Contacts of the helix formed by residues 184 - 205 (chain D) in PDB entry 3OX4
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 PRO 184 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41D PHE* 6.1 2.0 - - + -
182D GLY 3.4 9.2 - - - +
183D MET* 1.3 85.1 - - + +
185D LYS* 1.3 66.8 + - - +
186D GLY* 3.2 4.8 + - - +
187D LEU* 3.2 16.1 + - + +
188D THR* 2.9 22.7 + - - -
1385D NAD 3.6 17.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 185 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183D MET 3.9 0.4 + - - -
184D PRO* 1.3 71.1 - - - +
186D GLY* 1.3 62.6 + - - +
188D THR* 3.6 6.6 - - - -
189D ALA* 3.0 23.7 + - - +
228D LYS* 5.1 0.2 - - - +
231D CYS* 3.9 32.3 + - + +
232D ASP* 3.9 18.8 + - - +
333D SER 4.3 4.2 + - - -
334D ILE* 3.7 34.7 + - - +
335D GLY* 5.1 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 186 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184D PRO* 3.2 3.6 - - - +
185D LYS* 1.3 81.7 - - - +
187D LEU* 1.3 56.3 + - - +
189D ALA* 3.7 3.9 - - - +
190D ALA* 3.0 30.0 + - - +
279D VAL* 5.4 1.6 - - - +
334D ILE 5.8 0.9 - - - -
336D ILE* 5.5 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 187 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139D THR* 3.8 9.0 - - + -
183D MET* 3.8 16.8 - - + -
184D PRO* 3.2 19.8 + - + +
186D GLY* 1.3 70.9 - - - +
188D THR* 1.3 69.0 + - - +
190D ALA* 3.1 6.5 + - + +
191D THR* 2.8 58.3 + - + +
1385D NAD 3.2 62.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 188 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140D ALA* 5.9 1.4 - - + +
183D MET* 3.3 20.2 + - + +
184D PRO 2.9 18.1 + - - -
185D LYS* 3.6 7.5 - - - -
187D LEU* 1.3 76.2 - - - +
189D ALA* 1.3 57.2 + - - +
191D THR* 3.6 1.6 + - - -
192D GLY* 2.9 28.8 + - - -
227D LEU* 3.7 6.6 - - + +
230D ALA* 3.9 21.7 + - + -
231D CYS* 3.6 19.5 - - - -
240D ARG* 2.8 33.1 + - - +
243D MET* 5.6 0.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 189 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185D LYS 3.0 19.5 + - - +
186D GLY* 3.7 4.5 - - - +
188D THR* 1.3 76.9 - - - +
190D ALA* 1.3 56.9 + - - +
192D GLY* 3.9 0.2 - - - -
193D MET* 2.9 36.0 + - - +
227D LEU* 4.3 1.5 - - - +
231D CYS* 3.7 15.0 - - - -
334D ILE* 3.7 37.5 - - + +
336D ILE* 4.1 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 190 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186D GLY 3.0 19.0 + - - +
187D LEU* 3.8 8.1 - - + +
189D ALA* 1.3 77.4 - - - +
191D THR* 1.3 59.5 + - + +
193D MET* 3.4 3.4 + - - +
194D ASP 2.9 21.3 + - - -
276D PRO* 5.9 2.9 - - + -
278D GLY* 3.4 18.2 - - - -
279D VAL* 3.7 34.1 - - + +
336D ILE* 4.2 9.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 191 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139D THR* 3.9 11.2 - - - -
140D ALA* 3.3 19.3 + - - +
141D GLY* 2.8 35.6 - - - -
142D THR* 5.1 0.9 - - + -
183D MET* 3.8 6.1 - - - +
187D LEU* 2.8 49.1 + - + -
188D THR 3.6 3.1 + - - -
190D ALA* 1.3 73.0 - - + +
192D GLY* 1.3 67.1 + - - +
194D ASP* 3.3 7.7 + - + +
195D ALA 3.0 10.0 + - - -
278D GLY* 4.9 2.5 - - - -
