Contacts of the helix formed by residues 218 - 235 (chain B) in PDB entry 5OIV
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 SER 218 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B ARG* 3.4 5.6 + - - +
216B ARG 4.7 0.2 - - - -
217B PRO* 1.3 77.2 - - - +
219B ASP* 1.3 59.8 + - - +
220B GLY* 3.4 4.9 + - - -
221B GLU* 2.8 38.9 + - - +
222B TYR* 3.0 24.1 + - - -
374B GLU* 5.3 2.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 219 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B TYR* 3.8 2.4 + - - +
204B ARG* 2.9 31.9 + - - +
207B ASN* 4.3 5.0 + - - -
218B SER* 1.3 70.9 - - - +
220B GLY* 1.3 66.0 + - - +
222B TYR* 3.1 5.9 + - - +
223B ASP* 3.0 30.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 220 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B SER* 3.3 5.8 + - - -
219B ASP* 1.3 78.4 - - - +
221B GLU* 1.3 61.5 + - - +
223B ASP* 3.4 18.9 + - - +
224B ARG* 3.4 21.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 221 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B ASN* 3.4 16.1 + - - +
188B ASP* 4.8 0.2 - - - +
191B TYR* 6.5 1.3 - - + -
217B PRO* 3.5 11.6 - - + +
218B SER* 2.8 46.7 + - - +
220B GLY* 1.3 74.4 - - - +
222B TYR* 1.3 65.5 + - - +
224B ARG* 3.2 15.3 + - - +
225B TYR* 3.1 43.0 + - + +
374B GLU* 4.5 8.0 - - - +
377B ARG* 3.0 29.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 222 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B TYR* 6.0 0.2 - - - -
89B PHE* 4.6 16.3 + + - -
90B PRO* 5.3 0.4 - - + -
177B TRP* 4.4 14.3 + + - -
202B TYR* 3.3 15.9 - + - +
204B ARG* 3.6 48.2 - - + -
206B ASP* 3.3 19.1 - - - +
216B ARG* 3.2 24.3 + - - -
217B PRO* 4.0 17.9 - - + +
218B SER 3.0 12.2 + - - +
219B ASP 3.1 4.9 + - - +
221B GLU* 1.3 75.4 - - - +
223B ASP* 1.3 63.0 + - - +
225B TYR* 3.2 19.4 + + - -
226B LEU* 2.9 48.0 + - + +
504B SER* 3.7 12.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 223 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B PRO* 4.1 12.0 - - + +
199B LEU* 3.4 18.1 - - + +
202B TYR* 2.5 37.8 + - - -
219B ASP* 3.0 19.2 + - - +
220B GLY* 3.6 14.2 - - - +
221B GLU 3.2 0.4 - - - -
222B TYR* 1.3 77.4 - - - +
224B ARG* 1.3 58.5 + - - +
227B TRP* 2.9 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 224 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B ASP 5.5 0.4 + - - -
191B TYR* 3.1 52.6 + - + +
192B ALA* 3.7 24.7 + - - +
194B VAL* 3.3 28.4 + - + +
196B PRO* 4.2 10.1 - - + +
220B GLY 3.4 15.1 + - - +
221B GLU* 3.2 15.6 + - - +
223B ASP* 1.3 76.0 - - + +
225B TYR* 1.3 67.0 + - - +
227B TRP* 3.2 6.3 + - - +
228B LEU* 3.1 27.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 225 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B HIS* 2.9 28.3 + + + -
177B TRP* 3.7 43.1 - + + -
182B ASP* 3.3 21.1 + - + -
183B ASN* 3.5 20.6 - - - +
191B TYR* 3.4 42.2 - + - -
217B PRO* 3.9 9.8 - - + +
221B GLU* 3.1 35.7 + - + -
222B TYR* 3.2 33.8 + + - +
224B ARG* 1.3 76.7 - - - +
226B LEU* 1.3 64.3 + - + +
228B LEU 3.5 5.0 + - - -
229B LEU* 3.5 8.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 226 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B PHE* 4.0 28.0 - - + -
90B PRO* 4.1 15.9 - - + -
94B ARG* 4.1 23.7 + - + +
177B TRP* 4.3 7.4 - - + -
199B LEU* 3.9 19.2 - - + +
202B TYR* 4.6 8.3 - - + -
222B TYR* 2.9 52.7 + - + +
223B ASP* 4.0 2.7 - - - +
225B TYR* 1.3 81.4 - - + +
227B TRP* 1.3 65.9 + - - +
229B LEU* 3.2 22.7 + - + +
230B GLU* 3.3 15.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 227 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B VAL* 4.0 18.2 - - + -
