Contacts of the helix formed by residues 223 - 240 (chain C) in PDB entry 5PRC
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 LEU 223 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221C ARG 3.8 1.2 + - - -
222C PRO* 1.3 70.5 - - - +
224C SER* 1.3 63.8 + - - +
226C ALA* 2.8 25.4 + - + +
227C TYR* 3.3 18.6 - - + -
170M SER* 3.0 22.7 + - - +
171M GLU* 3.6 47.3 + - - +
183M TRP* 3.7 22.2 - - + +
186M ALA* 4.2 10.1 - - + +
187M PHE* 4.1 12.8 - - + -
190M ARG* 3.9 35.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 224 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187C TYR* 3.2 28.3 - - - -
222C PRO* 3.4 10.0 - - - +
223C LEU* 1.3 78.4 - - - +
225C ASP* 1.3 61.0 + - - +
227C TYR* 3.1 17.9 + - - +
228C ALA* 2.9 28.9 + - - +
96M PRO 4.9 1.8 - - - -
97M LYS* 2.7 37.2 + - - -
170M SER* 4.7 3.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 225 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192C MET* 5.4 2.1 - - - +
193C PHE* 5.2 1.2 - - - -
199C ARG* 2.9 30.6 + - - -
203C VAL* 3.4 6.0 - - + +
221C ARG* 3.0 49.1 + - + +
222C PRO* 2.9 24.8 + - - +
223C LEU 2.9 0.2 + - - -
224C SER* 1.3 84.7 + - - +
226C ALA* 1.3 60.4 + - - +
228C ALA* 3.6 7.6 - - - +
229C THR* 3.1 26.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 226 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203C VAL* 4.0 19.4 - - + +
222C PRO 4.3 0.2 + - - -
223C LEU* 2.8 20.6 + - + +
225C ASP* 1.3 71.5 - - - +
227C TYR* 1.3 65.7 + - - +
229C THR* 3.3 3.1 + - - +
230C PHE* 3.0 23.8 + - - +
186M ALA* 3.7 28.4 - - - +
189M ILE* 4.6 7.4 - - + +
190M ARG* 4.1 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 227 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185C LEU* 3.8 24.4 - - + +
187C TYR* 3.4 26.5 - + + -
223C LEU* 3.3 39.2 + - + -
224C SER* 3.1 14.5 + - - +
226C ALA* 1.3 77.4 - - - +
228C ALA* 1.3 63.7 + - - +
230C PHE* 3.1 7.9 + - - +
231C ALA* 2.9 21.3 + - - +
94M TYR* 5.2 11.4 - + - -
95M PRO* 4.9 3.6 - - + +
170M SER 4.9 4.0 - - - -
172M GLY 4.0 3.1 + - - -
174M PRO* 3.3 25.1 - - + +
179M PRO 4.9 0.4 - - - -
182M ASP* 4.3 5.4 - - + -
183M TRP* 3.2 40.4 - + + -
186M ALA* 3.6 23.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 228 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187C TYR* 3.9 19.6 - - + +
189C PRO* 4.7 0.9 - - - +
192C MET* 3.4 34.5 - - + -
193C PHE* 3.7 13.8 - - + -
224C SER 2.9 15.7 + - - +
225C ASP* 3.6 8.5 - - - +
227C TYR* 1.3 77.6 - - - +
229C THR* 1.3 57.7 + - - +
231C ALA* 3.0 5.2 + - - +
232C LEU 2.9 24.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 229 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193C PHE* 4.1 12.3 - - - -
200C GLN 4.6 0.5 + - - -
201C VAL* 2.6 42.5 + - + +
203C VAL* 3.7 12.9 - - + +
225C ASP 3.1 15.5 + - - -
226C ALA 3.3 4.0 + - - +
228C ALA* 1.3 78.9 - - - +
230C PHE* 1.3 63.8 + - - +
232C LEU* 3.2 5.8 + - - +
233C MET* 3.0 22.7 + - + +
339C HEM 3.9 35.4 - - + -
189M ILE* 5.8 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 230 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185C LEU* 3.6 26.9 - - + -
226C ALA 3.0 13.4 + - - +
227C TYR* 3.3 11.0 - - - +
229C THR* 1.3 76.3 - - - +
231C ALA* 1.3 57.5 + - - +
233C MET* 2.9 6.3 + - - +
234C MET* 2.8 49.5 + - + +
339C HEM 3.9 31.0 - - + -
162L TYR* 4.5 2.2 - + - -
165L LEU 4.1 12.8 - - - -
166L ASN* 3.5 30.5 - - - -
182M ASP* 4.8 7.6 - - - -
185M THR* 3.8 31.6 - - + -
186M ALA* 5.0 2.7 - - - -
189M ILE* 4.4 11.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 231 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180C THR* 4.0 16.5 - - + +
185C LEU* 3.9 27.5 - - + +
187C TYR* 4.3 12.6 - - + -
189C PRO* 4.1 8.1 - - + -
227C TYR 2.9 12.4 + - - +
228C ALA* 3.0 13.9 + - - +
230C PHE* 1.3 75.1 - - - +
232C LEU* 1.3 63.5 + - - +
234C MET* 3.2 6.9 + - - +
