Contacts of the helix formed by residues 230 - 245 (chain B) in PDB entry 2FBW
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 ASN 230 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B GLY 4.9 1.8 + - - -
155B LEU* 5.8 0.2 - - - +
185B MET* 4.2 5.2 - - - +
219B MET* 3.9 3.1 - - - +
222B THR* 2.6 31.0 + - + +
228B GLY 5.4 0.7 - - - +
229B LEU* 1.3 78.0 - - - +
231B PRO* 1.3 62.4 - - - +
232B GLY* 3.8 0.3 - - - -
233B LYS* 2.9 38.9 + - + +
234B ALA* 3.2 16.3 + - - +
114C PHE* 3.0 30.7 + - - +
115C LYS* 4.3 5.3 - - - +
116C LEU 5.2 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 231 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B CYS* 4.4 9.4 - - + -
181B PRO* 3.8 31.2 - - + +
182B ALA* 5.4 0.2 - - - -
185B MET* 3.7 25.1 - - + -
221B CYS* 3.8 27.4 - - + +
222B THR* 3.7 7.6 - - - +
225B CYS* 4.9 4.7 - - + -
229B LEU* 3.5 10.5 - - + +
230B ASN* 1.3 86.5 - - - +
232B GLY* 1.3 60.4 + - - +
234B ALA* 3.5 3.5 - - + +
235B ILE* 2.9 36.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 232 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B MET* 3.8 22.0 - - - -
221B CYS* 3.6 11.5 - - - -
222B THR* 3.3 7.0 + - - -
230B ASN 3.2 1.2 - - - -
231B PRO* 1.3 77.7 - - - +
233B LYS* 1.3 60.8 + - - +
235B ILE* 3.3 9.3 + - - +
236B ALA* 3.1 17.0 + - - +
114C PHE* 3.6 14.0 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
230B ASN* 2.9 32.8 + - + +
232B GLY* 1.3 71.3 - - - +
234B ALA* 1.3 67.5 + - - +
236B ALA* 3.1 4.2 + - + +
237B GLU* 3.0 48.4 + - + +
111C GLY 3.6 16.9 + - - -
114C PHE* 3.7 32.4 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
155B LEU* 4.4 4.7 - - + -
185B MET* 3.7 36.1 - - + -
188B TYR* 4.0 23.0 - - + -
230B ASN 3.2 8.3 + - - +
231B PRO 3.2 8.4 + - - +
233B LYS* 1.3 77.5 - - - +
235B ILE* 1.3 62.6 + - - +
237B GLU* 3.2 7.1 + - - +
238B ILE* 3.1 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 235 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B TYR* 3.9 16.8 - - - +
181B PRO* 3.9 30.5 - - + +
184B LEU* 4.0 23.8 - - + -
185B MET 5.1 1.8 - - - +
212B LEU* 3.8 19.1 - - + -
215B CYS* 3.6 29.2 - - + -
221B CYS* 5.3 2.0 - - - -
231B PRO 2.9 22.6 + - - +
232B GLY* 3.6 7.4 - - - +
234B ALA* 1.3 72.7 - - - +
236B ALA* 1.3 65.8 + - - +
238B ILE* 3.2 10.4 + - - +
239B LYS* 3.1 29.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 236 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B GLY 3.1 6.8 + - - +
233B LYS* 3.1 8.3 + - + +
235B ILE* 1.3 78.9 - - - +
237B GLU* 1.3 55.4 + - + +
239B LYS* 3.4 13.4 + - + +
240B LYS* 3.1 33.0 + - - +
108C TRP 4.1 7.6 - - - +
109C ASP* 5.0 2.4 - - - +
111C GLY* 4.7 6.1 - - - +
114C PHE* 3.3 39.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 237 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B TYR* 3.4 38.6 + - + +
233B LYS* 3.0 43.4 + - + +
234B ALA* 3.2 5.4 + - - +
236B ALA* 1.3 75.6 - - + +
238B ILE* 1.3 64.3 + - - +
240B LYS* 3.3 34.6 + - - +
241B MET* 3.0 29.3 + - - +
111C GLY* 4.6 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 238 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B LEU* 3.4 39.5 - - + +
187B ALA* 4.7 0.4 - - + -
