Contacts of the helix formed by residues 200 - 216 (chain D) in PDB entry 3OLJ
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 MET 200 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129D HIS* 3.5 49.1 - - + +
132D ALA* 3.7 15.3 - - + -
192D PHE* 3.6 35.0 - - + +
193D LEU* 4.1 5.6 - - - -
196D ALA* 2.9 36.6 + - + +
197D ILE 4.7 2.1 - - - +
198D GLU 3.7 0.8 - - - -
199D THR* 1.3 82.1 - - - +
201D PRO* 1.3 68.2 - - + +
202D CYS* 3.2 18.6 + - - -
203D VAL* 3.3 20.2 + - + +
204D LYS* 3.8 5.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 201 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192D PHE* 6.1 0.4 - - + -
199D THR 3.5 10.3 - - - +
200D MET* 1.3 83.3 - - + +
202D CYS* 1.3 63.6 + - - +
203D VAL 3.1 0.9 + - - -
204D LYS* 3.1 24.0 + - + +
205D LYS 4.6 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 202 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129D HIS* 4.1 13.9 - - - -
200D MET* 3.2 33.3 - - - -
201D PRO* 1.3 79.1 - - - +
203D VAL* 1.3 66.5 + - - +
204D LYS 3.7 0.2 + - - -
205D LYS* 4.7 5.5 + - - +
206D LYS* 5.2 1.6 + - - +
302D GLU* 5.5 0.9 - - - +
303D PHE* 3.2 32.3 - - + +
307D ALA* 3.7 41.9 - - + +
308D LEU* 4.5 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 203 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133D PHE* 3.6 47.1 - - + -
136D ALA* 5.1 3.8 - - + -
196D ALA* 3.9 22.2 - - + +
197D ILE* 4.1 17.7 - - + +
200D MET* 3.3 28.2 + - + +
201D PRO 3.1 0.6 - - - -
202D CYS* 1.3 79.4 - - - +
204D LYS* 1.3 65.3 + - - +
205D LYS 3.5 0.8 + - - -
206D LYS* 3.5 6.6 + - - +
207D ALA* 3.0 27.4 + - + +
303D PHE* 4.8 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 204 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197D ILE 5.3 9.6 - - - +
200D MET 3.8 3.6 + - - +
201D PRO* 3.1 21.7 + - + +
203D VAL* 1.3 80.2 - - - +
205D LYS* 1.3 59.9 + - - +
207D ALA* 4.5 3.4 - - - -
208D ASP* 2.8 57.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 205 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201D PRO 4.6 1.4 + - - -
202D CYS 4.7 4.2 + - - +
203D VAL 3.5 0.6 - - - -
204D LYS* 1.3 78.1 - - - +
206D LYS* 1.3 58.5 + - + +
208D ASP* 3.9 5.2 - - - +
209D TRP* 3.1 29.5 + - - +
212D ARG* 4.8 2.3 + - - -
299D ILE* 4.1 31.9 - - + +
302D GLU* 3.8 33.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 206 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133D PHE* 3.1 39.4 - - + -
202D CYS 5.2 1.7 + - - +
203D VAL 3.5 7.2 + - - +
204D LYS 3.3 0.4 - - - -
205D LYS* 1.3 77.2 - - + +
207D ALA* 1.3 64.7 + - - +
209D TRP* 3.3 2.6 + - - +
210D ALA* 3.0 23.0 + - - +
235D PHE* 3.1 50.4 + - + -
239D SER* 4.7 0.2 + - - -
299D ILE* 3.5 21.5 - - + -
300D GLU* 2.7 27.2 + - - +
303D PHE* 3.2 42.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 207 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133D PHE* 5.7 0.6 - - - -
137D SER* 6.1 1.1 - - - -
140D ILE* 3.8 23.3 - - + -
197D ILE* 4.3 18.8 - - + -
203D VAL* 3.0 31.1 + - + +
204D LYS* 3.8 4.7 - - - +
206D LYS* 1.3 76.8 - - - +
208D ASP* 1.3 59.2 + - - +
210D ALA* 3.4 2.5 + - - +
211D LEU* 3.0 37.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 208 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197D ILE* 6.1 1.0 - - - +
204D LYS* 2.8 59.1 + - - +
