Contacts of the helix formed by residues 194 - 214 (chain B) in PDB entry 1QAI
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 194 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B ILE* 5.5 0.4 - - - +
51B PRO* 6.2 1.0 - - - +
122B VAL* 3.8 11.3 - - - +
123B GLU 3.1 25.3 + - - -
124B ASP* 4.9 0.3 - - - +
125B ILE* 3.5 41.1 + - + +
192B PHE* 2.9 18.8 + - + -
193B LYS* 1.3 100.4 - - - +
195B SER* 1.3 66.1 + - - +
196B PRO* 3.3 4.5 - - - -
197B THR* 3.1 5.7 + - - +
198B LEU* 2.8 29.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 195 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B PHE* 3.6 28.5 - - - -
188B LEU* 2.9 37.3 - - - +
189B PRO 2.9 16.8 + - - -
190B GLN* 5.7 0.2 - - - -
192B PHE* 3.0 12.7 + - - -
194B ASN* 1.3 75.0 - - - +
196B PRO* 1.3 62.7 - - - +
199B PHE* 2.7 37.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 196 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B PHE* 3.7 23.3 - - + -
190B GLN* 6.0 0.4 - - - +
192B PHE 3.8 4.3 - - - +
193B LYS 3.5 13.9 - - - +
194B ASN 3.3 4.5 - - - -
195B SER* 1.3 94.4 - - - +
197B THR* 1.3 60.7 + - - +
199B PHE* 4.0 1.4 - - - +
200B ASP* 3.1 24.6 + - - +
223B VAL* 4.3 20.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 197 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B ILE* 3.4 34.6 + - + +
126B HIS 5.0 0.2 - - - -
127B PRO* 4.4 30.9 - - + +
193B LYS 5.4 1.0 + - - -
194B ASN* 3.1 4.5 + - - -
196B PRO* 1.3 78.0 - - - +
198B LEU* 1.3 64.4 + - - +
200B ASP* 3.3 5.4 + - - +
201B GLU* 2.9 48.4 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
48B LEU* 4.3 27.3 - - + +
50B ILE* 4.3 11.0 - - + -
125B ILE* 3.7 19.3 - - + -
158B LEU* 3.9 3.0 - - - +
188B LEU* 3.9 19.1 - - + -
192B PHE* 4.2 13.7 - - + -
194B ASN* 2.8 37.8 + - + +
195B SER 3.8 2.7 - - - +
197B THR* 1.3 72.0 - - - +
199B PHE* 1.3 64.0 + - - +
201B GLU* 3.5 19.7 + - - +
202B ALA* 3.1 22.5 + - - +
205B ARG* 5.0 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 199 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B LEU* 3.6 20.6 - - + -
154B ALA* 3.5 49.1 - - + -
155B PHE* 4.0 12.6 - + + -
157B CYS* 4.7 0.2 - - + -
158B LEU* 3.7 22.3 - - + +
188B LEU* 4.9 0.2 - - + -
195B SER 2.7 21.4 + - - +
196B PRO 4.0 2.2 - - - +
198B LEU* 1.3 69.4 - - - +
200B ASP* 1.3 61.7 + - - +
202B ALA* 3.2 3.1 + - - +
203B LEU* 2.9 37.1 + - + +
223B VAL* 3.2 43.3 - - + -
224B ASP* 3.8 3.6 - - - -
252B TYR* 3.5 25.6 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 200 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B VAL* 3.4 19.3 - - - +
196B PRO 3.1 18.6 + - - +
197B THR* 3.3 6.7 + - + +
199B PHE* 1.3 83.9 - - - +
201B GLU* 1.3 64.5 + - + +
203B LEU* 3.1 5.6 + - - +
204B HIS* 2.9 59.0 + - - -
221B GLN* 4.1 9.7 + - - +
222B TYR* 4.0 3.7 - - - -
223B VAL* 3.1 29.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 201 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B ILE* 4.7 3.8 - - - +
126B HIS 4.5 9.4 - - - +
127B PRO* 5.4 1.2 - - - +
128B THR* 4.8 8.1 + - - -
129B VAL* 6.3 0.2 - - - -
197B THR* 2.9 38.1 + - + +
198B LEU* 3.7 26.5 - - - +
200B ASP* 1.3 76.0 - - + +
202B ALA* 1.3 63.4 + - - +
204B HIS* 3.1 10.3 + - - +
205B ARG* 3.0 43.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 202 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B GLN* 3.4 30.6 + - + +
158B LEU* 4.1 16.4 - - + -
198B LEU 3.1 12.8 + - - +
199B PHE* 3.4 9.0 - - + +
201B GLU* 1.3 79.9 - - - +
203B LEU* 1.3 58.5 + - - +
205B ARG* 3.3 16.3 + - - +
206B ASP* 3.0 31.0 + - - +
252B TYR* 4.2 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 203 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B LEU* 3.8 22.2 - - + -
199B PHE* 2.9 21.7 + - + +
200B ASP* 3.1 3.6 + - - +
202B ALA* 1.3 74.1 - - - +
204B HIS* 1.3 61.0 + - - +
206B ASP* 4.4 1.8 - - + +
207B LEU* 3.0 48.2 + - + +
221B GLN* 3.4 17.4 + - - +
223B VAL 3.6 21.1 - - - +
226B LEU* 4.0 15.5 - - + -
247B LEU* 4.6 3.4 - - + -
