Contacts of the helix formed by residues 217 - 234 (chain P) in PDB entry 3E8E
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 LYS 217 (chain P).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158P HIS* 3.4 68.9 + - + +
161P ASP* 3.2 34.9 + - - +
162P LEU 5.4 1.1 - - - +
163P ILE* 4.0 22.3 - - + +
191P VAL 3.9 11.1 + - - +
192P LYS* 5.4 1.0 - - - +
193P GLY 5.7 1.7 - - - +
216P ASN* 1.3 80.0 - - + +
218P ALA* 1.3 57.8 + - - +
219P VAL* 2.9 6.5 + - - -
220P ASP* 3.0 14.4 + - - +
221P TRP* 4.0 1.7 + - - +
283P ASN* 5.9 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 218 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216P ASN* 3.0 19.7 + - - +
217P LYS* 1.3 77.4 - - - +
219P VAL* 1.3 60.5 + - - +
220P ASP 3.2 0.4 - - - -
221P TRP* 3.1 18.3 + - + +
222P TRP 3.1 17.5 + - - -
277P LEU* 3.7 23.6 - - + -
280P ARG* 3.1 14.3 + - - +
283P ASN* 3.7 25.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 219 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163P ILE* 3.8 18.6 - - + -
165P ARG* 4.5 7.0 - - + -
204P TYR 4.9 1.2 - - - +
206P ALA* 3.9 13.2 + - + +
208P GLU* 3.6 17.7 - - - +
209P ILE* 3.8 27.8 - - + -
215P TYR* 3.5 35.9 - - + -
216P ASN 3.3 13.7 + - - +
217P LYS 2.9 0.8 + - - -
218P ALA* 1.3 76.0 - - - +
220P ASP* 1.3 64.0 + - - +
222P TRP* 3.4 3.3 + - - +
223P ALA* 3.0 28.6 + - - +
280P ARG* 4.2 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 220 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154P PHE* 3.3 36.0 - - + -
158P HIS* 2.8 29.6 + - + +
163P ILE* 3.3 13.1 - - - +
164P TYR* 3.0 23.7 + - - +
165P ARG* 3.0 27.9 + - - -
167P LEU* 5.6 1.0 - - - +
217P LYS 3.0 9.1 + - - +
219P VAL* 1.3 80.5 - - - +
221P TRP* 1.3 59.4 + - - +
223P ALA* 3.5 6.6 + - - +
224P LEU* 3.0 21.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 221 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151P VAL* 3.9 14.6 - - + -
154P PHE* 3.7 31.4 - + + -
155P GLU* 4.4 2.0 - - - -
158P HIS* 3.5 30.2 + + - -
217P LYS* 5.3 0.8 - - + +
218P ALA* 3.1 24.5 + - + +
220P ASP* 1.3 74.0 - - - +
222P TRP* 1.3 68.8 + - - +
224P LEU* 3.3 27.4 + - + +
225P GLY 3.2 13.7 + - - -
272P LEU* 3.9 15.3 - - + +
280P ARG* 4.4 4.0 - - - -
281P PHE 3.6 17.7 - - - +
282P GLY* 3.4 31.5 + - - -
288P VAL* 3.8 32.5 - - + -
291P ILE* 3.3 24.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 222 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203P GLU 5.1 0.6 + - - -
204P TYR 3.8 7.5 - - - -
205P LEU 3.2 13.1 + - - -
206P ALA* 3.5 21.5 - - + -
207P PRO* 3.7 22.7 - - + -
218P ALA 3.1 6.1 + - - -
219P VAL 3.5 7.9 - - - +
221P TRP* 1.3 75.6 - - - +
223P ALA* 1.3 56.9 + - - +
225P GLY* 2.8 24.1 + - - -
226P VAL* 3.2 22.7 + - + +
238P PHE* 3.5 30.2 - + - -
250P ILE* 3.8 20.8 - - + +
253P GLY* 5.3 1.3 - - - -
272P LEU 3.7 11.7 - - - -
273P LEU* 3.3 50.8 - - + +
274P GLN 3.5 10.3 - - - -
275P VAL* 3.9 7.0 - - + -
280P ARG* 3.5 32.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 223 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167P LEU* 3.5 27.9 - - + +
204P TYR* 3.5 34.2 - - + +
219P VAL 3.0 17.3 + - - +
220P ASP* 3.6 9.9 - - - +
221P TRP 3.4 0.2 - - - -
222P TRP* 1.3 76.3 - - - +
224P LEU* 1.3 56.1 + - - +
226P VAL* 3.2 6.1 + - - +
227P LEU 2.9 23.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 224 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147P ALA* 4.4 7.6 - - - +
150P ILE* 3.8 29.6 - - + -
151P VAL* 3.5 26.9 - - + -
154P PHE* 4.5 2.0 - - + -
167P LEU* 3.5 8.7 - - + +
220P ASP 3.0 15.3 + - - +
221P TRP* 3.4 32.5 - - + +
222P TRP 3.1 0.2 - - - -
223P ALA* 1.3 71.7 - - - +
225P GLY* 1.3 59.5 + - - +
227P LEU* 3.3 10.2 + - + -
228P ILE* 3.0 48.7 + - + +
272P LEU* 4.5 13.5 - - + -
291P ILE* 4.6 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 225 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221P TRP 3.2 3.8 + - - -
222P TRP 2.8 16.2 + - - -
224P LEU* 1.3 73.1 - - - +
226P VAL* 1.3 60.6 + - - -
229P TYR* 3.2 21.8 + - - +
269P LEU* 3.3 13.7 - - - +
