Contacts of the helix formed by residues 213 - 237 (chain B) in PDB entry 1C3Q
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 213 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-6B HIS 5.5 0.2 - - - +
-4B HIS* 4.9 7.3 + - - -
176B ASP* 5.0 4.4 + - - +
211B GLU* 2.9 25.7 + - - +
212B GLU* 1.3 71.7 - - - +
214B PRO* 1.3 65.2 - - - +
215B LEU* 2.8 36.4 + - - +
216B PHE* 3.1 35.9 + - + -
217B ALA 2.9 22.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 214 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B ALA* 3.5 32.5 - - + +
119B ALA* 4.9 1.0 - - + +
164B VAL* 3.8 16.3 - - + +
208B CYS* 4.1 17.1 - - - -
211B GLU 4.9 0.7 - - - +
212B GLU 3.2 11.4 - - - +
213B ASN* 1.3 87.6 - - - +
215B LEU* 1.3 58.0 + - - +
216B PHE 3.3 0.2 - - - -
217B ALA* 3.7 9.5 - - + +
218B ALA* 2.9 31.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 215 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-4B HIS* 4.4 8.5 - - - +
164B VAL* 3.7 12.3 - - + +
174B ILE* 3.6 26.7 - - + +
175B ALA* 4.1 19.1 - - - -
176B ASP* 3.2 31.6 - - - +
179B HIS* 3.6 24.0 - - + -
181B TYR* 4.4 7.9 - - + -
213B ASN* 2.8 18.4 + - - +
214B PRO* 1.3 75.8 - - - +
216B PHE* 1.3 67.6 + - + +
218B ALA* 3.5 1.2 + - - +
219B ILE* 3.1 42.3 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
-6B HIS* 3.1 54.7 - + + -
-5B HIS* 4.0 4.5 - - - -
-4B HIS* 3.6 48.2 - + - -
1B MET* 3.6 38.8 - - + +
9B CYS* 5.4 0.9 - - - -
181B TYR* 4.8 0.7 - - - -
211B GLU* 4.0 13.5 - - + -
213B ASN* 3.1 31.7 + - + +
215B LEU* 1.3 85.6 - - + +
217B ALA* 1.3 66.6 + - - +
219B ILE* 3.3 2.5 + - + +
220B ALA* 3.0 25.3 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
204B VAL 5.1 0.2 - - - -
207B PHE* 3.4 14.8 - - - +
208B CYS* 3.7 44.2 - - - +
211B GLU* 3.6 13.6 - - + +
213B ASN 2.9 15.7 + - - +
214B PRO* 3.7 2.0 - - + +
215B LEU 3.3 0.2 - - - -
216B PHE* 1.3 77.8 - - - +
218B ALA* 1.3 56.6 + - - +
220B ALA* 3.4 3.4 + - - +
221B ALA* 2.9 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 218 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B ALA* 5.3 2.5 - - + -
164B VAL* 4.4 7.9 - - + -
166B ALA* 4.8 4.9 - - + -
174B ILE* 4.0 20.2 - - + -
204B VAL* 4.1 25.3 - - + +
214B PRO 2.9 21.3 + - - +
215B LEU 3.9 3.1 - - - +
217B ALA* 1.3 73.7 - - - +
219B ILE* 1.3 63.4 + - - +
221B ALA* 4.4 0.7 - - - -
222B ILE* 3.0 35.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 219 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B MET* 3.8 20.4 - - + -
174B ILE* 3.7 25.8 - - + -
181B TYR* 3.7 42.0 - - + -
183B LEU* 3.8 13.4 - - + +
215B LEU* 3.1 28.9 + - + +
216B PHE 3.7 4.0 - - - +
217B ALA 3.3 0.2 - - - -
218B ALA* 1.3 76.3 - - - +
220B ALA* 1.3 63.1 + - - +
223B SER* 2.9 30.7 + - - -
266B ILE* 3.5 31.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 220 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B MET* 4.0 2.9 - - + +
6B ALA* 3.7 33.5 - - + +
9B CYS* 3.8 10.3 - - + -
207B PHE* 3.6 22.9 - - + -
216B PHE 3.0 17.2 + - - +
217B ALA 3.7 0.9 - - - +
219B ILE* 1.3 76.3 - - - +
221B ALA* 1.3 63.0 + - - +
223B SER* 3.8 0.7 - - - -
224B SER* 2.9 30.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 221 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200B LEU* 4.8 0.9 - - - -
