Contacts of the helix formed by residues 229 - 250 (chain C) in PDB entry 4U1D
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 ASP 229 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226C ASP* 3.0 24.0 + - + +
228C SER* 1.3 78.5 - - - +
230C ALA* 1.3 65.4 + - - +
231C ASP* 2.9 18.7 + - - +
232C THR* 2.7 37.0 + - - +
233C LEU* 3.2 25.4 + - - +
235C ARG* 5.2 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 230 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228C SER 3.6 4.3 + - - +
229C ASP* 1.3 72.0 + - - +
231C ASP* 1.3 56.7 + - - +
233C LEU* 3.2 10.1 + - - +
234C GLN* 2.7 36.5 + - - +
270C SER* 5.7 0.4 + - - +
271C LYS* 5.6 6.5 - - + +
272C ARG* 3.9 37.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 231 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229C ASP* 2.9 17.3 + - - +
230C ALA* 1.3 75.5 - - - +
232C THR* 1.3 63.5 + - - +
234C GLN* 3.3 5.9 + - - +
235C ARG* 3.3 42.0 + - - +
272C ARG* 2.5 34.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 232 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176C GLU* 2.8 26.7 + - - +
225C VAL* 3.6 27.8 - - + -
226C ASP* 3.6 22.1 + - - +
227C LEU* 4.4 3.6 - - + -
229C ASP* 2.7 21.3 + - - +
231C ASP* 1.3 73.7 - - - +
233C LEU* 1.3 61.6 + - - +
235C ARG* 3.4 14.3 + - - +
236C TYR* 3.1 35.7 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 233 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227C LEU* 3.3 52.0 - - + +
228C SER 5.0 2.5 - - - +
229C ASP 3.2 15.9 + - - +
230C ALA* 3.6 10.3 - - - +
231C ASP 3.2 0.2 - - - -
232C THR* 1.3 75.6 - - - +
234C GLN* 1.3 58.1 + - - +
236C TYR* 3.8 6.9 - - + +
237C LEU* 2.7 38.4 + - + +
266C LEU* 4.9 10.5 - - + +
269C ILE* 3.6 35.9 - - + +
270C SER* 3.8 22.0 - - - +
271C LYS* 5.0 1.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 234 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230C ALA 2.7 20.9 + - - +
231C ASP* 3.3 10.5 + - - +
233C LEU* 1.3 72.8 - - - +
235C ARG* 1.3 57.8 - - + +
237C LEU* 4.2 8.1 - - - +
238C ASP* 3.1 34.3 + - - +
270C SER* 5.6 0.4 + - - -
272C ARG* 3.7 39.0 - - - +
273C ALA 3.7 11.6 - - - +
274C PRO* 4.0 23.0 - - - +
275C LYS* 4.4 18.1 - - - +
278C THR* 5.9 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 235 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176C GLU* 3.0 41.0 + - - +
177C ILE* 3.9 28.3 - - - +
180C SER* 3.5 33.7 + - - +
231C ASP* 3.3 21.9 + - - +
232C THR* 3.6 21.0 + - - +
233C LEU 3.1 0.4 - - - -
234C GLN* 1.3 78.4 - - + +
236C TYR* 1.3 67.4 + - + +
238C ASP* 3.1 8.3 + - - +
239C GLN* 3.0 30.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 236 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171C ASN* 3.9 14.7 + - - -
176C GLU* 5.0 8.5 - - + +
179C TYR* 4.0 28.0 - + - -
210C LEU* 3.9 17.5 - - + -
213C ALA* 5.2 0.7 - - + -
225C VAL* 3.7 30.4 - - + +
227C LEU* 3.6 33.4 - - + -
232C THR* 3.1 22.3 + - + +
233C LEU* 3.1 7.9 + - + +
235C ARG* 1.3 79.7 - - + +
