Contacts of the helix formed by residues 189 - 207 (chain D) in PDB entry 4O46
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 ALA 189 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183D TYR* 2.8 18.6 + - + +
184D TYR* 4.3 0.4 + - - -
187D GLN* 4.3 12.1 - - + +
188D ASN* 1.3 72.2 - - - +
190D PRO* 1.4 61.4 - - - +
191D GLU* 3.3 2.7 - - - -
192D GLN* 3.5 34.9 + - + +
193D ALA* 3.1 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 190 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184D TYR* 3.6 36.5 - - + +
188D ASN* 3.4 18.8 - - - +
189D ALA* 1.4 83.8 - - - +
191D GLU* 1.4 57.9 + - + +
193D ALA* 3.3 0.7 + - + +
194D CYS* 2.9 39.0 + - - -
233D TRP 5.9 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 191 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189D ALA 3.3 1.2 - - - -
190D PRO* 1.4 81.2 - - + +
192D GLN* 1.4 58.9 + - + +
194D CYS* 3.6 4.6 + - - +
195D HIS* 3.1 29.8 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
183D TYR* 3.5 39.8 + - + -
187D GLN* 5.8 0.8 - - - +
189D ALA* 3.5 30.4 + - + +
190D PRO 3.4 0.4 - - - -
191D GLU* 1.4 75.6 - - + +
193D ALA* 1.3 59.4 + - - +
195D HIS* 3.9 6.0 - - - +
196D LEU* 3.1 30.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 193 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180D SER* 3.3 35.7 - - - +
183D TYR* 3.7 8.2 - - - +
184D TYR* 3.6 20.9 - - + +
189D ALA 3.1 18.1 + - - +
190D PRO* 3.5 6.1 - - + +
192D GLN* 1.3 76.3 - - - +
194D CYS* 1.4 56.8 + - - +
197D ALA* 3.1 25.5 + - - +
233D TRP* 3.8 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 194 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190D PRO* 2.9 23.3 + - - +
191D GLU* 4.0 4.9 - - - +
193D ALA* 1.4 71.7 - - - +
195D HIS* 1.4 55.8 + - - +
197D ALA* 3.4 1.9 + - - +
198D LYS* 2.8 37.9 + - - +
230D LEU* 3.9 14.2 - - + +
233D TRP* 3.7 37.5 - - - -
234D THR* 4.1 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 195 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191D GLU 3.1 19.2 + - - +
192D GLN* 3.9 7.2 - - - +
194D CYS* 1.4 75.9 - - - +
196D LEU* 1.3 56.3 + - + +
198D LYS* 4.0 3.8 - - - +
199D THR* 2.6 56.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 196 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158D HIS* 3.5 35.4 - - + +
176D ALA* 3.9 15.9 - - + +
179D TYR* 3.6 25.8 - - + -
180D SER* 3.5 27.1 - - - +
183D TYR* 3.7 17.0 - - + -
192D GLN 3.1 17.7 + - - +
193D ALA 3.9 2.9 - - - +
195D HIS* 1.3 80.2 - - - +
197D ALA* 1.3 57.6 + - - +
199D THR* 4.0 4.5 - - - -
200D ALA* 3.1 31.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 197 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176D ALA 5.1 0.2 - - - -
180D SER* 4.1 10.7 - - - +
193D ALA 3.1 18.2 + - - +
194D CYS 3.9 1.8 - - - +
196D LEU* 1.3 74.1 - - - +
198D LYS* 1.4 64.4 + - - +
200D ALA* 3.9 2.1 - - - +
201D PHE* 3.1 24.6 + - - +
226D LEU* 3.8 29.2 - - + +
229D ASN* 5.8 0.7 - - + -
230D LEU* 3.7 22.1 - - + +
233D TRP* 4.2 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 198 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194D CYS 2.8 22.1 + - - +
195D HIS* 4.0 4.7 - - - +
197D ALA* 1.4 71.0 - - - +
199D THR* 1.4 54.0 - - - +