203B VAL* 3.8 8.0 - - + +
204B VAL* 3.6 29.2 - - + +
207B PHE* 3.4 31.1 - - + -
217B ALA 2.9 17.8 + - - +
218B ALA 3.7 3.6 - - - +
220B ALA* 1.3 78.1 - - - +
222B ILE* 1.3 57.9 + - - +
224B SER* 3.7 2.1 - - - -
225B TYR* 3.0 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 222 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B ARG* 4.8 2.0 - - + -
166B ALA* 4.0 21.1 - - + -
168B THR* 4.1 19.1 - - + -
172B ASP* 3.9 17.9 - - - +
174B ILE* 3.4 26.7 - - + -
183B LEU* 3.6 18.6 - - + -
185B ASN 4.6 3.9 - - - +
200B LEU* 4.0 25.8 - - + -
204B VAL* 4.2 11.9 - - + -
218B ALA 3.0 13.7 + - - +
221B ALA* 1.3 72.1 - - - +
223B SER* 1.3 60.9 + - - +
225B TYR* 3.7 2.2 - - + +
226B GLY* 2.8 26.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 223 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B ALA* 4.7 3.8 - - - -
183B LEU* 3.7 11.0 - - - +
185B ASN* 4.3 11.8 + - - +
219B ILE 2.9 21.7 + - - -
220B ALA* 3.8 4.5 - - - -
222B ILE* 1.3 76.8 - - - +
224B SER* 1.3 59.4 + - - +
226B GLY* 3.2 2.2 + - - -
227B VAL* 2.9 35.4 + - - +
260B VAL* 5.1 0.4 - - - -
264B ALA* 4.1 21.1 - - - -
266B ILE* 3.5 25.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 224 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B ALA 4.4 2.1 + - - -
10B LEU* 4.1 16.6 - - - +
39B LEU* 5.9 1.6 - - - -
203B VAL* 6.0 0.4 - - - -
207B PHE* 3.9 20.1 - - - -
220B ALA 2.9 18.6 + - - -
221B ALA 3.7 2.9 - - - -
223B SER* 1.3 76.4 - - - +
225B TYR* 1.3 58.0 + - - +
227B VAL* 3.3 3.3 + - - +
228B ALA* 3.0 29.6 + - - +
252B LEU* 5.5 1.3 - - - -
255B VAL* 4.6 6.2 - - - +
260B VAL* 3.9 31.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 225 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B LEU* 4.1 24.2 - - + +
196B ALA* 2.7 39.8 + - + +
199B LEU* 3.9 29.1 - - + +
200B LEU* 3.5 37.2 - - + -
203B VAL* 4.2 12.7 - - + +
221B ALA 3.0 18.6 + - - +
222B ILE* 3.7 2.7 - - + +
224B SER* 1.3 76.3 - - - +
226B GLY* 1.3 55.0 + - - +
228B ALA* 3.3 5.7 + - - +
229B ALA* 2.8 36.0 + - + +
248B LEU* 3.8 23.4 - - + +
252B LEU* 4.0 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 226 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B ASN* 3.1 31.2 - - - +
186B GLY* 4.6 0.7 - - - -
190B LEU* 5.9 0.4 - - - -
222B ILE 2.8 13.8 + - - -
223B SER 3.6 3.6 - - - -
225B TYR* 1.3 78.2 - - - +
227B VAL* 1.3 59.1 + - - +
229B ALA* 3.4 7.2 + - - +
230B GLN* 3.0 33.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 227 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B ASN* 4.4 4.9 - - - -
223B SER 2.9 23.2 + - - +
224B SER* 3.7 6.7 - - - +
226B GLY* 1.3 72.7 - - - +
228B ALA* 1.3 67.7 + - - +
230B GLN* 3.1 10.2 + - - +
231B LEU* 2.9 33.5 + - + +
255B VAL* 4.1 18.2 - - + -
259B ASP 4.0 17.0 - - - +
260B VAL* 4.6 7.0 - - - -
263B TRP* 4.2 17.5 - - + -
264B ALA* 3.9 30.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 228 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B SER 3.0 17.1 + - - +
225B TYR 3.5 4.5 - - - +
227B VAL* 1.3 77.9 - - - +
229B ALA* 1.3 57.0 + - - +
231B LEU* 3.2 3.7 + - - -
232B ALA* 2.9 30.7 + - - +
248B LEU* 4.3 3.1 - - + -
251B LYS* 3.6 29.2 - - + +
252B LEU* 3.8 25.8 - - + +
255B VAL* 4.5 9.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 229 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B GLY* 5.0 3.8 - - - -
