Contacts of the helix formed by residues 219 - 233 (chain B) in PDB entry 2YWB
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 GLY 219 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B SER* 3.3 14.6 + - - -
218B GLY* 1.3 81.5 - - - +
220B VAL* 1.3 61.7 + - - -
221B ASP* 3.1 4.6 + - - -
222B SER* 3.1 5.3 + - - -
223B SER* 2.9 25.6 + - - -
247B ARG* 6.1 1.3 - - - -
381B PHE* 6.6 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 220 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B GLY 3.7 2.0 + - - -
219B GLY* 1.3 70.7 - - - -
221B ASP* 1.3 59.5 + - - +
223B SER* 3.8 7.1 - - - -
224B THR* 2.5 49.7 + - - +
359B LYS* 4.2 16.2 - - + -
362B VAL* 4.7 1.6 - - + +
363B ARG* 3.9 49.6 - - + +
366B ALA* 4.0 14.8 - - + -
371B LEU* 4.2 7.6 - - + -
375B LEU 4.0 13.9 + - - +
376B ARG 4.1 10.8 - - - +
378B ARG 5.5 0.7 - - - +
----------------------------------------------------------
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 GLY* 3.1 1.7 + - - -
220B VAL* 1.3 81.2 - - - +
222B SER* 1.3 58.3 + - - +
224B THR* 3.2 4.3 + - - -
225B LEU* 2.9 27.2 + - - +
315B GLY* 2.7 35.2 - - - +
317B LEU* 3.5 18.1 - - - +
354B PHE* 3.3 25.3 - - - -
359B LYS* 4.8 15.9 - - + -
362B VAL* 3.7 13.6 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
214B LEU* 4.2 1.4 - - - +
215B ALA 3.5 24.0 - - - -
216B VAL* 3.7 9.5 - - - +
217B SER* 3.0 34.7 + - - -
218B GLY 3.8 0.7 + - - -
219B GLY 3.1 9.1 + - - -
221B ASP* 1.3 80.3 + - - +
223B SER* 1.3 60.7 + - - +
225B LEU* 3.4 11.5 + - - +
226B ALA* 3.2 22.0 + - - +
315B GLY* 5.8 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 223 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B VAL* 5.2 1.4 - - - +
218B GLY* 3.9 16.6 + - - -
219B GLY 2.9 18.8 + - - -
220B VAL* 3.8 8.5 - - - -
222B SER* 1.3 76.3 + - - +
224B THR* 1.3 60.0 + - - +
226B ALA* 3.4 6.4 + - - +
227B LEU* 3.1 31.7 + - - +
254B VAL* 4.6 2.6 - - - +
258B LEU* 4.0 30.9 - - - +
371B LEU* 4.5 15.2 - - - +
375B LEU* 5.4 5.2 + - - +
----------------------------------------------------------
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 VAL* 2.5 28.0 + - - +
221B ASP 3.6 3.8 - - - -
223B SER* 1.3 76.3 - - - +
225B LEU* 1.3 64.4 + - - +
227B LEU* 3.8 7.5 - - - +
228B LEU* 3.0 23.2 + - - +
354B PHE* 4.0 9.9 - - + -
362B VAL* 3.7 20.0 - - + +
365B LEU* 4.2 5.6 - - + -
366B ALA* 3.1 44.2 - - - +
369B LEU* 4.0 12.3 - - + -
371B LEU* 4.7 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 225 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B LEU* 4.2 13.2 - - + -
215B ALA 5.7 1.3 - - - +
221B ASP 2.9 13.6 + - - +
222B SER* 3.6 12.8 - - - +
223B SER 3.3 0.2 - - - -
224B THR* 1.3 77.3 - - - +
226B ALA* 1.3 62.5 + - - +
228B LEU* 3.3 6.0 + - + +
229B LEU* 3.1 35.4 + - + +
313B ALA* 3.7 29.6 - - + +
314B GLN 3.4 30.1 - - - +
315B GLY* 3.6 4.9 - - - +
351B LEU* 6.3 0.2 - - + -
353B PRO* 3.5 37.0 - - + -
354B PHE* 3.8 14.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 226 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B LEU* 4.1 10.5 - - + +
