Contacts of the helix formed by residues 225 - 248 (chain C) in PDB entry 2Z43
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 225 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220C TYR* 3.8 25.9 - - + +
221C PRO* 3.3 31.8 + - - +
222C GLY 2.8 5.2 + - - +
224C GLU* 1.3 95.7 + - - +
226C LEU* 1.3 57.2 + - - +
227C ALA 3.4 2.7 - - - -
228C VAL* 3.4 15.6 + - + +
229C ARG* 3.0 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 226 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222C GLY 3.3 1.8 + - - -
223C ARG* 3.2 36.0 + - + +
224C GLU 3.4 0.2 - - - -
225C ASN* 1.3 77.7 - - - +
227C ALA* 1.3 64.7 + - - +
229C ARG* 3.1 35.2 + - - +
230C GLN* 3.0 40.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 227 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223C ARG 4.7 1.0 + - - -
224C GLU 5.2 1.2 + - - +
225C ASN 3.4 0.4 - - - -
226C LEU* 1.3 78.9 - - - +
228C VAL* 1.3 61.7 + - + +
230C GLN* 3.3 7.4 + - - +
231C GLN* 2.9 28.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 228 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220C TYR* 4.5 12.8 - - + -
224C GLU 6.0 0.7 - - - +
225C ASN* 3.4 16.2 + - - +
226C LEU 3.3 0.2 - - - -
227C ALA* 1.3 77.7 - - + +
229C ARG* 1.3 65.6 + - - +
231C GLN* 3.2 9.2 + - - +
232C LYS* 3.1 47.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 229 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213C THR* 6.2 1.6 - - - -
216C PHE* 3.2 46.6 - - + +
217C ARG* 3.6 29.8 - - - +
220C TYR* 3.1 29.5 + - + +
221C PRO* 5.3 0.2 - - - -
222C GLY 4.0 22.0 + - - +
223C ARG* 4.8 2.2 - - - +
225C ASN 3.0 15.1 + - - +
226C LEU* 3.1 35.6 - - + +
228C VAL* 1.3 77.9 - - - +
230C GLN* 1.3 65.8 + - + +
232C LYS* 3.4 3.0 + - - +
233C LEU* 3.0 32.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 230 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226C LEU* 3.0 38.7 + - + +
227C ALA* 3.5 7.6 - - - +
229C ARG* 1.3 86.4 - - - +
231C GLN* 1.3 62.7 + - - +
233C LEU* 3.9 19.4 - - - +
234C ASN* 3.1 51.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 231 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227C ALA 2.9 16.4 + - - +
228C VAL* 3.6 10.0 - - - +
230C GLN* 1.3 78.0 - - - +
232C LYS* 1.3 79.3 + - - +
234C ASN* 3.5 5.6 + - - +
235C LYS* 3.3 41.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 232 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188C ILE* 5.7 3.0 - - + +
216C PHE* 4.0 18.0 - - + -
220C TYR* 3.8 44.9 - - + +
228C VAL* 3.1 30.4 + - + +
229C ARG 4.0 2.5 - - - +
231C GLN* 1.3 88.8 + - - +
233C LEU* 1.3 65.4 + - - +
235C LYS* 3.4 21.0 + - - +
236C HIS* 3.2 21.1 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
212C VAL* 4.5 4.9 - - + +
213C THR* 3.9 32.8 - - + -
216C PHE* 4.1 30.9 - - + -
229C ARG* 3.0 19.2 + - + +
230C GLN* 3.9 26.7 - - - +
232C LYS* 1.3 75.3 - - - +
234C ASN* 1.3 65.1 + - - +
236C HIS* 3.1 7.2 + - - +
237C LEU* 2.9 55.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 234 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230C GLN* 3.1 38.6 + - - +
231C GLN* 3.9 5.7 - - - +
233C LEU* 1.3 84.2 - - - +
235C LYS* 1.3 57.6 + - - +
237C LEU* 3.9 12.1 - - - +
238C HIS* 2.9 28.8 + - - +
281C PRO* 5.8 2.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 235 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231C GLN* 3.3 38.3 + - - +
232C LYS* 3.6 23.4 - - - +
233C LEU 3.1 0.4 - - - -
234C ASN* 1.3 77.1 - - - +
236C HIS* 1.3 65.4 + - - +
238C HIS* 3.4 7.4 + - + +
239C GLN* 3.1 26.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 236 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187C GLN* 3.1 43.9 + - + +
188C ILE* 4.0 25.4 - - + -
191C VAL* 3.3 34.1 - - + +
209C VAL* 5.0 2.2 - - + -
212C VAL* 4.0 16.7 - - + +
216C PHE* 3.9 18.2 - + + -
232C LYS 3.2 9.9 + - - +
233C LEU* 3.1 9.3 + - - +
235C LYS* 1.3 79.2 - - - +
237C LEU* 1.3 64.2 + - - +
239C GLN* 3.0 26.3 + - - +
240C LEU* 3.1 16.0 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
109C MET* 4.2 15.7 - - + +
