Contacts of the helix formed by residues 221 - 240 (chain X) in PDB entry 4HSC
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 THR 221 (chain X).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174X TYR* 3.6 4.7 - - - -
194X VAL* 6.1 5.6 - - + -
195X THR 5.8 4.3 - - - +
197X ARG* 5.8 2.2 - - + -
219X ASP* 2.6 36.8 + - - +
220X PRO* 1.3 76.6 - - - +
222X TYR* 1.3 68.3 + - - +
223X ALA* 3.6 8.0 + - - +
224X ASN* 3.3 22.3 + - - +
225X VAL* 3.1 19.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 222 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170X THR* 4.0 5.9 + - - -
171X ASP* 3.6 51.9 + - - +
173X THR 4.2 10.5 - - - -
174X TYR* 3.4 38.9 + + + -
221X THR* 1.3 75.3 - - - +
223X ALA* 1.3 62.0 + - + +
225X VAL* 4.0 0.7 - - - +
226X SER* 2.8 58.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 223 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221X THR* 3.1 8.5 + - - +
222X TYR* 1.3 88.9 - - + +
224X ASN* 1.3 64.1 + - - +
226X SER* 3.7 4.1 - - - -
227X THR* 3.0 33.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 224 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217X VAL* 3.9 12.3 - - + +
219X ASP* 3.0 45.4 + - - +
221X THR* 3.3 10.7 + - - +
223X ALA* 1.3 80.5 - - - +
225X VAL* 1.3 61.4 + - - +
227X THR* 3.4 6.8 + - - -
228X ALA* 2.9 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 225 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174X TYR* 3.6 31.9 - - + -
175X PRO* 3.8 19.3 - - + +
176X ALA* 5.4 0.4 - - + -
202X ILE* 4.6 12.1 - - + -
217X VAL* 4.3 10.8 - - + -
220X PRO* 3.8 22.7 - - + -
221X THR 3.1 17.0 + - - +
222X TYR 4.1 0.2 - - - +
224X ASN* 1.3 73.0 - - - +
226X SER* 1.3 67.2 + - - +
228X ALA* 3.1 6.6 + - - +
229X ILE* 2.8 46.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 226 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174X TYR* 5.3 1.8 - - - +
222X TYR* 2.8 52.9 + - - -
223X ALA* 3.7 6.1 - - - -
225X VAL* 1.3 76.6 - - - +
227X THR* 1.3 57.9 + - - +
229X ILE* 3.2 10.3 + - - +
230X ASP* 2.8 39.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 227 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223X ALA* 3.0 17.9 + - - +
224X ASN* 3.8 7.4 + - - -
225X VAL 3.2 0.2 - - - -
226X SER* 1.3 76.3 - - - +
228X ALA* 1.3 65.7 + - - +
230X ASP* 3.5 10.3 + - + +
231X ASN* 3.0 38.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 228 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202X ILE* 4.1 7.4 - - + -
215X VAL* 4.3 8.5 - - + +
217X VAL* 3.7 25.1 - - + -
224X ASN 2.9 19.1 + - - +
225X VAL 3.6 3.8 - - - +
227X THR* 1.3 76.9 - - - +
229X ILE* 1.3 57.1 + - - +
231X ASN* 3.4 10.3 + - - +
232X LEU* 3.0 32.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 229 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174X TYR* 5.8 0.7 - - + -
175X PRO* 3.9 12.1 - - + -
202X ILE* 3.9 15.3 - - + -
204X ILE* 4.8 1.6 - - + -
225X VAL* 2.8 36.1 + - + +
226X SER* 3.5 10.5 - - - +
228X ALA* 1.3 74.5 - - - +
230X ASP* 1.3 70.9 + - - +
232X LEU* 3.0 9.3 + - + +
233X VAL* 2.9 34.7 + - + +
302X TYR* 4.5 9.2 - - + +
304X VAL* 4.0 23.8 - - + -
344X TYR* 3.4 28.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 230 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226X SER* 2.8 29.9 + - - +
227X THR* 3.6 11.0 + - + +
229X ILE* 1.3 75.6 - - - +
231X ASN* 1.3 59.9 + - - +
233X VAL* 3.4 6.3 + - - +
234X ASN* 3.0 42.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 231 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227X THR* 3.0 37.3 + - - +