272P LEU* 3.7 28.9 - - - +
273P LEU* 3.8 11.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 226 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203P GLU 3.7 21.1 - - - +
204P TYR* 3.5 29.6 - - + +
222P TRP* 3.2 34.9 + - + +
223P ALA* 3.2 9.2 + - - +
225P GLY* 1.3 77.3 - - - +
227P LEU* 1.3 57.5 + - - +
229P TYR* 3.5 2.3 + - - +
230P GLU* 3.0 27.5 + - - +
236P PRO* 4.4 4.3 - - + -
237P PRO* 3.6 29.2 - - + +
238P PHE* 4.8 1.8 - - + -
273P LEU* 3.7 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 227 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128P MET* 4.5 1.6 - - + -
146P TYR* 6.2 0.2 - - + -
147P ALA* 5.6 0.4 - - - -
150P ILE* 4.0 17.0 - - + -
167P LEU* 3.8 20.0 - - + -
168P LYS* 4.3 2.9 - - - -
169P PRO* 3.8 34.8 - - + -
172P LEU* 3.7 30.7 - - + -
204P TYR* 3.5 9.2 - - + +
223P ALA 2.9 12.6 + - - +
224P LEU* 3.5 13.7 - - + +
226P VAL* 1.3 73.4 - - - +
228P ILE* 1.3 66.1 + - - +
230P GLU* 3.2 2.9 + - - +
231P MET* 2.9 49.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 228 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143P ALA* 4.9 2.1 - - + +
147P ALA* 3.7 29.2 - - + -
224P LEU* 3.0 33.7 + - + +
227P LEU* 1.3 75.8 - - - +
229P TYR* 1.3 64.1 + - - +
231P MET* 3.3 13.0 + - + +
232P ALA* 3.0 22.7 + - - +
265P LEU* 3.6 31.0 - - + -
268P LEU* 3.7 25.6 - - + -
269P LEU* 3.8 7.0 - - + -
272P LEU* 3.9 8.3 - - + -
291P ILE* 6.6 0.2 - - + -
296P TRP* 3.7 19.1 - - + -
297P PHE* 4.9 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 229 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225P GLY 3.2 16.9 + - - +
226P VAL 3.6 3.8 - - - +
228P ILE* 1.3 79.7 - - - +
230P GLU* 1.3 52.8 + - - +
232P ALA 3.7 0.2 - - - -
233P ALA* 2.7 47.5 + - + +
235P TYR* 3.2 35.8 + + - -
236P PRO 3.6 2.0 - - - -
237P PRO* 3.3 41.7 + - + +
255P VAL* 3.9 9.0 - - + -
256P ARG 2.6 30.1 + - - -
257P PHE* 3.6 26.2 - + - -
258P PRO* 3.6 15.1 - - + +
261P PHE* 3.8 18.0 - + - -
269P LEU* 4.1 8.4 - - + +
273P LEU* 4.9 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 230 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132P LEU* 3.9 8.9 - - + +
133P ARG* 2.8 33.5 + - - +
169P PRO* 4.2 7.3 - - + +
204P TYR* 2.7 30.4 + - - +
226P VAL 3.0 16.2 + - - +
227P LEU 3.7 3.4 - - - +
229P TYR* 1.3 76.4 - - - +
231P MET* 1.3 57.9 + - - +
234P GLY* 2.6 33.3 + - - -
235P TYR 3.5 16.4 - - - +
236P PRO* 3.7 17.3 - - + +
19Q ARG* 3.2 35.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 231 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128P MET* 3.7 37.2 - - - +
132P LEU* 3.8 13.3 - - + +
137P ARG* 3.5 5.0 - - - -
138P PHE* 2.9 42.8 + - + -
143P ALA* 3.2 31.9 - - + +
146P TYR* 4.0 14.8 - - + -
147P ALA* 4.2 13.5 - - + +
227P LEU* 2.9 30.7 + - + +
228P ILE* 3.5 23.1 - - + +
230P GLU* 1.3 79.8 - - + +
232P ALA* 1.3 59.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 232 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137P ARG* 3.5 11.1 + - - +
138P PHE 3.8 12.3 - - - +
140P GLU* 4.7 9.6 - - + -
143P ALA* 4.7 8.1 - - + -
228P ILE* 3.0 17.2 + - + +
231P MET* 1.3 76.9 - - - +
233P ALA* 1.3 60.2 + - - +
260P HIS* 3.0 20.9 + - + +
261P PHE* 3.6 21.5 - - + -
265P LEU* 3.9 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 233 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137P ARG* 3.9 13.9 - - - +
229P TYR* 2.7 27.1 + - + +
232P ALA* 1.3 73.7 - - - +
234P GLY* 1.3 57.8 + - - +
235P TYR* 3.3 42.4 - - + +
258P PRO* 3.8 16.4 - - + -
260P HIS* 4.2 6.8 - - - -
261P PHE* 3.7 7.8 - - + -
7Q TYR* 4.0 8.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 234 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132P LEU* 4.8 0.7 - - - -
133P ARG* 3.1 23.7 + - - -
136P GLY 3.0 27.7 - - - +
137P ARG* 3.8 2.3 - - - +
230P GLU 2.6 22.2 + - - -
232P ALA 3.6 1.0 - - - -
233P ALA* 1.3 73.9 - - - +
235P TYR* 1.3 58.2 + - - +
7Q TYR* 4.4 8.1 - - - -
10Q PHE* 3.6 8.5 - - - -
----------------------------------------------------------
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