Contacts of the helix formed by residues 219 - 232 (chain B) in PDB entry 4WLU
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 PRO 219 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B ASP* 4.5 2.2 - - - +
218B PHE* 1.3 87.6 - - + +
220B GLN* 1.3 65.9 + - - +
221B ASP* 3.2 17.9 - - - +
222B GLN* 3.1 28.9 + - + +
223B LEU* 2.9 20.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 220 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B PHE 3.8 1.2 + - - -
219B PRO* 1.3 72.4 - - - +
221B ASP* 1.3 52.4 + - - +
223B LEU* 3.7 17.3 - - - +
224B THR* 2.6 47.5 + - - +
311B PHE* 3.5 44.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 221 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B PRO* 3.4 18.5 - - - +
220B GLN* 1.3 76.4 - - - +
222B GLN* 1.3 81.3 + - - +
224B THR* 3.4 7.5 + - - -
225B ALA* 3.2 22.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 222 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B LEU* 4.8 14.5 - - + +
218B PHE* 3.6 29.0 - - + -
219B PRO* 3.1 31.0 + - + +
221B ASP* 1.3 90.3 + - - +
223B LEU* 1.3 57.7 + - - +
225B ALA* 3.2 6.4 + - - +
226B LEU* 2.8 36.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 223 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B ILE* 3.6 42.8 - - + -
218B PHE* 4.1 19.9 - - + +
219B PRO 2.9 16.4 + - - +
220B GLN* 3.7 24.5 - - - +
222B GLN* 1.3 76.8 - - - +
224B THR* 1.3 53.5 + - - +
226B LEU* 3.7 6.0 - - + +
227B THR* 2.5 40.7 + - - +
311B PHE* 3.9 26.7 - - + -
312B GLU* 6.1 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 224 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B GLN* 2.6 37.2 + - - +
221B ASP* 3.7 7.9 - - - -
222B GLN 3.2 0.2 - - - -
223B LEU* 1.3 73.9 - - - +
225B ALA* 1.3 59.1 + - - +
227B THR* 3.5 6.1 + - - -
228B GLY* 3.0 24.6 + - - -
311B PHE* 4.5 13.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 225 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B ASP 3.2 9.9 + - - +
222B GLN* 3.2 9.5 + - - +
224B THR* 1.3 75.5 - - - +
226B LEU* 1.3 56.0 + - - +
228B GLY* 3.2 1.6 + - - -
229B ARG* 2.7 36.1 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
180B PHE* 3.7 33.0 - - + -
181B VAL* 4.0 15.9 - - + +
184B LEU* 4.0 19.3 - - + -
209B ILE* 4.3 13.7 - - + -
218B PHE* 3.9 37.7 - - + -
222B GLN 2.8 21.2 + - - +
223B LEU* 3.7 6.1 - - + +
225B ALA* 1.3 73.1 - - - +
227B THR* 1.3 63.7 + - - +
229B ARG* 3.2 7.6 + - + +
230B ILE* 3.0 41.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 227 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B PRO* 4.0 25.3 + - + +
209B ILE* 4.9 3.0 - - - +
223B LEU* 2.5 31.8 + - - +
224B THR* 3.6 7.2 - - - -
226B LEU* 1.3 76.9 - - - +
228B GLY* 1.3 57.8 + - - +
230B ILE* 3.4 4.2 + - - +
231B GLN* 3.0 40.2 + - - +
311B PHE* 3.6 16.4 - - + -
315B MET* 3.7 31.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 228 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B THR 3.0 15.3 + - - -
225B ALA* 3.6 3.1 - - - -
227B THR* 1.3 74.1 - - - +
229B ARG* 1.3 64.2 + - - +
231B GLN* 3.3 13.3 + - - +
232B GLU* 3.0 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 229 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A HIS* 4.9 0.8 + - - -
180B PHE* 3.8 39.8 - - + +
183B GLU* 4.8 8.3 + - - -
225B ALA 2.7 21.6 + - - +
226B LEU* 3.2 10.5 + - + +
228B GLY* 1.3 73.7 - - - +
230B ILE* 1.3 60.6 + - - +
232B GLU* 3.8 1.6 - - - -
233B ALA* 3.1 26.2 + - - +
236B GLU* 2.7 42.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 230 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B ASP* 4.2 20.8 - - + +
176B ARG* 4.9 7.2 + - + -
177B ALA* 3.7 28.0 - - + +
180B PHE* 3.8 23.6 - - + -
196B VAL* 5.2 1.1 - - + -
205B ILE* 4.2 24.5 - - + +
207B PRO* 3.8 27.8 - - + -
209B ILE* 4.4 5.8 - - + -
226B LEU* 3.0 34.7 + - + +
227B THR 3.7 5.6 - - - +
229B ARG* 1.3 79.0 - - - +
231B GLN* 1.3 60.7 + - - +
232B GLU 3.4 0.3 + - - -
233B ALA* 3.5 12.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 231 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B ARG* 4.8 6.4 + - - -
202B GLY* 3.4 23.2 + - - +
203B LYS* 3.8 34.8 + - + +
205B ILE* 3.0 50.9 + - + +
206B ILE* 5.0 0.2 - - - +
207B PRO* 4.8 1.3 - - + -
227B THR* 3.0 35.8 + - + +
228B GLY* 3.3 12.3 + - - +
230B ILE* 1.3 77.6 - - - +
232B GLU* 1.3 66.0 + - - +
233B ALA 3.5 0.6 + - - -
315B MET* 4.1 13.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 232 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B ARG* 5.3 0.3 + - - -
110B ARG* 5.8 1.8 + - - +
202B GLY* 4.2 8.0 - - - -
203B LYS* 4.1 17.6 + - - -
228B GLY 3.0 15.1 + - - +
229B ARG* 3.8 2.0 - - - +
231B GLN* 1.3 84.1 - - + +
233B ALA* 1.3 57.9 + - - +
234B GLY 3.3 2.9 - - - -
235B THR* 3.0 34.7 + - + +
236B GLU* 2.9 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