205D LYS* 3.9 5.2 - - - +
207D ALA* 1.3 74.7 - - - +
209D TRP* 1.3 57.8 + - - +
211D LEU* 3.8 10.6 - - - +
212D ARG* 2.9 53.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 209 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205D LYS 3.1 18.2 + - - +
206D LYS 3.3 4.9 + - - +
208D ASP* 1.3 78.7 - - - +
210D ALA* 1.3 66.4 + - - +
212D ARG* 3.4 29.6 + - - +
213D TRP* 3.0 56.2 + + - +
227D ALA* 3.5 25.1 - - + -
230D ALA* 4.2 9.6 - - + -
231D VAL* 4.0 6.3 - - + -
235D PHE* 3.6 27.8 - + + -
292D ILE* 3.8 39.0 - - + -
295D ASN* 2.8 29.2 - - - +
296D ALA* 4.2 5.6 - - + -
299D ILE* 3.4 21.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 210 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140D ILE* 3.7 24.9 - - + -
206D LYS 3.0 13.3 + - - +
207D ALA 3.8 2.0 - - - +
209D TRP* 1.3 85.6 - - - +
211D LEU* 1.3 62.9 + - - +
213D TRP* 3.1 23.0 + - - +
214D ILE* 3.5 4.2 + - - +
228D PHE* 3.6 11.9 - - + -
231D VAL* 3.8 28.0 - - + -
235D PHE* 5.0 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 211 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140D ILE* 3.8 30.7 - - + -
143D GLU* 3.7 23.6 - - - +
197D ILE* 5.0 14.1 - - + -
207D ALA* 3.0 31.1 + - + +
208D ASP* 3.9 10.8 - - - +
209D TRP 3.3 0.2 - - - -
210D ALA* 1.3 73.1 - - - +
212D ARG* 1.3 65.1 + - - +
214D ILE* 3.1 12.8 + - + +
215D GLY* 3.1 17.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 212 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205D LYS 4.8 1.8 + - - -
208D ASP* 2.9 39.8 + - - +
209D TRP* 3.6 37.2 + - - +
210D ALA 3.3 0.4 - - - -
211D LEU* 1.3 74.8 - - - +
213D TRP* 1.3 59.4 - - + +
215D GLY* 3.4 2.5 + - - +
216D ASP* 2.9 31.1 + - - +
299D ILE* 5.8 0.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 213 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144D ASN* 4.7 1.9 - - - +
148D ARG* 3.6 11.6 + - - -
209D TRP* 3.0 60.2 - + - +
210D ALA* 3.1 10.3 + - - +
212D ARG* 1.3 76.3 - - + +
214D ILE* 1.3 63.9 + - - +
216D ASP* 3.9 11.9 + - - +
219D ALA* 3.9 22.2 - - + -
223D GLU* 4.3 11.7 - - + -
224D ARG* 3.8 33.9 + - + +
227D ALA* 3.5 22.9 - - + -
228D PHE* 3.9 15.7 - + + -
231D VAL* 5.9 0.2 - - + -
288D ARG* 3.5 27.1 - - - -
292D ILE* 3.9 28.5 - - + -
295D ASN* 6.2 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 214 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140D ILE* 3.4 41.5 - - + +
143D GLU* 4.0 29.8 - - + +
144D ASN* 3.7 17.9 - - + +
147D GLU* 4.1 10.8 - - - +
148D ARG* 3.0 47.1 + - + +
210D ALA 3.8 3.8 - - - +
211D LEU* 3.1 12.0 + - + +
213D TRP* 1.3 78.8 - - - +
215D GLY* 1.3 58.4 + - - +
228D PHE* 3.7 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 215 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211D LEU 3.1 12.7 + - - -
212D ARG* 3.4 3.1 + - - -
214D ILE* 1.3 76.8 - - - +
216D ASP* 1.3 57.5 + - - +
217D LYS* 3.1 24.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 216 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148D ARG* 2.9 24.9 + - - -
212D ARG 2.9 17.2 + - - +
213D TRP* 4.1 19.1 - - - +
214D ILE 3.3 2.2 - - - -
215D GLY* 1.3 72.7 - - - +
217D LYS* 1.3 60.5 + - - +
218D GLU* 2.8 37.1 + - - +
219D ALA* 2.8 31.2 + - + +
224D ARG* 4.3 2.3 - - - -
288D ARG* 5.8 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