Contacts of the helix formed by residues 184 - 196 (chain F) in PDB entry 1YPO
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 184 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182F ILE* 3.1 9.0 - - - +
183F ASN* 1.3 79.7 - - - +
185F THR* 1.3 63.6 - - - +
186F ALA* 3.5 12.4 - - - +
187F ASP* 2.4 52.6 + - - +
224F MET* 5.7 0.2 - - - -
227F LEU* 3.7 10.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 185 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182F ILE* 5.3 0.2 - - - -
184F SER* 1.3 70.3 - - - +
186F ALA* 1.3 56.6 + - - +
188F LEU* 2.8 14.2 + - + +
189F ASP* 2.7 44.7 + - - +
226F HIS 3.9 21.1 - - - +
227F LEU* 3.8 19.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 186 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151F HIS* 5.0 2.9 + - - -
184F SER* 3.5 13.4 - - - +
185F THR* 1.3 82.6 + - - +
187F ASP* 1.3 62.5 + - - +
189F ASP* 3.3 13.1 + - - +
190F PHE* 3.1 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 187 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151F HIS* 6.0 2.2 - - - -
154F ASN* 5.4 3.8 + - - -
156F TYR* 4.7 13.4 + - - +
180F LEU* 5.9 2.0 - - + -
181F LYS 4.0 8.9 - - - +
182F ILE* 3.7 17.0 - - + -
183F ASN* 3.5 18.6 + - - +
184F SER* 2.4 40.6 + - - +
186F ALA* 1.3 80.3 - - - +
188F LEU* 1.3 58.7 + - - +
190F PHE* 3.4 5.9 + - - +
191F ILE* 3.2 29.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 188 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182F ILE* 3.3 31.4 - - + +
184F SER 3.4 1.6 + - - +
185F THR* 2.8 21.5 + - - +
187F ASP* 1.3 73.0 - - - +
189F ASP* 1.3 59.5 + - - +
191F ILE* 3.3 3.0 + - + +
192F GLN* 2.8 34.8 + - + +
227F LEU 4.4 8.7 - - - +
228F PHE* 4.3 27.8 - - + -
246F ILE* 3.3 28.9 - - + -
249F GLY 4.3 13.9 - - - +
250F ALA* 6.1 0.4 - - - -
251F VAL* 4.9 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 189 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185F THR* 2.7 34.9 + - - +
186F ALA* 3.3 12.5 + - - +
188F LEU* 1.3 74.9 - - - +
190F PHE* 1.3 61.0 + - - +
192F GLN* 3.6 5.6 - - - +
193F GLN* 3.0 37.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 190 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147E ASP* 3.8 17.5 - - - -
149F ILE* 4.0 18.2 - - + -
151F HIS* 3.2 54.5 - + + +
156F TYR* 3.4 36.6 - + + -
158F PHE* 4.7 1.6 - + - -
186F ALA 3.1 10.5 + - - +
187F ASP* 3.7 8.7 - - - +
189F ASP* 1.3 74.0 - - - +
191F ILE* 1.3 85.7 + - + +
193F GLN* 3.3 9.3 + - + +
194F ALA* 2.8 44.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 191 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156F TYR* 4.0 19.7 - - + -
158F PHE* 4.5 11.2 - - + -
180F LEU* 3.9 29.6 - - + -
182F ILE* 5.5 1.1 - - + -
187F ASP 3.2 16.8 + - - +
188F LEU* 3.9 6.3 - - + +
190F PHE* 1.3 100.8 - - + +
192F GLN* 1.3 62.1 + - - +
194F ALA* 3.2 3.1 + - - +
195F ILE* 2.9 42.6 + - + +
246F ILE* 4.2 13.7 - - + -
263F ILE* 4.0 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 192 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188F LEU* 2.8 22.6 + - + +
189F ASP* 3.6 7.6 - - - +
191F ILE* 1.3 78.0 - - - +
193F GLN* 1.3 57.9 + - + +
194F ALA 3.2 0.2 + - - -
195F ILE* 3.6 7.8 - - - +
196F SER* 2.7 41.3 + - - -
246F ILE* 5.0 4.5 - - + +
248F ARG 4.0 5.1 + - - -
249F GLY* 3.0 38.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 193 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158E PHE 5.5 1.7 - - - +
160E SER* 4.1 13.4 - - - +
189F ASP* 3.0 25.9 + - - +
190F PHE* 3.9 6.3 - - + +
192F GLN* 1.3 85.6 - - + +
194F ALA* 1.3 62.0 + - - +
196F SER* 3.4 20.3 + - - -
197F TYR* 5.2 1.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 194 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158E PHE 5.3 0.2 - - - +
149F ILE* 5.5 4.3 - - + -
158F PHE* 3.9 26.2 - - + -
190F PHE* 2.8 33.3 + - + +
191F ILE* 3.4 7.6 - - - +
192F GLN 3.1 0.2 - - - -
193F GLN* 1.3 77.1 - - - +
195F ILE* 1.3 58.5 + - - +
196F SER 3.4 0.4 - - - -
197F TYR* 3.0 31.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 195 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197E TYR* 5.7 1.1 - - + -
158F PHE* 3.3 37.9 - - + -
191F ILE* 2.9 23.7 + - + +
192F GLN* 3.8 7.9 - - - +
194F ALA* 1.3 74.2 - - - +
196F SER* 1.3 55.7 + - - +
197F TYR* 3.1 9.6 - - - +
198F SER* 2.7 33.6 + - - -
200F PHE 5.7 0.4 - - - +
202F PHE* 3.8 39.9 - - + -
246F ILE* 4.1 33.0 - - + +
247F GLN* 5.4 2.9 - - - -
249F GLY* 6.1 1.1 - - - +
263F ILE* 4.4 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 196 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160E SER* 3.3 30.7 + - - -
261E PHE* 4.7 4.5 - - - -
192F GLN* 2.7 29.1 + - - -
193F GLN* 3.4 11.1 + - - -
194F ALA 3.4 1.4 - - - -
195F ILE* 1.3 76.5 - - - +
197F TYR* 1.3 61.2 + - - +
198F SER 3.0 13.3 + - - +
----------------------------------------------------------
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