212C VAL* 3.9 28.7 - - + -
213C THR* 6.4 0.2 - - + -
233C LEU* 2.9 40.0 + - + +
234C ASN* 3.9 13.5 - - - +
236C HIS* 1.3 77.1 - - - +
238C HIS* 1.3 56.5 + - - +
240C LEU* 3.1 17.3 + - + +
241C THR* 2.8 32.8 + - + +
253C ILE* 4.0 27.8 - - + -
281C PRO* 4.7 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 238 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234C ASN 2.9 19.5 + - - +
235C LYS* 3.7 7.6 - - + +
236C HIS 3.2 0.2 - - - -
237C LEU* 1.3 75.8 - - - +
239C GLN* 1.3 65.6 + - + +
241C THR* 2.6 27.2 + - - -
242C ARG* 2.9 40.3 + - + +
245C GLU* 6.1 0.7 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
188C ILE* 3.8 23.4 - - - +
191C VAL* 3.5 25.3 + - + +
192C ASP* 3.7 30.7 + - - +
195C GLN* 4.4 9.5 - - - +
235C LYS* 3.1 17.3 + - + +
236C HIS* 3.0 17.3 + - - +
238C HIS* 1.3 80.9 - - + +
240C LEU* 1.3 60.5 + - - +
242C ARG* 3.3 8.2 + - - +
243C LEU* 3.1 25.7 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
109C MET* 4.6 3.6 - - - -
191C VAL* 3.8 29.8 - - + -
194C LEU* 4.4 12.1 - - + -
207C ILE* 4.8 2.2 - - + -
209C VAL* 4.2 20.6 - - + -
212C VAL* 4.7 0.7 - - + -
236C HIS* 3.1 24.7 + - + +
237C LEU* 3.1 22.2 + - + +
239C GLN* 1.3 80.7 - - - +
241C THR* 1.4 63.8 + - - +
243C LEU* 3.2 10.3 + - + +
244C ALA* 3.1 21.5 + - - +
251C VAL* 3.9 23.5 - - + +
253C ILE* 4.0 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 241 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109C MET* 3.8 27.1 - - + +
237C LEU 2.8 16.6 + - - +
238C HIS* 2.6 36.8 + - - -
240C LEU* 1.4 76.6 - - - +
242C ARG* 1.3 55.0 + - - +
244C ALA* 3.3 9.0 + - - +
245C GLU* 2.9 44.1 + - - +
281C PRO* 3.6 27.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 242 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238C HIS* 2.9 43.5 + - + +
239C GLN* 3.6 10.3 - - - +
240C LEU 3.3 0.2 - - - -
241C THR* 1.3 73.8 - - - +
243C LEU* 1.3 66.6 + - - +
245C GLU* 4.3 17.7 + - - +
246C VAL* 2.9 62.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 243 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191C VAL* 3.9 20.6 - - + +
194C LEU* 3.7 38.6 - - + -
195C GLN* 3.6 37.0 - - + +
198C VAL* 4.7 5.2 - - + -
207C ILE* 4.6 11.2 - - + -
239C GLN* 3.1 16.0 + - - +
240C LEU* 3.2 10.7 + - + +
242C ARG* 1.3 76.0 - - - +
244C ALA* 1.3 63.5 + - - +
247C TYR* 3.0 48.7 + - + +
249C ILE* 4.6 4.1 - - + +
251C VAL* 5.2 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 244 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107C ARG* 3.5 9.2 - - - +
108C THR 3.9 21.8 - - - +
240C LEU 3.1 5.3 + - - +
241C THR* 3.4 12.8 - - - +
243C LEU* 1.3 80.3 - - - +
245C GLU* 1.3 56.8 + - - +
248C ASP 3.1 23.0 + - - -
249C ILE* 3.2 30.5 + - - +
251C VAL* 3.7 21.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 245 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107C ARG* 3.6 43.7 + - + +
108C THR* 5.6 0.4 - - - -
238C HIS* 6.1 0.3 - - - -
241C THR* 2.9 32.8 + - - +
242C ARG* 4.1 19.0 + - - +
244C ALA* 1.3 80.3 - - + +
246C VAL* 1.3 65.0 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
107C ARG* 5.1 2.3 + - - -
242C ARG* 2.9 63.2 + - + +
245C GLU* 1.3 74.6 - - - +
247C TYR* 1.3 85.4 + - + +
248C ASP* 3.8 0.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 247 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195C GLN* 4.4 22.8 + - + +
198C VAL* 3.9 24.2 - - + -
199C SER* 4.6 16.4 - - - -
205C LYS* 4.2 4.5 + - - -
243C LEU* 3.0 44.0 + - + +
246C VAL* 1.3 99.4 - - + +
248C ASP* 1.3 70.1 + - - +
249C ILE* 3.4 20.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 248 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C ARG* 5.7 0.7 - - - +
87C LYS* 2.7 34.0 + - - +
106C THR* 2.8 25.9 + - - -
107C ARG* 3.0 46.6 + - - +
205C LYS* 2.9 38.0 + - - +
244C ALA 3.1 9.2 + - - -
245C GLU 4.1 1.6 + - - -
246C VAL 3.6 3.6 + - - +
247C TYR* 1.3 77.8 - - - +
249C ILE* 1.3 58.4 + - - +
----------------------------------------------------------
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