237C LEU* 1.3 63.6 + - - +
239C GLN* 3.2 19.7 + - - -
240C ARG* 3.1 38.2 + - - +
266C LEU* 3.4 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 237 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233C LEU* 2.7 22.3 + - + +
234C GLN* 4.2 8.7 - - - +
236C TYR* 1.3 70.8 - - - +
238C ASP* 1.3 55.7 + - - +
240C ARG* 3.2 1.6 + - + +
241C PHE* 2.8 61.4 + - + -
263C VAL* 3.8 22.2 - - + +
266C LEU* 3.5 29.3 - - + +
267C MET* 3.8 22.9 - - + +
270C SER* 4.3 19.7 - - - +
272C ARG 5.7 0.4 - - - +
274C PRO* 4.8 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 238 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180C SER* 5.9 0.4 - - - +
234C GLN* 3.1 26.4 + - - +
235C ARG* 3.1 8.9 + - - +
237C LEU* 1.3 75.3 - - - +
239C GLN* 1.3 62.8 + - + +
241C PHE* 3.4 13.6 + - - +
242C GLN* 3.0 26.6 + - - +
275C LYS* 5.1 11.4 + - - +
278C THR* 5.0 16.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 239 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179C TYR* 3.8 16.2 - - - -
180C SER* 3.1 42.4 + - - +
183C VAL* 3.9 30.9 - - + +
184C LYS 5.8 0.2 - - - +
187C MET* 3.7 4.8 - - - +
206C LEU* 4.4 1.8 - - + +
235C ARG* 3.0 15.9 + - - +
236C TYR* 3.4 23.3 - - - +
237C LEU 3.2 0.2 - - - -
238C ASP* 1.3 76.4 - - + +
240C ARG* 1.3 88.5 + - - +
242C GLN* 3.1 11.0 + - - +
243C GLN* 2.8 27.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 240 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179C TYR* 5.1 3.2 + - - -
206C LEU* 3.2 42.4 + - - +
207C ARG* 5.7 2.2 - - - +
209C HIS* 5.4 0.6 - - - +
210C LEU* 3.8 29.8 - - - +
236C TYR* 3.1 33.1 + - - +
237C LEU* 3.8 6.3 - - - +
239C GLN* 1.3 106.3 + - - +
241C PHE* 1.3 66.5 + - - +
243C GLN* 3.2 23.8 + - + +
244C VAL* 3.1 18.4 + - - +
259C SER* 5.0 0.3 - - - +
262C ASP* 4.6 13.3 - - + +
263C VAL* 3.3 31.5 - - + +
266C LEU* 3.6 20.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 241 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237C LEU* 2.8 52.8 + - + +
238C ASP* 3.5 14.1 - - - +
239C GLN 3.3 0.2 - - - -
240C ARG* 1.3 71.6 - - - +
242C GLN* 1.3 60.2 + - - +
244C VAL* 3.4 6.9 + - - +
245C ASP* 3.3 18.2 + - - +
263C VAL* 3.8 14.3 - - + +
267C MET* 4.1 13.9 - - - -
274C PRO* 4.0 17.7 - - + -
278C THR* 4.5 19.7 - - - +
279C LEU* 3.6 20.6 - - + -
282C TYR* 3.3 52.9 - + + -
285C ASN* 5.1 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 242 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183C VAL* 5.6 0.5 - - - +
184C LYS* 3.5 39.8 + - - +
187C MET* 3.4 32.8 - - + +
188C HIS* 4.2 6.5 - - - +
238C ASP* 3.0 18.6 + - - +
239C GLN* 3.1 11.5 + - - +
241C PHE* 1.3 74.8 - - - +
243C GLN* 1.3 66.3 + - - +
245C ASP* 3.1 9.8 + - + +
246C VAL* 3.0 30.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 243 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187C MET* 3.5 25.1 - - + +
199C PHE* 3.4 15.7 - - + -
203C ALA* 3.8 33.8 + - + +
206C LEU* 4.0 11.1 - - - +
207C ARG* 3.8 3.5 - - - +