228X ALA* 3.6 7.8 - - - +
230X ASP* 1.3 77.2 - - - +
232X LEU* 1.3 64.4 + - + +
234X ASN* 3.5 10.7 + - - +
235X GLN* 3.1 38.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 232 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202X ILE* 4.2 14.1 - - + -
204X ILE* 4.1 25.6 - - + +
209X MET* 3.5 18.1 - - + +
212X LYS 3.1 28.5 - - - +
213X ALA* 4.1 17.0 - - - +
215X VAL* 3.9 35.0 - - + -
228X ALA 3.0 19.9 + - - +
229X ILE* 3.0 9.8 + - + +
231X ASN* 1.3 77.0 - - - +
233X VAL* 1.3 62.6 + - - +
235X GLN* 3.2 11.9 + - - +
236X TRP* 3.1 18.6 + - - +
304X VAL* 5.8 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 233 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204X ILE* 3.7 15.5 - - + -
206X LEU* 4.2 9.2 - - + -
229X ILE* 2.9 22.1 + - + +
230X ASP* 3.8 5.8 - - - +
232X LEU* 1.3 74.2 - - - +
234X ASN* 1.3 66.5 + - - +
236X TRP* 3.3 3.5 + - - +
237X HIS* 3.1 45.6 + - + +
302X TYR* 3.5 35.4 - - + +
422X PHE* 4.0 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 234 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230X ASP* 3.0 29.5 + - - +
231X ASN* 3.9 11.5 + - - +
232X LEU 3.2 0.2 - - - -
233X VAL* 1.3 77.8 - - - +
235X GLN* 1.3 60.2 + - + +
237X HIS* 3.4 13.8 + - - +
238X ASP* 2.9 43.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 235 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209X MET* 4.1 8.0 - - + +
212X LYS* 4.3 26.2 - - - +
215X VAL* 5.7 3.0 - - - +
231X ASN* 3.1 36.0 + - - +
232X LEU* 3.2 18.1 + - - +
234X ASN* 1.3 76.1 - - + +
236X TRP* 1.3 55.1 + - - +
238X ASP* 4.6 1.3 - - - -
239X ASN* 2.7 53.0 + - - +
240X TYR* 3.7 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 236 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206X LEU* 3.6 32.8 - - + +
207X PRO* 2.8 48.9 + - + +
209X MET* 3.7 10.5 - - + +
232X LEU 3.1 10.2 + - - +
233X VAL 3.4 7.6 - - - +
235X GLN* 1.3 79.4 - - - +
237X HIS* 1.3 86.2 + + - +
240X TYR* 2.7 48.9 + - + +
241X SER* 3.1 37.4 + - - -
244X ASN 4.6 7.9 - - - -
246X LEU* 4.1 26.2 - - + -
422X PHE* 3.6 31.0 - + - -
423X SER* 5.7 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 237 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233X VAL* 3.1 39.2 + - + +
234X ASN* 3.6 16.6 + - - +
236X TRP* 1.3 97.8 - + - +
238X ASP* 1.3 67.2 + - - +
239X ASN 3.7 0.2 + - - -
241X SER* 3.4 18.5 + - - -
242X GLY 4.8 1.9 + - - -
243X GLY* 4.9 2.6 + - - -
422X PHE* 3.3 25.0 - + - -
423X SER* 3.7 1.4 - - - -
424X ARG* 3.4 48.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 238 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234X ASN* 2.9 31.9 + - - +
235X GLN* 4.6 0.8 - - - -
237X HIS* 1.3 79.7 - - - +
239X ASN* 1.3 75.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 239 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235X GLN* 2.7 42.3 + - - +
238X ASP* 1.3 90.1 - - - +
240X TYR* 1.3 82.9 + - + +
242X GLY 5.3 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 240 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207X PRO 4.1 3.1 - - - +
208X GLY* 3.0 29.4 - - - +
209X MET* 3.7 36.8 - - + -
210X GLY 4.6 0.3 + - - -
212X LYS* 3.6 27.8 + - + +
235X GLN* 3.7 17.9 - - + -
236X TRP* 2.7 36.4 + - + +
239X ASN* 1.3 95.4 - - + +
241X SER* 1.3 60.2 + - - +
242X GLY 3.5 2.0 + - - -
----------------------------------------------------------
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