195B VAL 3.7 9.0 + - - +
196B PRO* 3.5 23.1 - - + -
197B GLY* 3.4 39.3 - - - -
198B LYS 3.7 19.3 - - - -
199B LEU* 3.9 17.0 - - + +
223B ASP 2.9 17.9 + - - +
224B ARG* 3.2 4.9 + - - +
226B LEU* 1.3 75.5 - - - +
228B LEU* 1.3 66.6 + - - +
230B GLU* 2.9 27.2 + - + +
231B GLU* 3.1 43.7 + - + +
247B SER* 4.7 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 228 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B TYR 3.6 16.2 - - - +
175B HIS* 3.6 29.6 - - + +
191B TYR* 3.9 22.0 - - + -
194B VAL* 4.3 10.5 - - + -
224B ARG 3.1 15.1 + - - +
225B TYR 3.7 1.8 - - - +
226B LEU 3.3 0.2 - - - -
227B TRP* 1.3 76.0 - - - +
229B LEU* 1.3 63.2 + - - +
231B GLU* 3.1 29.0 + - - +
232B MET* 3.1 27.3 + - - +
246B MET* 3.6 13.8 - - + +
247B SER* 4.2 5.8 - - - -
248B PHE* 3.6 30.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 229 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B PRO* 4.3 16.6 - - + -
94B ARG* 4.4 10.1 - - + +
95B TRP* 3.5 64.4 - - + -
175B HIS* 3.9 11.0 - - - +
177B TRP* 3.9 5.6 - - + -
225B TYR 3.5 12.8 + - - +
226B LEU* 3.2 21.9 + - + +
227B TRP 3.2 0.6 - - - -
228B LEU* 1.3 79.2 - - - +
230B GLU* 1.3 58.4 + - - +
232B MET* 3.2 13.2 + - + +
233B LYS* 2.9 40.7 + - + +
237B TYR* 4.6 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 230 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B ARG* 4.1 13.2 + - - -
199B LEU* 3.7 26.2 - - + -
200B PRO* 3.8 27.4 - - + +
226B LEU 3.3 4.1 + - - +
227B TRP* 2.9 27.2 + - + +
229B LEU* 1.3 78.4 - - - +
231B GLU* 1.3 63.7 + - - +
233B LYS* 3.3 31.5 + - - +
234B ALA* 3.0 24.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 231 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B TRP* 3.1 42.0 + - + +
228B LEU* 3.1 21.1 + - - +
230B GLU* 1.3 76.2 - - - +
232B MET* 1.3 62.3 + - - +
234B ALA* 3.4 14.0 + - - +
235B VAL* 3.6 13.3 + - - +
245B VAL* 3.8 20.0 - - + +
246B MET* 3.6 12.8 - - - +
247B SER* 2.6 49.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 232 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B TRP* 3.7 15.9 - - + -
112B GLY 4.2 2.0 - - - +
113B ILE* 3.4 25.6 - - + -
174B TYR* 5.3 8.1 - - + +
175B HIS* 4.7 2.9 - - + -
228B LEU 3.1 10.8 + - - +
229B LEU* 3.5 42.2 - - + +
231B GLU* 1.3 73.6 - - - +
233B LYS* 1.3 65.1 + - - +
235B VAL* 3.1 15.3 + - - +
237B TYR* 3.0 46.9 + - + -
242B LEU* 4.0 15.5 - - + -
246B MET* 3.6 24.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 233 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B ALA 4.9 1.8 + - - -
94B ARG* 2.8 35.8 + - - +
95B TRP 3.7 7.9 - - - +
96B ALA* 4.3 9.9 - - - -
100B LEU* 3.9 20.5 - - + +
200B PRO* 6.1 0.4 - - - +
229B LEU* 2.9 28.6 + - + +
230B GLU* 3.3 30.8 + - - +
232B MET* 1.3 75.2 - - - +
234B ALA* 1.3 58.0 + - - +
236B ARG* 2.9 21.8 + - - +
237B TYR* 3.2 31.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 234 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B GLU 3.0 16.8 + - - +
231B GLU* 3.6 9.4 - - - +
232B MET 3.2 0.4 - - - -
233B LYS* 1.3 76.4 - - - +
235B VAL* 1.3 64.3 + - + +
236B ARG* 3.4 3.2 + - - +
241B ARG* 4.3 7.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 235 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B GLU 3.7 9.4 - - - +
232B MET 3.4 11.0 - - - +
233B LYS 3.1 0.2 - - - -
234B ALA* 1.3 82.4 - - + +
236B ARG* 1.3 72.3 + - - +
237B TYR 3.1 2.8 + - - +
238B ASP* 3.1 18.6 + - - +
241B ARG* 3.4 42.8 + - + +
242B LEU* 3.8 24.9 - - + -
245B VAL* 3.7 35.0 - - + -
----------------------------------------------------------
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