187B HIS* 4.4 4.3 - - + +
190B LEU* 3.8 38.6 - - + -
225B TYR* 2.8 22.7 + - + +
226B GLY* 3.6 8.3 - - - +
227B VAL 3.2 0.2 - - - -
228B ALA* 1.3 72.4 - - - +
230B GLN* 1.3 58.3 + - - +
232B ALA* 3.5 1.5 + - - -
233B ALA* 3.0 27.5 + - - +
244B PHE* 3.6 9.2 - - + -
248B LEU* 3.9 12.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 230 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B HIS 4.0 2.3 - - - +
185B ASN* 2.9 44.4 + - - +
186B GLY 3.3 20.9 + - - +
187B HIS* 5.0 3.6 - - - +
226B GLY 3.0 22.8 + - - +
227B VAL* 3.1 8.3 + - + +
229B ALA* 1.3 73.9 - - - +
231B LEU* 1.3 65.7 + - + +
233B ALA* 3.1 8.3 + - - +
234B GLN* 2.9 38.8 + - - +
263B TRP* 4.7 17.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 231 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B VAL* 2.9 32.6 + - + +
228B ALA* 3.7 6.5 - - - +
230B GLN* 1.3 76.4 - - + +
232B ALA* 1.3 63.4 + - - +
234B GLN* 3.2 13.8 + - + +
235B GLN 3.1 18.7 + - - -
251B LYS* 3.2 28.1 + - + +
255B VAL* 4.3 14.1 - - + -
259B ASP* 4.2 23.3 - - - +
263B TRP* 5.0 15.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 232 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B ALA 2.9 18.0 + - - +
229B ALA* 3.7 6.3 - - - +
231B LEU* 1.3 75.7 - - - +
233B ALA* 1.3 58.2 + - - +
235B GLN* 3.4 2.3 + - - +
236B THR* 2.8 34.0 + - - -
244B PHE* 3.8 10.3 - - + -
247B GLU* 3.7 36.8 - - + +
248B LEU* 3.7 10.1 - - - +
251B LYS* 3.6 8.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 233 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B HIS* 3.4 43.3 - - + +
189B LEU* 4.4 4.2 - - + +
229B ALA 3.0 14.7 + - - +
230B GLN* 3.1 9.6 + - - +
232B ALA* 1.3 74.9 - - - +
234B GLN* 1.3 68.0 + - + +
236B THR* 3.6 2.3 - - - -
237B ALA* 3.0 23.2 + - - +
244B PHE* 3.7 11.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 234 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B HIS* 6.3 0.4 - - - -
230B GLN* 2.9 30.0 + - - +
231B LEU* 3.5 19.7 - - + +
233B ALA* 1.3 80.3 - - - +
235B GLN* 1.3 63.4 + - - +
237B ALA* 3.5 12.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 235 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A LYS* 6.0 5.3 - - - +
231B LEU 3.1 2.7 + - - +
232B ALA 3.7 2.7 - - - +
234B GLN* 1.3 79.8 - - - +
236B THR* 1.3 61.2 + - - +
237B ALA* 4.5 1.6 - - - +
239B LYS* 3.3 17.9 + - - +
247B GLU* 3.1 37.6 + - + +
251B LYS* 3.2 27.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 236 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B LEU* 4.5 6.7 - - + -
232B ALA 2.8 22.7 + - - -
233B ALA* 3.6 7.4 - - - -
234B GLN 3.2 0.2 - - - -
235B GLN* 1.3 76.3 - - - +
237B ALA* 1.3 80.6 + - - +
239B LYS* 3.2 30.4 + - + +
240B GLY 3.7 29.8 - - - +
243B SER* 4.0 2.8 - - - -
244B PHE* 3.3 31.5 + - + +
247B GLU* 3.8 7.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 237 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B LEU* 4.9 7.4 - - - +
233B ALA 3.0 14.8 + - - +
234B GLN 3.5 10.4 + - - +
235B GLN 4.5 1.8 - - - +
236B THR* 1.3 84.9 - - - +
238B ASP* 1.3 72.2 + - + +
239B LYS* 3.4 5.0 + - + +
240B GLY 4.9 0.5 + - - -
----------------------------------------------------------
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