Contacts of the helix formed by residues 209 - 229 (chain D) in PDB entry 5Y1Z
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 CYS 209 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133D ILE* 4.3 4.3 - - - -
136D ALA* 3.7 26.2 - - - +
137D GLU* 3.8 22.9 - - + -
146D MET* 4.0 11.9 - - + -
154D LEU* 3.4 17.6 - - - +
158D LEU* 4.8 0.2 - - - +
207D TYR* 4.2 2.6 - - - +
208D GLY* 1.3 78.2 - - - +
210D THR* 1.3 66.2 + - - +
211D GLU* 3.6 18.2 - - - +
212D ALA* 3.5 27.1 + - - +
213D PHE* 3.6 10.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 210 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146D MET* 3.9 9.6 - - + +
154D LEU* 4.1 8.5 - - + -
158D LEU* 5.0 0.9 - - + -
209D CYS* 1.3 75.1 - - - +
211D GLU* 1.3 74.3 + - - +
213D PHE* 3.1 5.2 + - - +
214D LEU* 3.1 22.0 + - - +
249D MET* 3.7 35.7 - - - +
252D ILE* 3.9 28.5 - - + -
253D GLU* 2.8 35.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 211 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129D GLU* 5.0 2.4 - - - +
132D LYS* 4.0 34.0 - - + +
133D ILE* 4.3 12.3 - - + -
136D ALA* 3.4 27.0 - - + +
143D SER* 6.0 2.1 - - - -
146D MET* 5.7 0.7 - - - +
209D CYS* 3.3 8.6 - - - +
210D THR* 1.3 91.2 + - - +
212D ALA* 1.3 58.2 + - - +
214D LEU* 3.2 7.1 + - - +
215D ALA* 2.8 28.2 + - - +
253D GLU* 4.5 6.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 212 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133D ILE* 3.6 34.5 - - + +
137D GLU* 4.1 6.5 - - - +
206D MET 5.7 0.4 - - - +
207D TYR* 4.0 14.5 - - + -
208D GLY 4.7 2.2 - - - +
209D CYS* 3.5 19.6 - - - +
210D THR 3.2 0.4 - - - -
211D GLU* 1.3 78.8 - - - +
213D PHE* 1.3 62.0 + - - +
215D ALA* 3.4 2.1 + - - +
216D ASP* 3.0 25.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 213 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158D LEU* 3.9 31.4 - - + -
161D ALA* 4.6 1.1 - - + -
162D ILE* 3.6 37.0 - - + -
165D MET* 3.2 26.2 - - + -
198D LEU* 4.0 21.1 - - + -
202D ALA* 5.0 0.2 - - + -
207D TYR* 3.5 40.9 - + + -
209D CYS 3.6 5.7 + - - +
210D THR 3.1 9.0 + - - +
212D ALA* 1.3 75.5 - - - +
214D LEU* 1.3 65.9 + - - +
216D ASP* 3.1 4.0 + - - +
217D ALA* 3.0 21.8 + - - +
245D CYS* 3.8 6.5 - - - -
249D MET* 3.3 26.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 214 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132D LYS* 6.4 0.4 - - - +
210D THR 3.1 10.7 + - - +
211D GLU* 3.6 9.6 - - - +
213D PHE* 1.3 77.9 - - - +
215D ALA* 1.3 63.2 + - - +
217D ALA* 3.2 3.0 + - + -
218D LYS* 3.0 57.3 + - + +
242D ILE* 4.3 4.9 - - + +
245D CYS* 3.6 30.1 - - + -
246D GLU* 3.5 38.1 - - + +
249D MET* 4.2 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 215 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92D TRP* 3.6 9.6 - - - -
108D ARG* 3.3 26.8 + - - +
129D GLU* 3.4 28.9 - - - +
133D ILE* 4.1 15.7 - - + -
211D GLU 2.8 15.4 + - - +
