Contacts of the helix formed by residues 218 - 231 (chain B) in PDB entry 2W99
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
----------------------------------------------------------
217B ASN* 1.3 89.1 + - - +
219B GLU* 1.3 71.6 + - - +
220B ALA* 3.2 8.1 + - - +
221B ASP* 2.9 32.2 + - - +
222B GLN* 2.9 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 219 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B VAL* 5.7 2.3 - - - +
178B LEU* 3.2 18.9 - - + +
186B LEU* 3.1 60.2 - - + +
217B ASN 4.0 5.3 - - - +
218B SER* 1.3 77.2 + - - +
220B ALA* 1.3 58.5 + - - +
222B GLN* 3.8 4.1 - - - +
223B LEU* 2.8 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 220 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B SER* 3.2 6.1 + - - +
219B GLU* 1.3 77.4 - - - +
221B ASP* 1.3 57.4 + - - +
223B LEU* 3.2 14.8 - - + +
224B GLY* 2.6 34.5 + - - -
244B LEU 6.1 0.7 - - - +
246B ARG* 5.5 15.0 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
216B GLY* 4.3 0.7 - - - -
217B ASN* 4.0 11.8 + - - +
218B SER* 2.9 30.6 + - - +
220B ALA* 1.3 76.7 - - - +
222B GLN* 1.3 52.1 + - - +
224B GLY* 3.4 0.9 + - - -
225B LYS* 2.7 62.1 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
178B LEU* 2.3 43.5 + - + +
179B TRP* 2.8 24.6 - - - +
180B TYR 3.7 0.5 + - - -
181B ARG 4.0 9.2 + - - +
214B PHE* 3.4 25.0 + - + +
216B GLY 3.9 9.9 - - - +
217B ASN 4.4 7.5 + - - +
218B SER 2.9 15.7 + - - +
219B GLU 3.8 3.1 - - - +
221B ASP* 1.3 73.2 + - - +
223B LEU* 1.3 56.1 + - - +
225B LYS* 3.2 10.3 - - + +
226B ILE* 2.7 55.1 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
183B PRO* 5.0 11.4 - - + +
187B LEU* 4.2 38.6 - - + -
219B GLU 2.8 16.3 + - - +
220B ALA* 3.2 19.3 - - + +
222B GLN* 1.3 77.3 - - - +
224B GLY* 1.3 56.2 + - - +
226B ILE* 3.4 14.8 + - + +
227B PHE* 3.1 59.1 + - + -
238B TRP* 5.9 0.9 - - + -
246B ARG* 5.6 7.6 - - + +
278B PHE* 5.6 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 224 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B ALA 2.6 18.7 + - - -
221B ASP* 3.7 1.3 - - - -
223B LEU* 1.3 69.1 - - - +
225B LYS* 1.3 60.2 + - - +
226B ILE 3.1 0.9 - - - -
227B PHE* 3.1 14.7 + - - +
228B ASP* 2.4 35.3 + - - +
250B PRO* 5.8 8.5 - - - -
252B ARG* 4.6 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 225 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B PHE* 3.0 34.9 - - + +
215B CYS 3.6 15.9 + - - +
216B GLY* 3.3 29.0 - - - -
221B ASP* 2.7 40.2 + - - +
222B GLN* 3.2 13.5 - - + +
224B GLY* 1.3 70.9 - - - +
226B ILE* 1.3 62.1 + - - +
228B ASP* 3.1 29.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 226 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B ARG 4.8 10.1 - - - +
183B PRO* 5.1 15.7 - - + -
198B TRP* 3.6 37.0 - - + +
214B PHE* 3.4 35.2 - - + -
222B GLN* 2.7 49.0 + - + +
223B LEU* 3.4 12.8 - - + +
224B GLY 3.1 0.2 - - - -
225B LYS* 1.3 74.0 - - - +
227B PHE* 1.3 67.4 + - + +
229B LEU 3.1 12.1 + - - -
230B ILE* 3.2 20.7 + - + +
278B PHE* 6.3 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 227 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B LEU* 6.4 0.2 - - + -
223B LEU* 3.1 42.8 + - + -
224B GLY* 3.1 13.8 + - - +
226B ILE* 1.3 78.7 - - + +
228B ASP* 1.3 60.3 + - - +
230B ILE* 4.1 12.8 - - + -
231B GLY* 2.8 27.3 + - - -
232B LEU* 3.8 21.8 + - + +
233B PRO* 3.2 31.0 - - + -
238B TRP* 3.2 35.7 - + - -
248B ALA* 6.1 0.7 - - - -
250B PRO* 5.2 7.2 - - + -
252B ARG* 4.1 16.2 - - - -
253B GLY 4.2 1.9 - - - +
278B PHE* 4.8 16.8 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 228 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B PHE* 5.4 0.7 - - + -
224B GLY 2.4 26.1 - - - +
225B LYS* 3.1 23.8 - - - +
226B ILE 3.1 0.2 - - - -
227B PHE* 1.3 78.1 - - - +
229B LEU* 1.3 57.2 + - + +
252B ARG* 3.3 32.7 + - - +
253B GLY 4.2 4.9 - - - +
255B ARG* 3.6 24.2 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
213B LEU* 4.2 15.5 - - + -
214B PHE* 3.7 31.2 - - + -
225B LYS 4.0 0.2 + - - -
226B ILE 3.1 2.0 + - - -
228B ASP* 1.3 79.7 - - + +
230B ILE* 1.3 66.1 + - + +
255B ARG* 3.0 58.7 + - + +
256B PRO 3.9 11.4 - - - +
257B VAL* 4.2 22.2 - - + +
260B VAL* 3.8 29.2 - - + -
261B VAL* 5.9 1.6 - - + -
273B LEU* 5.7 0.4 - - + -
276B LEU* 6.5 0.4 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
198B TRP* 5.5 4.5 - - + -
214B PHE* 6.5 0.2 - - + -
226B ILE* 3.2 23.9 + - + +
227B PHE* 4.1 14.1 - - + -
229B LEU* 1.3 83.9 - - + +
231B GLY* 1.3 76.8 + - - +
233B PRO* 5.0 3.1 - - + -
254B PRO* 3.5 18.4 - - - +
255B ARG 4.2 0.5 + - - +
273B LEU* 3.6 29.2 - - + +
276B LEU* 2.9 33.9 - - + +
277B THR* 5.1 4.0 - - - -
278B PHE* 5.2 9.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 231 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B PHE* 2.8 18.9 + - - -
229B LEU 3.6 1.0 - - - -
230B ILE* 1.3 83.9 - - - +
232B LEU* 1.3 68.5 + - - -
233B PRO* 3.0 12.7 - - - +
253B GLY* 3.2 28.0 - - - -
254B PRO* 3.9 1.6 - - - -
----------------------------------------------------------
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