Contacts of the helix formed by residues 214 - 238 (chain B) in PDB entry 2WVL
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 VAL 214 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B GLY 2.7 35.6 + - - +
213B VAL* 1.3 69.8 - - - +
215B PHE* 1.3 72.7 + - + +
216B ARG* 3.0 9.9 + - - +
217B ARG* 3.3 23.8 + - - +
218B TYR* 4.4 0.7 + - - +
314B LYS* 3.9 42.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 215 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B TRP* 4.4 30.1 - + - -
202B ARG 5.0 7.0 - - - -
212B GLY 5.1 0.7 - - - -
214B VAL* 1.3 86.6 - - + +
216B ARG* 1.3 95.9 + - - +
217B ARG 3.3 1.1 - - - -
218B TYR* 3.7 12.8 + - + +
219B GLY* 3.2 19.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 216 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B GLY 3.7 18.9 + - - -
213B VAL* 3.7 42.1 - - + +
215B PHE* 1.3 107.0 - - - +
217B ARG* 1.3 82.0 + - - +
219B GLY* 3.5 1.0 + - - -
220B ARG* 3.3 26.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 217 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B VAL* 4.0 31.0 + - - +
214B VAL* 3.5 15.3 - - - +
216B ARG* 1.3 106.8 - - - +
218B TYR* 1.3 59.9 + - - +
219B GLY 3.3 0.7 + - - -
220B ARG* 3.7 7.4 - - - +
221B VAL* 3.0 30.6 + - - +
316B ASP* 6.2 4.3 - - + -
319B ILE* 4.3 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 218 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B VAL 4.4 0.8 + - - +
215B PHE* 3.7 16.8 + - + +
217B ARG* 1.3 79.4 - - - +
219B GLY* 1.3 62.9 + - - +
221B VAL* 3.4 15.6 - - + +
222B SER* 3.1 23.1 + - - -
248B ASN* 5.0 6.3 - - + +
319B ILE* 3.8 28.6 - - + +
322B MET* 4.3 26.2 - - + -
400B GDD 3.8 28.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 219 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B PHE 3.2 16.4 + - - -
216B ARG* 3.9 2.0 - - - -
217B ARG 3.2 0.6 - - - -
218B TYR* 1.3 74.4 - - - +
220B ARG* 1.3 54.7 + - - +
221B VAL 2.8 15.9 + - - -
222B SER* 2.9 22.8 + - - -
223B GLU* 3.1 17.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 220 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B ARG 3.3 13.9 + - - +
217B ARG* 3.7 15.5 - - - +
219B GLY* 1.3 71.7 - - - +
221B VAL* 1.3 67.5 + - + +
223B GLU* 4.0 14.4 + - - +
224B ARG* 3.2 53.9 + - - +
323B LEU* 4.9 11.2 - - - +
347B GLU* 4.3 8.5 + - - +
351B ALA* 5.1 11.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 221 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B ARG 3.0 19.1 - - - +
218B TYR* 3.4 20.0 - - + +
219B GLY 2.8 6.1 + - - -
220B ARG* 1.3 89.5 - - + +
222B SER* 1.3 57.5 + - - +
224B ARG* 3.2 7.6 + - - +
225B ASN* 2.7 43.4 + - - +
319B ILE* 4.2 33.0 - - + +
322B MET* 5.5 7.0 - - + -
323B LEU* 4.1 19.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 222 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B TYR* 3.1 25.0 + - - -
219B GLY* 2.9 16.3 + - - -
221B VAL* 1.3 77.7 - - - +
223B GLU* 1.3 58.8 + - - +
224B ARG 3.1 1.3 - - - -
225B ASN* 3.5 9.5 - - - +
226B ASN* 2.6 47.7 + - - -