188B TYR* 3.8 26.5 - - + +
191B MET* 4.1 11.4 - - + -
203B LEU* 4.2 8.3 - - + -
206B LEU* 3.7 28.3 - - + -
212B LEU* 3.7 15.5 - - + -
234B ALA 3.1 14.0 + - - +
235B ILE* 3.2 10.1 + - - +
237B GLU* 1.3 76.4 - - - +
239B LYS* 1.3 53.7 + - - +
241B MET* 3.0 8.5 + - - +
242B MET* 2.6 43.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 239 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B LEU* 4.2 21.5 - - + -
213B TYR* 4.2 15.2 + - + -
215B CYS* 3.2 40.3 + - - -
216B HIS* 4.9 0.2 - - - +
217B THR* 4.1 13.1 + - - -
235B ILE* 3.1 32.5 + - + +
236B ALA* 3.6 13.7 - - + +
237B GLU 3.3 0.2 - - - -
238B ILE* 1.3 74.3 - - - +
240B LYS* 1.3 62.7 + - - +
242B MET* 3.3 10.6 + - - +
243B ALA* 3.0 24.4 + - - +
109C ASP* 5.0 5.4 + - - +
10D TRP* 4.0 42.0 - - + +
14D ARG* 5.8 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 240 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B ALA 3.1 18.2 + - - +
237B GLU* 3.5 34.9 + - - +
238B ILE 3.2 0.2 - - - -
239B LYS* 1.3 74.8 - - + +
241B MET* 1.3 65.2 + - - +
243B ALA* 3.2 11.7 + - - -
244B THR* 3.0 23.7 + - + +
109C ASP 3.6 23.6 - - - +
110C MET* 3.4 26.6 + - - +
111C GLY* 3.9 7.4 + - - +
10D TRP* 5.4 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 241 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B TYR* 3.8 32.8 - - - -
191B MET* 4.3 15.3 - - + +
192B ILE* 4.6 7.6 - - + -
199B THR* 3.7 29.6 - - + -
203B LEU* 4.0 18.2 - - + -
237B GLU* 3.0 17.6 + - - +
238B ILE* 3.5 6.7 - - - +
240B LYS* 1.3 76.5 - - + +
242B MET* 1.3 64.3 + - - +
244B THR* 3.2 5.7 + - - -
245B TYR* 3.0 31.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 242 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B LEU* 3.3 40.4 - - + +
206B LEU* 3.7 30.3 - - + +
207B GLN* 3.5 30.5 - - - +
212B LEU* 3.8 8.5 - - + -
213B TYR* 3.4 27.4 - - + +
238B ILE* 2.6 36.3 + - + +
239B LYS 3.6 4.3 - - - +
240B LYS 3.3 0.2 - - - -
241B MET* 1.3 72.1 - - - +
243B ALA* 1.3 57.0 + - - +
245B TYR* 3.4 10.6 - - - -
4D LYS* 3.2 22.2 + - - -
7D SER* 3.4 11.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 243 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B LYS 3.0 15.8 + - - +
240B LYS* 3.8 6.1 - - - +
241B MET 3.1 0.6 - - - -
242B MET* 1.3 77.1 - - - +
244B THR* 1.3 65.0 + - + +
4D LYS* 4.3 5.8 + - - -
7D SER* 4.4 5.8 - - - +
10D TRP* 4.0 16.6 - - + -
11D THR* 3.5 27.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 244 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240B LYS* 3.0 18.7 + - + +
241B MET* 3.2 6.3 + - - -
243B ALA* 1.3 88.2 - - + +
245B TYR* 1.3 66.2 + - - +
246B LYS* 3.6 8.3 + - - +
4D LYS* 4.4 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 245 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200B GLU* 3.8 28.7 - - + -
203B LEU* 3.7 35.0 - - + -
204B ALA* 3.7 12.9 - - + +
207B GLN* 3.1 31.4 + - - +
241B MET* 3.0 26.3 + - - +
242B MET* 3.4 24.0 - - - -
244B THR* 1.3 76.8 + - - +
246B LYS* 1.3 68.0 + - - +
247B GLU 3.8 15.9 + - - -
3D SER 5.0 0.2 + - - -
4D LYS* 2.6 44.8 + - - +
----------------------------------------------------------
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