1385D NAD 3.5 19.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 192 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140D ALA* 3.5 11.0 - - - -
188D THR 2.9 19.0 + - - -
189D ALA 3.9 0.4 - - - -
191D THR* 1.3 77.6 + - - +
193D MET* 1.3 56.8 + - - +
195D ALA* 3.2 5.7 + - - +
196D LEU* 3.0 23.9 + - - +
223D ILE* 4.0 6.6 - - - +
227D LEU* 3.9 11.0 - - - -
243D MET* 3.7 17.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 193 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189D ALA 2.9 24.9 + - - +
190D ALA 3.7 4.0 - - - +
192D GLY* 1.3 76.0 - - - +
194D ASP* 1.3 59.7 + - - +
196D LEU* 3.2 18.2 + - + +
197D THR* 2.8 32.3 + - - -
227D LEU* 4.1 13.9 - - + -
278D GLY 5.2 0.4 - - - -
282D ALA* 3.7 26.7 - - + +
285D LEU* 4.1 24.5 - - + -
327D VAL* 4.2 12.1 - - + +
330D LEU* 4.4 8.3 - - - -
331D ALA* 4.1 20.6 - - + -
334D ILE* 3.8 18.2 - - + -
336D ILE* 4.1 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 194 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141D GLY 3.8 1.6 - - - +
142D THR* 3.7 15.2 - - - +
190D ALA 2.9 16.6 + - - +
191D THR* 3.5 11.1 - - - +
193D MET* 1.3 77.0 - - - +
195D ALA* 1.3 57.7 + - - +
197D THR* 3.1 7.1 + - - -
198D HIS* 2.9 37.0 + - - -
263D HIS* 3.3 6.2 + - - -
277D HIS* 3.1 22.8 + - - -
278D GLY* 4.0 12.7 + - - +
281D ASN* 3.7 5.4 - - - +
501D FE2 2.1 31.2 - - - -
1385D NAD 5.4 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 195 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140D ALA 4.2 2.2 - - - +
141D GLY* 3.5 21.9 + - - +
191D THR 3.0 14.1 + - - +
192D GLY* 3.3 10.5 - - - +
194D ASP* 1.3 78.1 - - - +
196D LEU* 1.3 61.4 + - - +
198D HIS* 3.2 9.6 + - - +
199D ALA* 3.0 19.6 + - - +
223D ILE* 3.7 14.1 - - + -
243D MET* 5.0 0.9 - - + -
247D GLN* 4.0 20.0 - - + -
250D ALA* 3.5 7.7 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
192D GLY 3.0 13.7 + - - +
193D MET* 3.2 27.8 + - + +
195D ALA* 1.3 75.4 - - - +
197D THR* 1.3 62.4 + - - +
199D ALA* 3.2 4.4 + - - +
200D PHE* 3.0 47.4 + - + -
220D ALA* 4.3 21.1 - - + -
223D ILE* 3.4 25.5 - - + +
285D LEU* 4.4 5.6 - - + -
307D MET* 4.3 16.6 - - + -
327D VAL* 4.7 5.2 - - + -
330D LEU* 4.0 26.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 197 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193D MET 2.8 21.7 + - - -
194D ASP* 3.3 10.1 - - - -
196D LEU* 1.3 72.9 - - - +
198D HIS* 1.3 61.1 + - - +
200D PHE* 3.3 1.0 + - - +
201D GLU* 2.9 38.9 + - + +
262D VAL* 3.5 33.2 - - + -
263D HIS* 3.3 26.0 - - + +
281D ASN* 3.8 16.4 + - - +
282D ALA* 4.5 0.3 + - - -
285D LEU* 3.8 23.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 198 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141D GLY 3.1 28.8 + - - -
142D THR* 3.6 17.2 + - - -
143D ALA* 5.4 0.4 - - - +
194D ASP* 2.9 19.7 + - - -
195D ALA* 3.2 9.6 - - - +
197D THR* 1.3 75.6 - - - +
199D ALA* 1.3 62.2 + - - +
202D ALA* 2.9 29.3 + - - +
250D ALA* 3.8 10.5 - - + +
254D PHE* 3.5 30.9 - + + +
259D LEU* 3.9 15.3 - - + +
263D HIS* 3.2 16.8 + + - -
501D FE2 2.2 31.2 - - - -
1385D NAD 3.6 8.4 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 199 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195D ALA 3.0 12.0 + - - +
