Contacts of the helix formed by residues 202 - 224 (chain D) in PDB entry 5DYE
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 202 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122D LEU* 4.0 21.5 - - + -
128D GLN* 3.6 29.6 - - + +
200D SER* 3.2 10.4 + - - +
201D PRO* 1.3 79.9 - - - +
203D HIS* 1.3 61.1 + - - +
204D TRP* 3.2 10.5 - - - -
205D VAL* 3.3 25.4 + - + +
206D PHE* 3.9 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 203 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189D SER* 3.8 39.2 - - - -
190D PHE* 4.4 4.8 + - - -
193D ALA* 4.0 5.3 - - + +
198D ARG 5.5 0.2 + - - -
199D PHE* 3.9 34.4 - + + -
200D SER* 3.1 27.0 + - - +
201D PRO 3.8 0.2 - - - -
202D ALA* 1.3 73.1 - - - +
204D TRP* 1.3 63.8 + - - +
205D VAL 3.2 1.1 - - - -
206D PHE* 3.3 26.2 + + - +
207D TRP* 3.4 38.3 + + - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 204 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128D GLN* 3.0 42.1 + - + -
132D MET* 3.7 33.7 - - + -
201D PRO 4.1 5.2 - - - -
202D ALA* 3.8 16.2 - - - +
203D HIS* 1.3 76.6 - - - +
205D VAL* 1.3 75.0 + - + +
206D PHE 3.4 0.2 - - - -
207D TRP* 4.1 6.1 - - - +
208D VAL* 3.2 42.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 205 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122D LEU* 5.4 1.6 - - + -
128D GLN* 4.5 10.3 - - + +
131D ALA* 3.9 13.9 - - + +
132D MET* 3.7 38.1 - - + +
135D GLU* 4.6 8.3 - - + +
180D THR* 5.3 0.7 - - + -
202D ALA* 3.3 24.9 + - + +
203D HIS 3.2 0.6 - - - -
204D TRP* 1.3 106.3 - - + +
206D PHE* 1.3 68.7 + - + +
209D GLY* 2.9 28.3 + - - +
210D PRO* 3.6 1.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 206 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120D ASN* 3.5 42.6 - - + -
121D ALA* 4.1 9.2 - - - -
122D LEU* 5.0 8.1 - - + -
135D GLU* 5.1 3.1 - - + -
180D THR* 4.0 24.9 - - + -
183D SER* 4.3 12.6 + - - +
186D PRO* 3.5 14.8 - - - +
189D SER* 3.4 24.5 - - - +
200D SER* 4.0 15.3 - - - -
202D ALA* 3.9 14.1 - - + -
203D HIS* 3.3 35.3 + + + +
205D VAL* 1.3 83.4 - - + +
207D TRP* 1.3 60.8 + - - +
210D PRO* 3.2 24.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 207 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70D PRO* 5.1 6.1 - - + -
91D VAL* 5.6 2.0 - - + -
95D LEU* 3.5 39.5 - - + -
186D PRO* 3.7 26.4 - - + +
189D SER* 6.3 0.2 - - - -
190D PHE* 3.7 35.1 - + + -
203D HIS* 3.4 46.4 + + - -
204D TRP* 4.2 7.4 - - - +
205D VAL 3.4 0.2 - - - -
206D PHE* 1.3 80.4 - - - +
208D VAL* 1.3 70.4 + - + +
210D PRO* 3.6 0.9 - - - +
211D ILE* 3.3 45.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 208 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132D MET* 3.3 24.5 - - + -
204D TRP* 3.2 30.2 + - + +
207D TRP* 1.3 79.7 - - + +
209D GLY* 1.3 65.9 + - - +
211D ILE* 5.0 3.1 - - - -
212D VAL* 3.0 46.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 209 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132D MET* 4.1 20.8 - - - +
135D GLU* 3.9 13.7 - - - -