248B ASN* 4.2 14.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 223 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B GLY* 3.1 17.2 + - - +
220B ARG* 4.1 16.0 - - - +
222B SER* 1.3 78.2 + - - +
224B ARG* 1.3 56.6 + - - +
226B ASN* 4.0 11.2 - - - +
227B ARG* 3.0 33.2 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
220B ARG* 3.2 31.9 + - - +
221B VAL 3.4 6.3 - - - +
222B SER 3.1 0.8 - - - -
223B GLU* 1.3 76.4 - - - +
225B ASN* 1.3 59.2 + - - +
227B ARG* 3.1 46.8 + - - +
228B ALA* 2.9 36.4 + - - +
231B GLN* 3.1 20.0 + - - -
323B LEU* 3.9 19.1 - - + -
327B LEU* 4.4 6.2 - - + +
343B SER* 3.3 27.3 + - - -
344B VAL* 4.1 10.1 - - - +
347B GLU* 2.7 51.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 225 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B VAL* 2.7 23.7 + - - +
222B SER* 3.1 7.9 + - - +
224B ARG* 1.3 72.0 - - - +
226B ASN* 1.3 64.5 + - - +
228B ALA* 3.3 5.5 + - - +
229B LEU* 3.3 24.3 + - - +
247B ALA* 3.8 6.1 - - + -
248B ASN* 3.1 30.8 + - - +
322B MET* 3.7 22.8 + - - +
323B LEU* 3.4 12.9 - - - +
326B CYS* 3.4 24.6 - - - +
327B LEU* 3.3 21.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 226 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222B SER* 2.6 34.6 + - - +
223B GLU* 4.0 11.6 - - - +
225B ASN* 1.3 68.8 - - - +
227B ARG* 1.3 65.9 + - - +
229B LEU* 2.9 14.0 + - - +
230B ASN* 3.0 19.3 + - - +
244B VAL* 3.3 16.8 - - - +
245B LYS* 3.2 31.0 + - + +
246B THR 3.3 0.3 + - - -
247B ALA* 2.9 35.6 + - - +
248B ASN* 4.7 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 227 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223B GLU* 3.0 27.8 + - - +
224B ARG* 3.1 38.7 + - - +
226B ASN* 1.3 72.5 - - - +
228B ALA* 1.3 62.9 + - - +
230B ASN* 3.3 11.1 + - + +
231B GLN* 2.9 39.2 + - + +
347B GLU* 3.0 40.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 228 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B ARG* 2.9 19.0 + - - +
225B ASN 3.3 10.5 - - - +
226B ASN 3.1 0.2 - - - -
227B ARG* 1.3 76.2 - - - +
229B LEU* 1.3 58.5 + - + +
231B GLN* 3.1 16.1 + - - +
232B LEU* 2.9 26.3 + - - +
326B CYS* 5.0 0.9 - - - -
327B LEU* 4.0 24.0 - - + -
330B VAL* 4.2 23.7 - - + +
344B VAL* 4.9 2.5 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
225B ASN 3.3 12.8 + - - +
226B ASN 2.9 8.5 + - - +
228B ALA* 1.3 79.2 - - - +
230B ASN* 1.3 63.1 + - - +
232B LEU* 3.1 10.4 + - + +
233B ILE* 3.0 27.4 + - + +
244B VAL* 3.9 17.9 - - + -
247B ALA* 4.4 8.1 - - + -
272B PRO* 4.2 12.1 - - + +
275B LEU* 3.3 46.2 - - + -
276B VAL* 4.7 7.9 - - + -
279B LEU* 5.2 5.1 - - + +
326B CYS* 3.9 16.6 - - - -
330B VAL* 3.7 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 230 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B ASN* 3.0 21.9 + - - +
227B ARG* 3.6 11.1 - - + +
229B LEU* 1.3 74.2 - - - +
231B GLN* 1.3 62.4 + - + +
233B ILE* 3.2 3.5 + - - +
234B GLY* 2.9 25.6 + - - -
240B GLU* 5.7 0.3 - - - -
241B THR* 3.3 32.4 + - + +
242B ASP* 4.1 5.9 - - - +
243B VAL* 3.3 15.4 - - - +
