Contacts of the helix formed by residues 232 - 251 (chain C) in PDB entry 3J8B
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 GLY 232 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227C PRO 3.5 0.2 + - - -
228C LEU* 2.6 33.5 + - - -
231C ARG* 1.3 69.1 - - - +
233C CYS* 1.3 64.8 + - - +
234C ILE 2.9 4.0 + - - -
235C LEU* 3.0 21.5 + - - +
236C THR* 4.0 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 233 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228C LEU 3.8 3.0 + - - -
229C ARG 4.3 7.9 + - - +
230C VAL 4.0 14.1 + - - +
232C GLY* 1.3 75.0 - - - +
234C ILE* 1.3 64.7 + - - +
236C THR* 3.0 25.4 + - - -
237C LEU* 3.4 4.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 234 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230C VAL 4.9 0.6 + - - -
231C ARG* 3.6 18.1 + - - +
232C GLY 2.9 0.4 + - - -
233C CYS* 1.3 76.7 - - - +
235C LEU* 1.3 66.0 + - - +
237C LEU* 3.0 24.7 + - - +
238C VAL* 3.4 4.0 + - - +
276C VAL* 6.3 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 235 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232C GLY* 3.0 12.6 + - - +
234C ILE* 1.3 77.8 - - - +
236C THR* 1.3 64.9 + - - +
238C VAL* 2.9 20.9 + - - +
239C GLU* 3.0 12.0 + - - +
276C VAL* 5.9 5.8 - - + -
288C GLU 6.2 0.2 - - - +
291C ARG* 6.2 4.5 - - + -
292C ILE* 6.1 5.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 236 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232C GLY 4.0 0.8 + - - -
233C CYS* 3.0 17.0 + - - -
235C LEU* 1.3 77.3 - - - +
237C LEU* 1.3 63.4 + - - +
239C GLU* 2.9 11.9 + - - +
240C ARG* 2.9 22.3 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
169C ILE* 5.0 17.3 - - + -
195C ILE* 5.5 10.3 - - + -
233C CYS 3.4 3.6 + - - +
234C ILE* 3.0 14.9 + - - +
236C THR* 1.3 78.2 - - - +
238C VAL* 1.3 63.0 + - - +
240C ARG* 3.0 18.9 + - - +
241C MET* 3.1 11.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 238 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234C ILE 3.4 3.4 + - - +
235C LEU* 2.9 14.2 + - - +
237C LEU* 1.3 77.3 - - - +
239C GLU* 1.3 64.1 + - - +
241C MET* 3.0 20.8 + - - +
242C ASP* 3.1 11.7 + - - +
272C ILE* 5.4 14.8 - - + +
273C ILE* 5.7 3.6 - - - +
276C VAL* 5.3 11.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 239 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235C LEU 3.0 10.4 + - - +
236C THR* 2.9 15.5 + - - +
238C VAL* 1.3 75.9 - - - +
240C ARG* 1.3 58.4 + - - +
242C ASP* 3.0 10.8 + - - +
243C GLU* 2.8 30.3 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
173C TYR* 5.1 15.5 - - + -
236C THR 2.9 11.0 + - - +
237C LEU* 3.0 12.3 + - - +
239C GLU* 1.3 76.3 - - - +
241C MET* 1.3 63.6 + - - +
243C GLU* 3.0 6.8 + - - +
244C GLU* 2.9 29.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 241 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192C LEU* 6.2 5.8 - - + -
237C LEU 3.1 6.4 + - - +
238C VAL* 3.0 18.0 + - - +
240C ARG* 1.3 78.1 - - - +
242C ASP* 1.3 56.0 + - - +
244C GLU* 4.5 3.3 - - - +
245C PHE* 3.1 26.2 + - - +
269C VAL* 5.8 6.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 242 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238C VAL 3.1 9.1 + - - +
239C GLU* 3.0 12.4 + - - +
241C MET* 1.3 75.2 - - - +
243C GLU* 1.3 60.3 + - - +
245C PHE* 3.0 9.4 + - - +
246C THR* 2.8 29.1 + - - -
269C VAL* 5.4 13.2 - - + +
295C LEU* 6.3 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 243 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239C GLU 2.8 18.2 + - - +
240C ARG* 3.0 6.9 + - - +
242C ASP* 1.3 73.0 - - - +
244C GLU* 1.3 64.9 + - - +
246C THR* 2.9 10.6 + - - -
247C LYS* 2.9 20.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 244 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240C ARG 2.9 15.5 + - - +
241C MET* 4.5 2.9 - - - +
243C GLU* 1.3 75.9 - - - +
245C PHE* 1.3 63.5 + - - +
247C LYS* 3.0 20.5 + - - +
248C ILE* 3.0 11.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 245 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241C MET 3.1 21.1 + - - +
242C ASP* 3.0 10.9 + - - +
244C GLU* 1.3 78.0 - - - +
246C THR* 1.3 60.6 + - - +
248C ILE* 2.9 22.4 + - - +
249C MET* 3.2 6.9 + - - +
262C HIS* 5.9 0.9 - - - +
265C ASP* 6.5 1.3 - - + -
269C VAL* 6.0 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 246 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242C ASP 2.8 11.2 + - - -
243C GLU* 3.3 11.7 - - - -
245C PHE* 1.3 74.7 - - - +
247C LYS* 1.3 62.9 + - - +
249C MET* 2.9 19.6 + - - +
250C GLN* 3.1 13.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 247 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243C GLU 2.9 11.2 + - - +
244C GLU* 3.0 16.1 + - - +
246C THR* 1.3 77.0 - - - +
248C ILE* 1.3 59.6 + - - +
250C GLN* 4.1 6.9 - - - +
251C ASN* 3.3 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 248 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183C MET* 3.9 27.1 - - + -
244C GLU 3.0 8.5 + - - +
245C PHE* 2.9 14.6 + - - +
247C LYS* 1.3 76.7 - - - +
249C MET* 1.3 59.2 + - - +
251C ASN* 2.9 4.6 + - - -
252C THR* 2.9 32.4 + - - -
262C HIS* 5.4 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 249 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245C PHE 3.2 6.0 + - - +
246C THR* 2.9 12.4 + - - +
248C ILE* 1.3 78.1 - - - +
250C GLN* 1.3 61.7 - - - +
252C THR* 4.1 13.3 + - - +
254C PRO* 6.1 0.7 - - - +
259C TYR* 6.0 4.4 - - - +
262C HIS* 5.4 12.7 - - + +
462C PRO* 5.6 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 250 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246C THR 3.1 13.3 + - - +
247C LYS* 4.1 7.4 - - - +
249C MET* 1.3 77.6 - - - +
251C ASN* 1.3 61.2 + - - +
252C THR 3.5 8.1 - - - +
441C LEU* 4.1 27.8 + - + +
460C GLN 6.0 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 251 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182C TYR 6.4 0.2 - - - -
183C MET* 5.2 8.7 - - + +
247C LYS 3.3 16.5 + - - +
248C ILE* 2.9 6.3 + - - +
250C GLN* 1.3 76.5 - - - +
252C THR* 1.3 64.1 + - - +
441C LEU* 5.4 3.4 - - - -
----------------------------------------------------------
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