196D LEU* 3.2 11.4 + - + +
198D HIS* 1.3 75.3 - - - +
200D PHE* 1.3 57.6 + - + +
202D ALA* 4.7 0.7 - - - -
203D TYR* 2.9 31.6 + - - +
216D ALA* 3.5 36.0 - - - +
219D ALA* 4.2 14.4 - - + -
220D ALA* 4.2 12.3 - - + +
250D ALA* 4.3 4.4 - - - +
303D VAL* 5.8 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 200 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196D LEU* 3.0 45.9 + - + +
197D THR 3.6 6.1 - - - +
199D ALA* 1.3 75.9 - - - +
201D GLU* 1.3 58.1 + - + +
203D TYR* 3.3 5.9 + - - +
204D SER* 2.8 34.1 + - - -
285D LEU* 4.3 14.1 - - + -
289D LEU* 3.8 32.5 - - + -
300D LEU* 3.9 15.9 - - + -
303D VAL* 3.3 39.5 - - + +
307D MET* 4.0 3.6 - - - -
323D THR* 3.6 24.7 - - + -
327D VAL* 3.7 26.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 201 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197D THR* 2.9 30.5 + - + +
200D PHE* 1.3 71.9 - - + +
202D ALA* 1.3 55.9 + - - +
204D SER* 3.2 5.3 + - - +
205D SER* 2.7 36.4 + - - -
258D SER 4.3 2.0 - - - -
259D LEU* 3.5 20.7 - - + +
260D GLY* 3.0 26.0 + - - +
261D TYR 3.3 1.0 + - - -
262D VAL* 2.9 39.7 + - + +
263D HIS* 2.6 36.4 + - - -
288D VAL* 4.7 0.5 - - - +
289D LEU* 6.3 0.7 - - + -
292D ASN* 5.3 1.6 + - - -
366D ASN* 4.3 2.3 - - - +
367D PRO* 5.7 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 202 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198D HIS 2.9 18.8 + - - +
199D ALA 3.9 1.6 - - - +
201D GLU* 1.3 77.4 - - - +
203D TYR* 1.3 62.4 + - - +
204D SER 3.5 0.3 + - - -
205D SER* 3.5 11.0 + - - -
208D ALA* 3.6 14.2 - - - +
212D THR* 4.6 2.2 + - - -
216D ALA* 4.6 1.3 - - + -
253D ALA* 3.6 34.3 - - + +
254D PHE* 3.6 16.6 - - - +
257D ALA* 3.7 7.5 - - + +
258D SER 3.6 11.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 203 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199D ALA 2.9 19.4 + - - +
200D PHE 3.6 4.5 - - - +
202D ALA* 1.3 77.5 - - - +
204D SER* 1.3 57.6 + - - +
205D SER 4.5 0.2 - - - +
208D ALA* 4.3 2.8 - - - +
213D ASP* 3.4 41.1 - - + +
216D ALA* 4.1 6.9 - - + +
217D LEU* 3.5 35.5 - - + +
299D ARG* 2.7 86.2 + - + -
300D LEU* 6.4 0.2 - - + -
302D ASP* 3.2 22.6 + - + +
303D VAL* 3.6 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 204 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200D PHE* 2.8 21.6 + - - +
201D GLU* 3.8 5.8 - - - -
203D TYR* 1.3 79.1 - - - +
205D SER* 1.3 66.1 + - - +
206D THR* 4.6 0.3 - - - +
289D LEU* 5.2 2.4 - - - +
292D ASN* 5.0 4.4 - - - +
296D VAL* 4.1 12.4 - - - +
299D ARG* 4.5 10.5 - - - +
300D LEU* 4.0 21.7 - - - +
367D PRO* 3.3 41.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 205 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201D GLU 2.7 17.3 + - - -
202D ALA* 3.6 12.3 - - - -
203D TYR 3.4 1.5 - - - +
204D SER* 1.3 80.6 - - - +
206D THR* 1.3 58.0 + - - +
207D ALA 2.9 16.6 + - - -
208D ALA* 3.2 16.1 + - - +
257D ALA* 2.6 30.8 + - - -
258D SER 4.2 0.2 - - - -
259D LEU 4.1 7.4 - - - -
299D ARG* 5.6 0.5 + - - -
365D THR* 3.3 19.0 - - - -
367D PRO* 4.8 0.9 - - - -
----------------------------------------------------------
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