Contacts of the helix formed by residues 219 - 237 (chain O) in PDB entry 6GYK
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 GLN 219 (chain O).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160O ILE* 3.6 11.2 - - - +
217O ALA* 3.7 16.8 - - - +
218O LYS* 1.3 92.9 + - - +
220O ARG* 1.3 65.3 + - - +
221O GLU* 3.4 13.0 - - + +
222O GLU* 2.9 37.8 + - + +
223O ILE* 3.9 3.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 220 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65O PRO 5.3 1.4 + - - -
67O LEU* 3.4 40.7 - - + +
128O SER* 5.1 5.3 - - - -
129O GLU* 3.1 38.5 + - - +
160O ILE* 4.0 6.8 - - - +
219O GLN* 1.3 71.2 - - - +
221O GLU* 1.3 62.1 + - + +
222O GLU 3.1 2.5 - - - -
223O ILE* 3.0 8.9 + - + +
224O TYR* 2.9 69.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 221 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219O GLN* 3.4 7.7 - - + +
220O ARG* 1.3 77.6 - - + +
222O GLU* 1.3 59.1 + - + +
224O TYR* 4.0 11.8 - - + +
225O GLN* 2.9 49.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 222 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200O PRO* 3.5 22.9 - - + +
201O LYS 5.1 1.2 - - - +
202O ILE* 3.7 18.6 - - + +
216O GLY 4.5 0.5 - - - +
217O ALA* 3.4 7.9 - - + -
218O LYS* 3.1 24.9 + - - +
219O GLN* 2.9 36.6 + - + +
220O ARG 3.1 0.8 - - - -
221O GLU* 1.3 77.4 - - + +
223O ILE* 1.3 60.2 + - - +
225O GLN* 4.6 2.2 - - - +
226O ALA* 2.9 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 223 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65O PRO* 4.1 21.3 - - + -
67O LEU* 4.9 11.2 - - + -
160O ILE* 4.0 26.9 - - + +
162O GLY* 5.0 4.3 - - - +
202O ILE* 4.3 7.2 - - + -
214O LEU* 3.4 46.3 - - + +
215O THR 4.6 0.2 - - - +
217O ALA* 3.6 28.0 - - + -
219O GLN 3.9 6.5 - - - +
220O ARG* 3.0 10.8 + - - +
222O GLU* 1.3 74.8 - - - +
224O TYR* 1.3 64.0 + - + +
226O ALA 3.2 0.7 + - - -
227O PHE* 2.9 26.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 224 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64O VAL* 3.4 20.6 - - + +
65O PRO* 3.6 44.6 + - + -
67O LEU* 5.9 1.1 - - + -
220O ARG* 2.9 59.4 + - + +
221O GLU* 4.0 9.6 - - + +
223O ILE* 1.3 80.3 - - + +
225O GLN* 1.3 58.6 + - + +
227O PHE* 3.4 3.8 + - - +
228O GLU* 2.9 45.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 225 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199O LYS* 4.0 20.2 + - - +
200O PRO* 4.2 19.3 - - + +
221O GLU* 2.9 35.5 + - + +
222O GLU* 4.1 3.7 - - - +
224O TYR* 1.3 74.5 - - + +
226O ALA* 1.3 59.6 + - - +
228O GLU* 3.8 11.0 - - - +
229O ALA* 2.9 31.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 226 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197O MET* 3.4 20.6 - - + +
200O PRO* 4.1 0.6 - - - +
202O ILE* 3.7 26.0 - - + -
204O LEU* 4.4 1.8 - - + -
214O LEU* 3.7 15.3 - - + -
222O GLU 2.9 21.0 + - - +
223O ILE 3.2 4.9 + - - +
225O GLN* 1.3 77.5 - - - +
227O PHE* 1.3 57.8 + - - +
229O ALA 3.3 0.5 + - - -
230O ILE* 2.9 32.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 227 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61O SER* 4.5 6.5 - - - -
63O ILE* 3.1 45.3 - - + -
65O PRO* 3.7 26.5 - - + -
164O CYS* 3.5 30.7 - - - -
166O VAL* 4.6 13.0 - - + -
212O ILE* 5.1 4.9 - - + -
214O LEU* 3.9 7.1 - - + +
223O ILE 2.9 11.5 + - - +
224O TYR 3.9 2.2 - - - +
226O ALA* 1.3 75.8 - - - +
228O GLU* 1.3 68.1 + - + +
230O ILE* 3.4 14.2 - - + +
231O TYR* 2.9 59.5 + + + +
234O LEU* 5.4 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 228 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224O TYR* 2.9 31.1 + - + +
225O GLN* 4.1 9.1 - - - +
