Contacts of the helix formed by residues 184 - 194 (chain D) 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 D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182D ILE* 3.1 14.9 + - - +
183D ASN* 1.3 82.2 - - - +
185D THR* 1.3 61.3 + - - +
186D ALA* 3.9 8.0 + - - +
187D ASP* 3.1 44.9 + - - +
188D LEU* 3.2 2.1 + - - +
224D MET* 5.7 0.4 - - - -
227D LEU* 3.5 20.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 185 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A ARG* 3.4 36.7 + - - +
184D SER* 1.3 70.4 - - - +
186D ALA* 1.3 61.3 + - - +
187D ASP 3.1 1.3 - - - -
188D LEU* 3.3 8.2 + - + +
189D ASP* 2.9 34.7 + - - +
226D HIS 4.6 11.7 - - - +
227D LEU* 3.8 21.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 186 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151D HIS* 5.1 2.7 + - - -
184D SER* 3.3 8.0 + - - +
185D THR* 1.3 79.3 + - - +
187D ASP* 1.3 63.8 + - - +
189D ASP* 3.4 9.3 + - - +
190D PHE* 3.2 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 187 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151D HIS* 5.7 6.1 - - - -
154D ASN* 5.5 1.7 + - - -
156D TYR* 3.9 17.9 + - - -
180D LEU* 5.7 1.7 - - + +
181D LYS 3.8 9.2 - - - +
182D ILE* 3.4 14.9 - - + +
183D ASN* 3.4 18.5 + - - +
184D SER* 3.1 31.9 + - - +
186D ALA* 1.3 84.1 - - - +
188D LEU* 1.3 57.7 + - - +
190D PHE* 3.6 6.3 + - - +
191D ILE* 3.4 28.6 + - - +
265D GLN* 5.3 0.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 188 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A ARG* 4.4 9.2 - - - +
213A TYR* 2.8 52.0 + - + +
182D ILE* 4.0 21.3 - - + -
184D SER 3.2 8.9 + - - +
185D THR* 3.3 12.1 + - + +
186D ALA 3.2 0.2 - - - -
187D ASP* 1.3 77.8 - - - +
189D ASP* 1.3 62.5 + - - +
190D PHE 3.2 2.0 + - - -
191D ILE* 4.1 3.0 - - - +
192D GLN* 3.4 16.6 + - - +
227D LEU* 4.6 7.6 - - + +
228D PHE* 3.6 44.4 - - + -
246D ILE* 4.6 9.7 - - + +
249D GLY 4.1 9.9 - - - +
251D VAL* 5.0 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 189 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A ARG* 2.9 23.8 + - - -
210A ASN* 2.9 28.6 + - - +
212A SER* 4.6 3.6 + - - -
213A TYR* 2.9 16.7 + - - -
185D THR* 2.9 23.5 + - - +
186D ALA* 3.4 9.3 + - - +
188D LEU* 1.3 76.7 - - - +
190D PHE* 1.3 60.2 + - - +
192D GLN* 4.0 3.5 - - - +
193D GLN* 3.5 19.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 190 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147C ASP* 3.7 27.8 - - - -
149D ILE* 3.9 22.2 - - + -
151D HIS* 3.5 48.5 - + + +
156D TYR* 3.8 30.5 - + + -
158D PHE* 5.4 1.1 - + - -
186D ALA 3.2 15.3 + - - +
187D ASP* 3.9 5.2 - - - +
188D LEU 3.2 0.6 - - - -
189D ASP* 1.3 75.6 - - - +
191D ILE* 1.3 83.0 + - + +
192D GLN 2.9 5.8 + - - -
193D GLN* 2.9 22.1 + - + -
194D ALA* 3.0 22.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 191 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156D TYR* 4.0 24.7 - - + -
158D PHE* 4.2 14.6 - - + -
180D LEU* 3.8 28.5 - - + -
182D ILE* 5.1 2.7 - - + -
187D ASP 3.4 16.9 + - - +
188D LEU* 3.8 6.0 + - - +
190D PHE* 1.3 97.1 - - + +
192D GLN* 1.3 57.9 + - - +
194D ALA* 3.6 3.3 + - - +
195D ILE* 3.3 27.6 + - + +
246D ILE* 4.2 22.0 - - + -
263D ILE* 3.9 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 192 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A SER* 3.2 25.1 - - - +
213A TYR* 3.4 36.8 - - + +
214A PRO* 3.7 3.6 - - - +
188D LEU* 3.4 17.4 + - + +
189D ASP 4.0 3.4 - - - +
190D PHE 2.9 0.6 - - - -
191D ILE* 1.3 77.6 - - - +
193D GLN* 1.3 59.7 + - - +
194D ALA 3.0 1.8 - - - -
195D ILE* 3.4 18.3 - - - +
196D SER* 2.8 31.4 + - - -
246D ILE* 5.6 1.8 - - + -
248D ARG* 3.3 7.6 + - - +
249D GLY* 2.8 40.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 193 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A SER* 3.5 12.5 + - - +
147C ASP* 3.7 24.4 + - - +
157C LEU* 5.5 7.3 - - - +
158C PHE 5.2 6.0 + - - +
160C SER* 3.9 32.3 + - - +
189D ASP 3.5 12.6 + - - +
190D PHE* 2.9 16.7 + - + +
192D GLN* 1.3 78.9 - - - +
194D ALA* 1.3 57.7 + - - +
195D ILE 3.4 0.2 - - - -
196D SER* 3.3 18.8 + - - -
197D TYR* 5.2 1.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 194 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197C TYR* 4.9 0.5 + - - -
149D ILE* 4.9 8.5 - - + +
158D PHE* 3.5 33.2 - - + -
190D PHE* 3.0 27.0 + - + +
191D ILE* 3.7 5.8 - - - +
192D GLN 3.0 0.4 - - - -
193D GLN* 1.3 79.5 - - - +
195D ILE* 1.3 60.8 + - - +
196D SER 3.5 0.2 - - - -
197D TYR* 3.4 26.2 + - - -
----------------------------------------------------------
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