235C SER* 2.9 22.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 232 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189C PRO* 3.3 29.5 - - + +
193C PHE* 3.7 37.0 - - + -
194C LEU* 4.3 17.9 - - + -
201C VAL* 3.8 32.1 - - + -
228C ALA 2.9 7.2 + - - +
229C THR 3.4 7.2 - - - +
231C ALA* 1.3 76.3 - - - +
233C MET* 1.3 65.8 + - + +
235C SER* 3.3 5.7 + - - +
236C ILE* 2.9 44.6 + - + +
271C ILE* 4.9 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 233 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201C VAL* 4.0 7.9 - - + -
229C THR* 3.0 11.8 + - + +
230C PHE 2.9 8.7 + - - +
232C LEU* 1.3 98.8 - - + +
234C MET* 1.3 61.9 + - - +
236C ILE* 3.9 12.2 - - + +
237C SER* 2.8 35.1 + - - -
271C ILE* 5.4 0.9 - - + -
339C HEM 2.1 113.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 234 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180C THR* 3.9 18.6 - - - +
181C ALA* 4.2 11.1 - - + +
183C SER* 3.8 23.6 - - - -
185C LEU* 4.3 8.1 - - + -
230C PHE* 2.8 37.6 + - + +
231C ALA* 3.3 9.4 - - - +
233C MET* 1.3 75.0 - - - +
235C SER* 1.3 62.4 + - - +
237C SER* 3.4 3.4 + - - -
238C ASP* 3.1 23.6 + - - +
339C HEM 3.9 13.0 - - - -
165L LEU* 3.9 27.1 - - + +
166L ASN* 4.2 14.4 - - + +
260L PRO* 4.0 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 235 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179C TYR* 3.5 45.5 + - - -
180C THR* 4.4 0.6 - - - +
189C PRO* 4.0 14.0 - - - +
194C LEU* 5.6 2.8 - - - +
231C ALA 2.9 13.0 + - - -
232C LEU* 3.3 11.7 - - - +
234C MET* 1.3 76.2 - - - +
236C ILE* 1.3 52.8 + - - +
238C ASP* 3.1 6.3 + - - +
239C SER* 2.8 42.9 + - - -
306C ARG* 4.5 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 236 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194C LEU* 5.8 0.9 - - + -
232C LEU* 2.9 39.7 + - + +
233C MET* 3.9 19.5 - - + +
235C SER* 1.3 75.4 - - - +
237C SER* 1.3 64.4 + - - +
239C SER* 3.2 8.4 + - - -
240C LEU* 2.9 26.2 + - + +
267C ALA* 5.8 0.2 - - + -
271C ILE* 4.6 15.5 - - + -
305C CYS* 4.0 18.4 - - - -
339C HEM 4.2 32.3 - - + -
340C HEM 3.6 30.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 237 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233C MET 2.8 22.1 + - - -
234C MET* 3.5 5.6 - - - -
236C ILE* 1.3 76.9 - - - +
238C ASP* 1.3 65.6 + - - +
240C LEU* 2.9 8.8 + - - +
241C GLY 3.0 9.5 + - - -
242C THR* 3.0 38.0 + - - -
244C CYS 4.2 0.9 + - - -
339C HEM 3.5 31.8 - - - +
165L LEU* 3.8 15.3 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
154C LEU* 5.1 1.7 - - - +
178C LYS 4.7 5.4 - - - +
179C TYR 5.4 0.6 - - - +
181C ALA* 4.1 27.3 + - + +
234C MET 3.1 10.5 + - - +
235C SER* 3.6 7.9 - - - +
237C SER* 1.3 78.5 - - - +
239C SER* 1.3 63.6 + - - +
241C GLY* 2.8 17.7 + - - +
242C THR 5.0 0.4 - - - -
306C ARG* 2.8 22.7 + - - +
311C GLY* 4.3 5.2 - - - -
165L LEU* 5.3 5.2 - - + +
261L GLU* 4.2 14.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 239 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235C SER* 2.8 25.7 + - - -
236C ILE 3.4 9.2 - - - -
238C ASP* 1.3 71.8 - - - +
240C LEU* 1.3 58.4 + - - +
241C GLY 3.3 0.4 - - - -
304C ASP* 5.2 1.7 + - - -
305C CYS* 3.8 25.7 + - - +
306C ARG* 3.5 40.1 + - - +
309C HIS* 3.7 9.7 - - - +
310C GLN* 4.1 1.0 + - - -
311C GLY 2.9 24.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 240 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236C ILE* 2.9 21.2 + - + +
237C SER 2.9 3.3 + - - +
239C SER* 1.3 82.9 - - - +
241C GLY* 1.3 64.2 + - - +
242C THR* 3.8 14.4 - - + -
246C PHE* 5.0 0.4 - - + -
305C CYS* 4.4 1.1 - - + -
309C HIS* 3.4 39.7 - - + +
311C GLY 3.4 6.0 - - - +
312C VAL* 3.3 5.2 - - - -
313C THR* 3.2 35.1 + - + +
339C HEM 3.7 30.1 - - + -
340C HEM 3.8 34.1 - - + -
----------------------------------------------------------
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