212D ALA 3.6 6.7 - - - +
213D PHE 3.2 0.2 - - - -
214D LEU* 1.3 76.6 - - - +
216D ASP* 1.3 63.3 + - - +
218D LYS* 3.5 12.8 + - - +
219D TRP 4.0 0.2 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
108D ARG* 4.6 7.4 + - - -
191D HIS* 5.2 3.1 + - - -
193D MET* 3.9 17.9 - - + +
198D LEU* 4.0 5.8 - - + -
201D ASN* 3.9 7.8 + - - -
206D MET* 6.0 0.5 - - - +
207D TYR* 2.8 37.4 + - + +
212D ALA 3.0 12.8 + - - +
213D PHE 3.1 6.9 + - - +
215D ALA* 1.3 76.6 - - - +
217D ALA* 1.3 66.4 + - - +
219D TRP* 2.9 36.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 217 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165D MET* 5.1 2.0 - - - -
195D LEU* 6.1 0.2 - - + -
198D LEU* 3.7 30.2 - - + +
213D PHE* 3.0 16.5 + - + +
214D LEU 3.7 3.8 - - - +
216D ASP* 1.3 75.1 - - - +
218D LYS* 1.3 56.8 + - - +
220D ILE* 2.8 33.5 + - + +
241D VAL* 6.2 0.2 - - + -
242D ILE* 3.7 16.5 - - + +
245D CYS* 4.1 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 218 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92D TRP* 3.7 28.6 - - + +
129D GLU* 4.2 16.0 + - - +
132D LYS* 5.8 3.6 - - - +
214D LEU* 3.0 47.1 + - + +
215D ALA* 3.7 2.5 - - - +
216D ASP 3.1 0.6 - - - -
217D ALA* 1.3 74.0 - - - +
219D TRP* 1.3 64.5 + - - +
220D ILE 3.1 0.4 - - - -
221D LEU* 3.0 7.3 + - + +
222D HIS* 3.0 22.7 + - - +
242D ILE* 4.0 24.0 - - + -
246D GLU* 4.2 14.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 219 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88D ASP* 3.5 21.3 - - + -
92D TRP* 3.6 9.6 - + - -
107D PRO* 4.0 25.6 - - + +
108D ARG* 3.4 46.6 - - + +
190D PHE 5.9 0.2 - - - -
191D HIS* 3.5 56.1 + + + +
193D MET* 3.8 15.9 - - + -
215D ALA 4.0 1.1 - - - -
216D ASP* 2.9 31.2 + - - +
218D LYS* 1.3 77.4 - - - +
220D ILE* 1.3 57.3 + - - +
222D HIS* 3.4 36.1 - + - -
223D ASN* 2.8 48.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 220 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173D PHE* 3.7 34.4 - - + +
193D MET* 3.4 31.6 - - + +
194D ASP* 3.9 16.6 - - - -
195D LEU* 3.8 30.7 - - + +
198D LEU* 4.2 9.6 - - + -
217D ALA* 2.8 18.2 + - + +
219D TRP* 1.3 77.7 - - - +
221D LEU* 1.3 57.4 + - - +
223D ASN* 3.9 2.7 - - - +
224D CYS* 3.0 27.0 + - - +
238D ALA* 4.5 8.5 - - + -
241D VAL* 5.2 6.3 - - + -
242D ILE* 4.5 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 221 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95D HIS* 5.7 2.9 - - + +
217D ALA 4.0 0.2 + - - -
218D LYS* 3.0 10.8 + - + +
220D ILE* 1.3 78.6 - - - +
222D HIS* 1.3 66.4 + - - +
224D CYS* 3.2 0.7 + - - +
225D ILE* 2.9 47.9 + - + +
235D THR* 4.1 4.7 - - + +
238D ALA* 3.9 21.3 - - + -
239D LYS* 3.9 36.8 - - + -
242D ILE* 4.2 30.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 222 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88D ASP* 2.6 22.3 + - - -
90D TYR* 3.5 10.0 + - + -
91D CYS 3.4 25.1 - - - -