201D PHE* 3.3 4.3 + - + +
202D ASP* 2.8 72.0 + - - +
230D LEU* 3.5 22.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 199 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195D HIS* 2.6 47.2 + - + +
196D LEU* 4.0 5.8 - - - -
198D LYS* 1.4 74.0 - - - +
200D ALA* 1.3 53.4 + - - +
202D ASP* 3.7 5.3 - - - -
203D ASP* 2.8 60.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 200 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167D PRO* 4.5 2.3 - - - +
172D ARG* 6.2 1.1 - - - +
173D LEU* 3.9 10.0 - - + +
176D ALA* 3.5 28.3 - - + -
196D LEU* 3.1 20.6 + - + +
197D ALA 3.9 4.5 - - - +
199D THR* 1.3 75.9 - - - +
201D PHE* 1.4 60.8 + - - +
203D ASP* 3.7 5.1 + - - +
204D ALA* 3.2 24.1 + - - +
226D LEU* 4.4 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 201 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173D LEU* 5.3 0.2 - - - -
197D ALA 3.1 19.5 + - - +
198D LYS* 3.7 5.8 - - + +
200D ALA* 1.4 73.7 - - - +
202D ASP* 1.4 71.8 + - - +
204D ALA* 3.4 5.6 + - - +
205D ILE* 2.9 38.6 + - + +
223D MET* 3.3 53.2 - - + +
224D GLN* 5.5 0.2 - - - -
226D LEU* 4.4 13.8 - - + +
227D ARG* 4.1 19.3 - - + -
230D LEU* 5.1 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 202 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198D LYS* 2.8 62.6 + - - +
199D THR* 3.9 4.7 + - - +
201D PHE* 1.4 80.4 - - - +
203D ASP* 1.4 63.7 + - - +
205D ILE* 3.7 6.8 - - - +
206D ALA* 2.9 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 203 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167D PRO* 3.6 21.7 - - + +
172D ARG* 4.0 14.5 + - - +
199D THR* 2.8 45.8 + - - +
200D ALA* 4.1 5.4 - - - +
202D ASP* 1.4 75.1 - - - +
204D ALA* 1.3 60.6 + - - +
206D ALA* 3.5 5.9 + - - +
207D GLU* 3.4 30.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 204 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167D PRO* 3.5 19.9 - - - +
168D THR* 3.4 22.0 - - + +
173D LEU* 3.8 11.7 - - + -
200D ALA 3.2 19.3 + - - +
201D PHE 3.7 4.3 - - - +
203D ASP* 1.3 73.7 - - - +
205D ILE* 1.4 64.5 + - - +
207D GLU 3.5 0.2 - - - -
208D LEU* 3.3 22.3 + - - +
223D MET* 3.9 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 205 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201D PHE* 2.9 28.9 + - + +
202D ASP* 3.7 8.7 - - - +
203D ASP 3.4 0.2 - - - -
204D ALA* 1.4 74.4 - - - +
206D ALA* 1.4 62.7 - - - +
207D GLU 3.3 0.9 + - - -
208D LEU* 3.4 33.0 + - + +
223D MET* 4.1 7.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 206 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202D ASP 2.9 17.3 + - - +
203D ASP* 3.6 9.9 - - - +
205D ILE* 1.4 76.1 - - - +
207D GLU* 1.3 67.1 + - + +
208D LEU 3.7 0.8 + - - -
209D ASP* 4.7 5.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 207 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166D GLN* 5.4 1.6 - - - +
167D PRO* 3.5 34.6 - - + +
168D THR* 3.3 3.5 - - + +
203D ASP* 3.4 16.8 + - - +
204D ALA 3.5 5.1 + - - -
205D ILE 3.2 0.4 - - - -
206D ALA* 1.3 84.9 - - + +
208D LEU* 1.3 58.3 + - - +
209D ASP* 3.0 11.4 - - - +
210D THR* 2.6 53.9 + - + +
----------------------------------------------------------
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