216B VAL* 4.2 15.0 - - + -
222B SER 3.2 10.9 + - - +
223B SER* 3.4 10.5 - - - +
224B THR 3.2 0.2 - - - -
225B LEU* 1.3 80.3 - - - +
227B LEU* 1.3 56.3 + - - +
229B LEU* 3.3 7.2 + - - +
230B ALA* 2.9 29.5 + - - +
236B HIS* 4.8 3.5 + - - -
238B ALA* 4.7 0.9 - - + -
258B LEU* 4.9 2.5 - - + -
263B VAL* 3.6 31.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 227 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223B SER 3.1 18.0 + - - +
224B THR* 3.3 11.9 + - - +
226B ALA* 1.3 75.8 - - - +
228B LEU* 1.3 58.7 + - - +
230B ALA* 3.8 4.7 - - + +
231B LYS* 2.8 32.2 + - - +
258B LEU* 4.6 4.3 - - + -
261B LEU* 3.7 38.6 - - + +
263B VAL* 4.2 12.6 - - + -
366B ALA* 4.7 1.3 - - - +
369B LEU* 3.8 36.6 - - + +
371B LEU* 3.8 37.9 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
196B LEU* 3.7 21.3 - - + -
199B LEU* 4.1 23.3 - - + +
200B LEU* 3.4 29.3 - - + +
203B VAL* 4.5 12.1 - - + -
224B THR 3.0 16.5 + - - +
225B LEU* 3.5 7.0 - - + +
227B LEU* 1.3 76.7 - - - +
229B LEU* 1.3 59.7 + - + +
231B LYS* 3.2 5.0 + - - +
232B ALA* 2.9 30.0 + - - +
353B PRO* 4.0 23.3 - - + -
354B PHE* 4.0 24.9 - - + -
365B LEU* 6.0 0.7 - - + -
369B LEU* 3.6 8.6 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
203B VAL* 3.3 32.3 - - + -
212B VAL* 4.0 22.0 - - + -
214B LEU* 3.8 31.6 - - + -
225B LEU* 3.1 20.3 + - + +
226B ALA* 3.6 6.5 - - - +
228B LEU* 1.3 81.8 - - + +
230B ALA* 1.3 61.9 + - - +
232B ALA* 3.1 9.4 + - - +
234B VAL* 3.1 40.2 + - + -
236B HIS* 4.2 19.3 - - + +
313B ALA* 4.1 8.1 - - + -
351B LEU* 4.5 4.5 - - + -
353B PRO* 6.3 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 230 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B ALA 2.9 16.3 + - - +
227B LEU* 3.8 5.4 - - + +
229B LEU* 1.3 76.7 - - - +
231B LYS* 1.3 62.9 + - - +
233B GLY* 3.0 14.6 + - - -
234B VAL 5.1 0.9 - - - -
236B HIS* 3.8 21.9 - - + -
261B LEU 5.1 3.8 - - - +
262B GLY* 4.3 23.3 - - - +
263B VAL* 4.3 5.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 231 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B LEU* 6.2 0.2 - - + -
200B LEU* 3.7 26.5 - - + -
204B ARG* 3.7 8.1 + - - -
227B LEU 2.8 18.8 + - - +
228B LEU 3.6 3.6 - - - +
230B ALA* 1.3 77.8 - - - +
232B ALA* 1.3 60.0 + - - +
233B GLY 3.2 1.2 + - - -
369B LEU* 3.9 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 232 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200B LEU* 4.2 6.5 - - + +
203B VAL* 3.6 27.8 - - + -
204B ARG* 2.9 46.5 + - + +
228B LEU 2.9 16.2 + - - +
229B LEU 3.1 6.7 + - - +
231B LYS* 1.3 76.2 - - - +
233B GLY* 1.3 59.6 + - - +
234B VAL* 3.4 9.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 233 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B ALA 3.0 15.4 + - - -
231B LYS 3.2 1.6 + - - -
232B ALA* 1.3 79.5 - - - +
234B VAL* 1.3 64.6 + - - +
235B ASP* 3.7 1.0 + - - -
----------------------------------------------------------
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