136D LEU* 3.5 16.8 - - - +
205D VAL 2.9 16.4 + - - -
208D VAL* 1.3 77.1 - - - +
210D PRO* 1.4 65.0 - - - +
212D VAL* 4.2 1.3 - - - +
213D GLY 3.2 17.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 210 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71D ALA* 3.5 18.3 - - + +
135D GLU* 3.8 22.2 - - + +
139D THR* 3.6 15.8 - - - +
183D SER* 4.7 1.3 - - - +
184D MET* 3.6 22.2 - - - +
185D ASN 4.2 0.9 - - - +
186D PRO* 3.7 8.3 - - + -
205D VAL 3.6 5.2 - - - +
206D PHE* 3.2 27.8 - - - +
207D TRP 3.6 2.9 - - - +
209D GLY* 1.4 86.9 - - - +
211D ILE* 1.3 59.1 + - - +
213D GLY* 3.3 0.7 + - - -
214D ALA* 2.9 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 211 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70D PRO* 4.0 4.3 - - + +
71D ALA* 3.6 24.9 - - - +
74D LEU* 4.0 33.4 - - + -
186D PRO* 4.0 6.7 - - + -
207D TRP* 3.3 43.4 + - + +
208D VAL* 3.6 3.7 + - - +
209D GLY 3.5 0.6 - - - -
210D PRO* 1.3 75.1 - - - +
212D VAL* 1.3 56.5 + - + +
214D ALA* 3.3 2.6 + - - +
215D VAL* 2.8 53.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 212 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132D MET* 4.9 6.1 - - + -
136D LEU* 4.0 11.9 - - + -
208D VAL* 3.0 42.0 + - + +
209D GLY* 4.2 2.5 - - - +
211D ILE* 1.3 75.6 - - + +
213D GLY* 1.3 60.5 + - - +
215D VAL* 4.0 4.9 - - - +
216D LEU* 2.9 52.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 213 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136D LEU* 3.7 32.7 - - - +
140D PHE* 3.5 23.6 - - - -
209D GLY 3.2 14.0 + - - -
210D PRO 3.7 2.9 - - - -
211D ILE 3.3 0.2 - - - -
212D VAL* 1.3 76.6 - - - +
214D ALA* 1.3 58.8 + - - +
216D LEU* 3.5 1.7 + - - -
217D ALA* 3.2 16.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 214 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71D ALA* 3.1 34.3 - - + +
72D ILE* 4.4 3.4 - - + +
75D ALA* 3.4 15.0 - - + +
139D THR* 4.5 6.5 - - + +
140D PHE 4.6 1.2 - - - +
143D ALA* 3.8 20.4 - - + -
147D PHE* 3.9 3.6 - - - -
210D PRO 2.9 15.9 + - - +
211D ILE 3.7 0.9 - - - +
213D GLY* 1.3 75.7 - - - +
215D VAL* 1.3 60.1 + - - +
217D ALA* 3.4 5.5 + - - +
218D ALA 3.3 15.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 215 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74D LEU 3.4 28.0 - - - +
75D ALA* 3.6 11.7 - - - +
78D VAL* 3.5 32.5 - - + -
211D ILE* 2.8 34.1 + - + +
212D VAL* 4.0 4.9 - - - +
214D ALA* 1.3 73.1 - - - +
216D LEU* 1.3 59.5 + - + +
218D ALA* 3.2 16.6 + - - +
219D ILE* 3.3 20.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 216 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136D LEU* 4.0 16.8 - - + -
140D PHE* 3.9 14.5 - - + -
212D VAL* 2.9 43.5 + - + +
213D GLY* 4.0 4.0 - - - +
215D VAL* 1.3 75.2 - - + +
217D ALA* 1.3 61.4 + - - +
219D ILE* 4.0 24.3 + - + +
220D LEU* 3.7 15.8 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
140D PHE* 3.7 35.0 - - + +
143D ALA* 3.7 11.9 - - + -
144D LEU* 4.1 10.4 - - + +