244B VAL* 2.8 47.8 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
224B ARG* 3.1 30.8 + - - +
227B ARG* 2.9 29.0 + - + +
228B ALA* 3.4 9.4 - - - +
230B ASN* 1.3 74.9 - - + +
232B LEU* 1.3 67.9 + - - +
234B GLY* 4.5 1.6 - - - +
235B GLY 3.0 19.8 + - - -
340B VAL* 3.4 23.8 - - + +
343B SER* 3.3 28.7 + - - -
344B VAL* 5.0 4.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 232 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B ALA 2.9 12.2 + - - +
229B LEU* 3.1 13.7 + - + +
231B GLN* 1.3 78.8 - - - +
233B ILE* 1.3 67.2 + - + +
235B GLY* 3.5 5.7 + - - -
236B VAL* 3.7 14.3 + - - +
276B VAL* 3.9 38.8 - - + -
279B LEU* 4.4 15.5 - - + -
330B VAL* 3.7 25.4 - - + -
333B SER* 4.0 12.1 - - - +
335B LEU* 4.2 12.5 - - + +
336B ALA* 3.9 31.9 - - + +
340B VAL* 4.1 7.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 233 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B GLU* 4.2 12.3 - - + +
12B PHE* 3.6 30.7 - - + -
17B LEU* 4.4 15.0 - - + -
229B LEU* 3.0 15.1 + - + +
230B ASN* 3.2 5.8 + - - +
231B GLN 3.2 0.2 - - - -
232B LEU* 1.3 75.8 - - - +
234B GLY* 1.3 58.4 + - - +
236B VAL* 2.8 22.9 + - - +
237B SER* 3.0 16.2 + - - +
241B THR* 4.0 20.2 - - + -
243B VAL* 4.5 4.3 - - + -
244B VAL* 3.9 24.5 - - + -
279B LEU* 3.9 30.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 234 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B ASN 2.9 18.6 + - - -
231B GLN* 4.0 1.6 - - - -
233B ILE* 1.3 73.0 - - - +
235B GLY* 1.3 61.6 + - - +
236B VAL 2.8 2.1 + - - -
237B SER* 3.6 11.4 - - - -
238B GLY* 2.8 25.9 + - - -
239B PHE 3.6 16.9 + - - -
240B GLU* 4.7 5.4 - - - -
241B THR* 4.5 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 235 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B GLN 3.0 16.8 + - - -
232B LEU 4.0 2.2 - - - -
233B ILE 3.1 0.2 + - - -
234B GLY* 1.3 75.3 - - - +
236B VAL* 1.3 58.6 + - - +
238B GLY* 4.6 1.7 + - - -
337B THR* 3.3 33.3 - - - +
340B VAL* 4.1 6.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 236 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B PHE* 3.5 28.3 - - + -
232B LEU 3.8 10.1 - - - +
233B ILE 2.8 8.6 + - - +
235B GLY* 1.3 80.3 - - - +
237B SER* 1.3 67.7 + - - +
238B GLY* 3.2 2.7 + - - -
283B GLY 5.8 0.2 - - - +
285B VAL* 4.0 17.3 - - + -
335B LEU* 3.6 43.1 - - + +
337B THR* 5.2 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 237 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B GLU* 5.1 5.4 + - - -
11B ARG 5.8 2.7 - - - -
12B PHE* 4.8 7.2 - - - -
233B ILE* 3.0 17.0 + - - +
234B GLY* 3.6 6.8 + - - -
236B VAL* 1.3 81.3 - - - +
238B GLY* 1.3 60.5 + - - +
239B PHE* 3.1 40.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 238 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B GLY 2.8 14.8 + - - -
235B GLY 5.3 1.3 - - - -
236B VAL 3.2 3.5 - - - -
237B SER* 1.3 75.6 - - - +
239B PHE* 1.3 74.6 + - - +
240B GLU* 4.8 4.6 - - - +
----------------------------------------------------------
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