239C GLN 2.8 13.8 + - - +
240C ARG* 3.3 22.6 - - - +
242C GLN* 1.3 76.8 - - - +
244C VAL* 1.3 60.1 + - - +
247C SER* 2.9 28.3 + - - -
259C SER* 2.8 26.1 + - - +
262C ASP* 3.2 23.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 244 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240C ARG 3.1 10.1 + - - +
241C PHE 3.6 8.7 - - - +
242C GLN 3.2 0.2 - - - -
243C GLN* 1.3 74.8 - - - +
245C ASP* 1.3 65.6 + - - +
247C SER* 3.3 6.8 + - - -
248C VAL* 3.0 28.0 + - + +
256C ALA* 4.4 4.9 - - + +
259C SER* 3.5 37.7 - - - +
260C ILE* 4.1 5.4 - - + +
263C VAL* 3.9 9.4 - - + -
282C TYR* 4.1 19.7 - - + -
285C ASN* 4.0 25.6 - - + +
286C LEU* 4.7 6.5 - - + -
289C VAL* 5.7 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 245 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241C PHE 3.3 9.1 + - - +
242C GLN* 3.1 16.4 + - + +
244C VAL* 1.3 78.5 - - - +
246C VAL* 1.3 60.3 + - + +
248C VAL* 3.2 4.0 + - - +
249C LYS* 2.9 61.9 + - - +
281C ASN* 3.6 16.7 + - - +
285C ASN* 3.1 29.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 246 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187C MET* 3.8 31.0 - - + +
188C HIS* 5.7 0.4 - - - -
191C LEU* 4.1 25.6 - - + +
199C PHE* 3.6 28.5 - - + -
242C GLN* 3.0 20.8 + - + +
245C ASP* 1.3 77.0 - - + +
247C SER* 1.3 56.7 + - - +
249C LYS* 3.2 6.3 + - - +
250C LEU* 2.8 50.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 247 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199C PHE* 3.2 23.4 - - - -
243C GLN 2.9 23.0 + - - -
244C VAL* 3.4 7.2 - - - -
246C VAL* 1.3 77.8 - - - +
248C VAL* 1.3 61.0 + - - +
250C LEU* 3.5 1.1 + - - -
251C GLU 3.1 2.9 + - - -
252C LEU* 3.0 35.4 + - - +
255C GLU* 3.7 12.5 + - - +
256C ALA* 3.5 28.0 + - - -
259C SER* 4.0 2.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 248 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244C VAL* 3.0 17.1 + - + +
245C ASP 3.6 6.3 - - - +
247C SER* 1.3 76.6 - - - +
249C LYS* 1.3 65.1 + - + +
251C GLU* 3.1 15.9 + - - +
253C TRP* 3.8 26.5 - - + -
256C ALA* 4.2 5.2 - - + -
285C ASN* 3.9 24.0 - - + +
288C LYS* 3.8 31.0 - - + -
289C VAL* 3.7 26.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 249 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191C LEU* 3.6 40.9 - - + +
194C GLN* 4.5 6.1 + - - -
245C ASP* 2.9 50.1 + - - +
246C VAL 3.8 0.2 - - - +
248C VAL* 1.3 80.1 - - + +
250C LEU* 1.3 63.1 + - - +
251C GLU* 3.2 7.8 + - - +
281C ASN* 6.1 1.1 - - - +
285C ASN* 5.9 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 250 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190C CYS 4.2 11.9 - - - +
191C LEU* 3.7 21.8 - - + -
194C GLN* 3.4 43.7 - - - +
196C LYS* 3.2 42.0 + - + +
199C PHE* 4.3 17.3 - - + -
246C VAL* 2.8 35.6 + - + +
247C SER 4.1 0.2 - - - +
249C LYS* 1.3 75.2 - - - +
251C GLU* 1.3 71.0 + - - +
252C LEU* 3.1 19.6 + - + +
----------------------------------------------------------
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