92D TRP* 4.0 19.5 + + + +
95D HIS* 2.9 33.0 + - + +
218D LYS 3.0 15.2 + - - +
219D TRP* 3.4 36.5 - + - +
221D LEU* 1.3 77.3 - - - +
223D ASN* 1.3 64.8 + - - +
225D ILE* 3.2 2.4 + - - +
226D ILE* 2.9 51.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 223 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185D TYR* 3.9 13.4 + - - +
189D ILE* 3.4 35.7 - - + +
190D PHE 5.4 0.2 + - - -
191D HIS 2.7 27.7 + - - -
192D PRO* 3.6 7.3 - - - +
193D MET 3.8 7.6 + - - +
219D TRP* 2.8 31.7 + - - +
220D ILE* 4.0 3.3 - - - +
222D HIS* 1.3 89.0 - - - +
224D CYS* 1.3 57.8 + - - +
226D ILE* 3.3 1.8 + - - +
227D TYR* 2.9 33.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 224 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173D PHE* 3.8 16.4 - - + -
185D TYR* 5.9 0.2 - - - -
220D ILE 3.0 19.0 + - - +
221D LEU 3.2 3.3 + - - +
223D ASN* 1.3 77.2 - - - +
225D ILE* 1.3 58.1 + - - +
228D ASN* 2.9 58.5 + - - +
229D GLY 3.7 0.3 + - - -
234D LEU* 3.5 11.4 - - - -
235D THR* 3.3 38.4 + - + +
238D ALA* 4.2 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 225 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95D HIS* 3.5 49.8 - - + +
221D LEU* 2.9 40.7 + - + +
222D HIS 3.7 3.4 - - - +
224D CYS* 1.3 76.2 - - - +
226D ILE* 1.3 65.5 + - - +
229D GLY* 2.9 26.7 + - - -
230D GLY* 4.3 16.2 - - - +
235D THR* 3.5 22.7 - - + -
239D LYS* 6.0 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 226 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88D ASP* 4.7 1.8 - - - +
90D TYR* 3.5 55.0 - - + +
95D HIS* 4.0 13.7 - - + +
188D TYR* 4.0 15.9 - - + +
189D ILE* 3.9 16.8 - - + -
222D HIS* 2.9 56.6 + - + +
223D ASN* 3.8 8.5 - - - +
225D ILE* 1.3 79.5 - - - +
227D TYR* 1.3 64.4 + - - +
229D GLY* 4.2 1.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 227 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177D VAL* 5.8 0.2 - - + -
182D HIS* 3.4 33.1 + + + +
184D ASP* 2.7 36.9 + - - -
185D TYR* 3.5 45.5 - + + -
188D TYR* 4.1 26.9 - + + -
189D ILE* 4.1 4.5 - - + -
223D ASN 2.9 16.6 + - - +
224D CYS 4.4 0.7 - - - +
226D ILE* 1.3 80.9 - - - +
228D ASN* 1.3 78.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 228 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173D PHE* 5.7 1.0 - - - -
185D TYR* 6.1 0.2 - - - -
224D CYS* 2.9 41.6 + - - +
227D TYR* 1.3 101.4 - - - +
229D GLY* 1.3 59.2 + - - +
232D HIS* 3.5 43.8 + - + +
234D LEU* 3.9 23.8 - - - +
235D THR* 4.3 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 229 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225D ILE* 2.9 19.9 + - - +
226D ILE 4.2 1.8 + - - -
227D TYR 3.7 1.0 - - - -
228D ASN* 1.3 79.7 - - - +
230D GLY* 1.3 59.0 + - - -
231D ASN 3.3 4.0 + - - -
232D HIS 3.5 2.1 + - - -
235D THR* 2.7 28.4 + - - -
----------------------------------------------------------
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