147D PHE* 3.9 6.1 - - + -
213D GLY 3.2 13.6 + - - +
214D ALA 3.5 10.1 - - - +
215D VAL 3.2 0.4 - - - -
216D LEU* 1.3 76.1 - - - +
218D ALA* 1.3 54.0 + - - +
220D LEU* 3.4 2.6 + - - +
221D TYR* 2.7 36.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 218 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75D ALA 3.7 21.8 - - - +
78D VAL* 5.1 1.1 - - + -
79D GLY* 4.1 8.5 - - - +
147D PHE* 3.7 5.8 - - + -
214D ALA 3.3 8.0 + - - +
215D VAL* 3.2 12.4 + - + +
217D ALA* 1.3 75.9 - - - +
219D ILE* 1.3 60.8 + - + +
222D PHE* 2.8 59.3 + - + +
223D TYR* 3.7 4.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 219 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78D VAL* 5.1 8.1 - - + -
215D VAL* 3.3 23.4 + - + +
216D LEU* 4.1 28.5 - - + +
217D ALA 3.4 0.2 - - - -
218D ALA* 1.3 77.0 - - - +
220D LEU* 1.3 62.9 + - - +
223D TYR* 3.6 27.3 - - + +
224D LEU* 3.3 31.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 220 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B PHE* 3.6 25.6 - - + -
19B LEU* 3.4 31.6 - - + -
140D PHE* 3.7 18.2 - - + -
144D LEU* 4.3 9.4 - - + -
216D LEU 3.7 10.7 + - - +
217D ALA 3.4 7.5 + - - +
218D ALA 3.2 0.4 - - - -
219D ILE* 1.3 78.4 - - - +
221D TYR* 1.3 57.7 + - - +
224D LEU* 3.1 27.6 + - + +
225D LEU* 2.7 58.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 221 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B ALA 5.3 2.0 - - - -
144D LEU* 4.3 13.2 - - + -
147D PHE* 3.6 36.6 - - + -
148D ALA* 3.5 30.6 + - + +
151D ASP* 2.7 37.4 + - + +
153D ARG* 4.2 6.3 - - - -
217D ALA 2.7 20.6 + - - +
218D ALA 4.4 0.2 - - - +
220D LEU* 1.3 74.0 - - - +
222D PHE* 1.3 82.8 + + - +
225D LEU* 3.5 13.1 - - + +
226D PHE* 2.7 66.9 + + - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 222 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75D ALA 5.3 0.7 - - - -
76D LEU* 4.6 4.0 - - + -
79D GLY* 4.1 14.8 - - - +
81D GLN* 3.2 45.3 - - + -
147D PHE* 3.8 48.2 - + + -
151D ASP* 5.9 2.9 - - + -
153D ARG* 4.5 9.9 - - - -
218D ALA* 2.8 36.6 + - + +
221D TYR* 1.3 94.7 - + - +
223D TYR* 1.3 70.8 + - + +
226D PHE 3.0 19.4 - - - +
227D PRO* 3.3 10.7 - - - +
228D ASN* 4.1 4.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 223 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78D VAL* 2.6 30.2 + - + -
79D GLY* 3.0 23.7 - - - -
80D ASN* 2.7 28.0 + - - -
218D ALA 4.4 1.3 - - - -
219D ILE* 3.6 37.8 + - + +
221D TYR 3.5 0.2 - - - -
222D PHE* 1.3 86.4 - - + +
224D LEU* 1.3 68.6 + - + +
227D PRO* 4.0 15.3 - - - +
228D ASN* 5.8 4.7 - - + -
235D ARG* 4.7 16.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 224 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B LYS* 3.2 22.0 + - + -
15B PHE* 6.2 0.7 - - + -
219D ILE* 3.3 22.2 + - + +
220D LEU* 3.1 31.7 + - + +
223D TYR* 1.3 81.9 - - + +
225D LEU* 1.3 67.7 + - + +
227D PRO* 3.7 3.6 - - - +
----------------------------------------------------------
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