3.8 13.6 + - - +
233B TYR* 5.9 1.0 - - - -
234B VAL* 3.6 25.6 - - - +
376B GLY 3.7 14.6 - - - +
377B PHE* 4.0 16.0 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 198 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B GLU* 4.9 0.8 + - - +
196B PRO* 3.4 5.2 - - + +
197B TYR* 1.3 83.2 - - + +
199B GLU* 1.3 61.3 + - - +
201B VAL* 3.2 15.8 + - - +
202B ARG* 3.2 35.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 199 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B ARG* 2.7 47.1 + - - +
196B PRO* 3.2 35.1 - - + +
198B ARG* 1.3 76.9 - - - +
200B THR* 1.3 68.2 + - - +
202B ARG* 3.0 31.8 + - - +
203B GLU* 3.0 25.1 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
195B ARG* 3.6 15.8 + - - +
196B PRO 2.5 21.7 + - - -
197B TYR* 3.2 12.1 - - - -
199B GLU* 1.3 81.7 - - - +
201B VAL* 1.3 63.2 + - - +
203B GLU* 3.6 1.6 + - - +
204B PHE* 3.1 21.5 + - - +
374B LEU* 3.9 16.6 - - + +
376B GLY* 3.4 30.3 + - - +
377B PHE* 3.5 32.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 201 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B TYR* 3.0 49.4 + - + +
198B ARG* 3.4 8.5 - - - +
200B THR* 1.3 75.4 - - - +
202B ARG* 1.3 66.7 + - + +
204B PHE* 3.2 7.0 + - - +
205B LEU* 3.0 38.2 + - + +
234B VAL* 4.2 15.9 - - + -
238B HIS* 4.2 17.3 - - + +
377B PHE* 4.7 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 202 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B ARG* 3.4 32.1 + - - +
199B GLU* 3.0 41.1 + - - +
201B VAL* 1.3 79.1 - - + +
203B GLU* 1.3 62.1 + - - +
205B LEU* 3.2 10.8 + - - +
206B GLU* 3.0 34.7 + - - +
241B ARG* 6.0 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 203 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B ARG* 2.5 42.8 + - - +
199B GLU 3.0 14.9 + - - +
200B THR 4.1 2.9 - - - +
202B ARG* 1.3 74.4 - - - +
204B PHE* 1.3 67.2 + - - +
206B GLU* 3.1 19.3 + - + +
207B ILE* 2.9 43.8 + - + +
372B HIS* 4.5 8.7 + - - +
374B LEU* 3.2 16.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 204 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200B THR 3.1 16.1 + - - +
201B VAL* 3.3 10.8 - - - +
203B GLU* 1.3 79.4 - - - +
205B LEU* 1.3 67.5 + - + +
207B ILE* 3.4 5.9 + - - +
208B LEU* 3.2 51.9 + - + +
220B ILE* 3.9 21.1 - - + -
231B ILE* 3.9 23.6 - - + -
234B VAL* 4.0 31.0 - - + -
235B LEU* 4.1 8.5 - - + -
337B VAL* 4.1 14.1 - - + -
339B VAL* 4.5 8.3 - - + -
374B LEU* 3.7 24.2 - - + +
377B PHE* 4.1 14.4 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 205 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B VAL* 3.0 26.6 + - + +
202B ARG* 3.6 9.9 - - - +
203B GLU 3.2 0.2 - - - -
204B PHE* 1.3 88.8 - - + +
206B GLU* 1.3 66.6 + - - +
208B LEU* 3.1 4.8 + - - +
209B GLU* 2.8 29.9 + - - +
234B VAL* 4.5 6.7 - - + +
235B LEU* 5.6 0.2 - - + -
238B HIS* 3.7 41.5 - - + +
241B ARG* 3.2 40.8 - - - +
242B LEU* 4.3 18.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 206 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B ARG* 3.0 30.8 + - - +