227O PHE* 1.3 84.5 - - + +
229O ALA* 1.3 58.7 + - - +
230O ILE 3.4 0.2 - - - -
231O TYR* 4.2 4.2 - - - +
232O PRO* 3.6 17.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 229 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197O MET* 4.0 20.3 - - + +
199O LYS 5.1 4.7 - - - +
200O PRO* 5.3 0.4 - - + -
225O GLN 2.9 19.4 + - - +
226O ALA 3.6 3.6 - - - +
227O PHE 3.2 0.2 - - - -
228O GLU* 1.3 75.7 - - - +
230O ILE* 1.3 61.2 + - - +
231O TYR 3.6 0.2 - - - -
232O PRO* 4.3 4.1 - - - +
233O VAL* 4.1 13.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 230 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175O LEU* 5.9 0.4 - - + -
195O TYR* 3.7 42.8 - - + +
197O MET* 4.2 3.4 - - + -
204O LEU* 3.7 22.4 - - + -
206O ILE* 4.2 18.6 - - + -
212O ILE* 4.9 2.7 - - + -
226O ALA 2.9 17.7 + - - +
227O PHE* 3.4 19.3 - - + +
229O ALA* 1.3 81.6 - - - +
231O TYR* 1.3 65.2 + - - +
232O PRO 3.5 1.3 - - - -
233O VAL* 3.4 19.9 + - + +
234O LEU* 3.1 36.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 231 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61O SER* 3.4 45.6 + - - -
63O ILE* 4.6 10.9 - - + +
166O VAL* 5.0 10.1 - - + -
168O PHE* 4.9 14.6 - + - -
227O PHE* 2.9 44.3 + + + +
228O GLU* 4.5 4.5 - - - +
230O ILE* 1.3 79.3 - - - +
232O PRO* 1.3 70.0 - - + +
234O LEU* 3.2 8.5 + - + +
235O SER* 2.9 49.6 + - - -
238O ARG* 5.6 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 232 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228O GLU 3.6 15.3 - - - +
229O ALA 4.3 6.3 - - - +
230O ILE 3.7 1.6 - - - -
231O TYR* 1.3 99.2 - - + +
233O VAL* 1.3 58.4 + - + +
235O SER* 3.3 8.9 + - - +
236O GLU* 2.9 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 233 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175O LEU* 3.6 23.7 - - + +
179O HIS* 3.5 34.5 - - + +
195O TYR* 5.6 2.9 - - + +
229O ALA 4.1 18.4 - - - +
230O ILE* 3.4 20.2 + - + +
231O TYR 3.2 0.6 - - - -
232O PRO* 1.3 78.2 - - + +
234O LEU* 1.3 62.1 + - + +
236O GLU* 3.4 12.7 + - - +
237O PHE* 3.2 32.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 234 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166O VAL* 3.9 13.2 - - + -
168O PHE* 3.2 27.6 - - + -
170O ILE* 3.7 27.8 - - + +
175O LEU* 4.5 4.5 - - + -
206O ILE* 3.7 30.5 - - + -
212O ILE* 3.7 31.2 - - + -
227O PHE* 5.4 1.6 - - + -
230O ILE* 3.1 32.8 + - + +
231O TYR* 3.6 9.0 - - + +
233O VAL* 1.3 77.5 - - + +
235O SER* 1.3 64.1 + - - +
236O GLU 3.3 0.5 + - - -
237O PHE 3.4 15.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 235 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168O PHE* 4.0 9.1 - - - -
231O TYR* 2.9 40.6 + - - -
232O PRO* 3.3 9.2 + - - -
234O LEU* 1.3 75.4 - - - +
236O GLU* 1.3 60.6 + - - +
238O ARG* 3.1 53.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 236 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171O ARG* 5.5 0.7 + - - -
178O SER* 5.7 0.3 + - - -
179O HIS* 5.2 2.9 + - - -
232O PRO 2.9 15.4 + - - +
233O VAL* 3.6 13.0 - - - +
234O LEU 3.2 0.6 - - - -
235O SER* 1.3 80.2 - - - +
237O PHE* 1.3 84.7 + - + +
238O ARG* 3.3 7.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 237 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170O ILE* 3.3 10.2 - - + +
171O ARG* 2.7 65.9 + - + +
174O GLY* 3.3 38.6 - - - -
175O LEU* 3.8 17.5 - - + -
178O SER* 3.6 20.0 - - - -
179O HIS* 4.3 4.5 - + - -
233O VAL* 3.2 36.6 + - + +
234O LEU 3.4 5.1 + - - +
236O GLU* 1.3 102.2 - - + +
238O ARG* 1.3 58.1 + - - +
----------------------------------------------------------
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