252B TYR* 3.7 39.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 204 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B VAL* 3.2 31.2 - - + +
200B ASP* 2.9 55.6 + - - -
201B GLU* 3.5 9.9 - - - +
203B LEU* 1.3 76.5 - - - +
205B ARG* 1.3 64.4 + - + +
207B LEU 3.3 0.5 + - - -
208B ALA* 3.0 25.5 + - - +
211B ARG* 4.2 18.0 + - - -
221B GLN* 3.2 41.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 205 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B ARG* 3.9 9.1 + - - +
45B GLN* 2.9 33.3 + - - +
48B LEU* 5.9 5.7 - - - +
198B LEU 5.0 1.2 + - - -
201B GLU* 3.0 36.8 + - - +
202B ALA* 3.4 20.7 - - - +
204B HIS* 1.3 80.2 - - + +
206B ASP* 1.3 60.8 - - - +
208B ALA* 3.6 13.9 + - - +
209B ASP* 3.6 8.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 206 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B ALA* 4.9 0.5 - - - +
44B ARG* 3.0 54.5 + - - +
45B GLN* 2.8 29.1 + - - +
202B ALA 3.0 9.8 + - - +
203B LEU* 4.0 5.6 - - + +
204B HIS 3.2 0.4 - - - -
205B ARG* 1.3 77.9 - - - +
207B LEU* 1.3 59.0 + - - +
209B ASP* 3.4 7.2 - - - +
210B PHE 5.0 0.7 + - - -
246B THR* 5.0 2.4 - - - +
250B LEU* 3.2 27.8 - - + +
252B TYR* 3.0 28.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 207 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B LEU* 3.0 40.6 + - + +
204B HIS 3.8 0.9 - - - +
206B ASP* 1.3 75.3 - - - +
208B ALA* 1.3 67.2 + - - +
209B ASP 3.2 2.5 - - - -
210B PHE* 3.0 10.4 + - + +
211B ARG* 2.9 24.7 + - + +
219B LEU* 3.9 24.5 - - + -
221B GLN* 4.0 15.0 - - - +
226B LEU* 4.2 20.2 - - + -
243B LEU* 4.1 16.2 - - + -
246B THR* 4.1 16.8 - - + -
247B LEU* 3.9 20.9 - - + -
250B LEU* 4.2 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 208 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B HIS 3.0 17.3 + - - +
205B ARG* 3.7 12.6 - - - +
206B ASP 3.4 0.6 - - - -
207B LEU* 1.3 76.6 - - - +
209B ASP* 1.3 65.2 + - - +
211B ARG* 3.0 16.6 + - - +
212B ILE* 3.0 29.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 209 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B ARG* 3.4 32.6 + - - -
205B ARG 3.6 9.0 - - - +
206B ASP 3.4 8.5 - - - +
208B ALA* 1.3 72.9 - - - +
210B PHE* 1.3 63.2 + - - +
212B ILE* 3.2 8.8 + - - +
213B GLN* 3.0 35.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 210 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B ASP 5.0 0.6 + - - +
207B LEU* 3.0 20.9 + - + +
209B ASP* 1.3 79.9 - - - +
211B ARG* 1.3 65.2 + - - +
213B GLN* 3.2 11.7 + - - +
214B HIS* 3.0 53.0 + + + +
217B LEU* 4.3 10.3 - - + -
219B LEU* 4.0 24.9 - - + -
228B LEU* 4.2 14.1 - - + -
239B GLY 3.8 16.6 - - - -
242B ALA* 3.7 5.2 - - + -
243B LEU* 3.5 43.7 - - + -
246B THR* 3.6 24.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 211 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B HIS* 4.2 13.8 + - - -
207B LEU* 2.9 16.7 + - - +
208B ALA* 3.0 13.9 + - - +
210B PHE* 1.3 78.1 - - - +
212B ILE* 1.3 66.9 + - + +
214B HIS 3.3 21.9 - - - +
215B PRO* 3.4 7.1 - - - +
219B LEU* 2.7 55.5 + - + +
220B LEU* 4.4 0.8 - - - +
221B GLN* 3.5 34.0 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
208B ALA* 3.0 30.2 + - + +
209B ASP* 3.6 9.4 - - - +
210B PHE 3.2 0.2 - - - -
211B ARG* 1.3 82.9 - - + +
213B GLN* 1.3 67.7 + - + +
215B PRO* 3.3 16.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 213 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B ASP* 3.0 27.3 + - - +
210B PHE* 3.2 13.8 + - - +
212B ILE* 1.3 80.5 - - + +
214B HIS* 1.3 81.4 + - + +
215B PRO* 3.5 5.4 - - - +
246B THR* 5.4 2.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 214 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B PHE* 3.0 57.3 + + + +
211B ARG* 3.3 9.9 - - - +
213B GLN* 1.3 100.9 + - + +
215B PRO* 1.3 59.9 - - - +
216B ASP* 3.2 3.4 - - - +
217B LEU* 3.1 49.0 + - + +
238B GLN 5.7 0.2 - - - -
239B GLY* 5.6 1.3 - - - -
242B ALA* 3.8 19.0 - - + +
----------------------------------------------------------
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