203B GLU* 3.1 20.3 + - + +
205B LEU* 1.3 75.6 - - - +
207B ILE* 1.3 64.7 + - + +
209B GLU* 3.2 14.3 + - - +
210B LYS* 3.0 25.2 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
203B GLU* 2.9 36.2 + - + +
204B PHE* 3.6 6.7 - - - +
206B GLU* 1.3 77.3 - - + +
208B LEU* 1.3 58.1 - - + +
210B LYS* 3.3 4.9 + - - +
211B THR* 3.0 48.6 + - + +
218B VAL* 5.2 1.6 - - + -
335B ALA* 4.2 2.0 - - + -
337B VAL* 3.6 27.1 - - + -
372B HIS* 3.3 53.2 - - + +
374B LEU* 4.6 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 208 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B PHE* 3.2 49.1 + - + +
205B LEU* 3.1 6.5 + - + +
207B ILE* 1.3 76.7 - - + +
209B GLU* 1.3 67.7 + - - +
212B LEU* 3.0 33.1 + - + +
218B VAL* 3.2 43.7 - - + -
235B LEU* 3.5 22.0 - - + -
242B LEU* 3.5 23.1 - - + -
308B VAL* 4.4 13.5 - - + -
337B VAL* 5.6 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 209 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B LEU* 2.8 25.0 + - - +
206B GLU* 3.6 15.4 + - - +
208B LEU* 1.3 71.8 - - - +
210B LYS* 1.3 57.4 + - - +
212B LEU* 4.3 0.2 - - - +
213B SER* 2.9 37.2 + - - +
241B ARG* 3.5 47.6 + - + +
242B LEU* 4.0 8.9 - - + +
243B PRO* 4.3 9.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 210 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B GLU 3.0 16.0 + - - +
207B ILE* 3.5 6.7 - - - +
208B LEU 3.2 0.2 - - - -
209B GLU* 1.3 73.8 - - - +
211B THR* 1.3 72.0 + - + +
213B SER* 3.2 5.4 + - - -
214B GLN* 3.0 51.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 211 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B ILE* 3.0 24.4 + - + +
208B LEU 3.8 0.2 + - - -
210B LYS* 1.3 76.4 - - + +
212B LEU* 1.3 74.1 + - - +
214B GLN* 3.0 19.8 - - - +
216B GLY 2.9 28.0 + - - -
217B LYS 4.9 1.1 - - - -
218B VAL* 2.7 28.4 + - + +
333B ARG 3.9 12.8 - - - +
334B ASN 4.9 0.2 - - - -
335B ALA* 3.4 31.2 - - + -
370B SER* 5.1 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 212 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B LEU* 3.0 29.6 + - + +
211B THR* 1.3 86.3 + - - +
213B SER* 1.3 55.1 + - - +
215B GLY* 3.0 18.7 + - - -
216B GLY 4.0 4.3 - - - +
218B VAL* 4.3 4.0 - - + -
242B LEU* 4.7 7.9 - - + -
243B PRO* 3.2 39.7 - - + +
245B ALA* 4.2 6.3 - - + -
306B PRO* 3.6 18.8 - - + +
307B MET* 3.4 43.5 - - - +
308B VAL* 4.0 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 213 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B GLU* 2.9 24.3 + - - +
210B LYS* 3.2 4.9 + - - -
212B LEU* 1.3 77.7 - - - +
214B GLN* 1.3 57.0 + - - +
215B GLY 3.2 1.2 + - - -
243B PRO* 3.9 16.5 - - - +
434B SO4 5.7 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 214 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B LYS* 3.0 48.7 + - + +
211B THR* 3.0 28.5 + - - +
213B SER* 1.3 76.7 - - - +
215B GLY* 1.3 58.2 + - - +
216B GLY 3.5 3.5 + - - +
332B PRO 4.3 3.6 + - - -
333B ARG* 3.1 59.8 + - + +
----------------------------------------------------------
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