Contacts of the helix formed by residues 226 - 237 (chain C) in PDB entry 3A4Y
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 GLU 226 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141C HIS 5.0 3.4 - - - +
142C LEU* 3.6 24.9 - - + -
143C PRO* 4.0 6.6 - - - +
168C LYS* 5.1 1.8 - - - +
170C VAL* 3.9 7.4 - - - +
171C LEU* 2.9 34.9 - - + +
223C PHE* 4.4 2.0 + - - +
225C VAL* 1.3 80.9 - - - +
227C ARG* 1.3 83.2 + - - +
229C GLN* 3.1 9.2 - - - +
230C GLU* 3.1 43.3 + - - +
261C TYR* 2.7 29.7 + - - -
379C GLY* 6.2 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 227 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141C HIS* 6.0 0.8 - - - -
168C LYS* 4.1 4.4 - - - +
222C THR* 4.0 3.6 - - - -
223C PHE* 3.4 49.8 - - + +
225C VAL 3.8 0.2 - - - -
226C GLU* 1.3 83.5 - - - +
228C ALA* 1.3 67.2 + - - +
230C GLU* 2.8 21.8 + - - +
231C ILE* 2.9 18.9 + - + +
339C VAL* 4.0 31.0 + - + -
340C GLY* 4.4 1.7 - - - -
377C PHE* 2.6 29.8 + - + +
378C SER* 3.1 8.1 - - - +
379C GLY* 3.1 20.8 - - - +
435C SO4 2.7 42.9 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
222C THR* 4.0 16.3 - - - +
223C PHE 3.1 15.5 + - - +
224C ALA* 4.6 0.2 - - - -
226C GLU 3.5 0.2 - - - -
227C ARG* 1.3 75.7 - - - +
229C GLN* 1.3 81.4 + - - +
231C ILE* 3.1 6.1 + - - +
232C LEU* 3.0 28.8 + - + +
249C LEU* 4.0 14.8 - - + -
254C ALA* 3.7 18.4 - - + -
310C LEU* 4.1 3.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 229 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224C ALA 3.0 17.8 + - - -
225C VAL 3.0 29.7 + - - +
226C GLU* 3.1 7.2 - - - +
228C ALA* 1.3 83.5 - - - +
230C GLU* 1.3 63.3 + - - +
232C LEU* 3.1 12.1 + - - +
233C TYR 3.0 17.7 + - - -
249C LEU* 5.9 0.2 - - - +
254C ALA 3.5 7.5 + - - +
257C VAL* 3.8 6.8 - - - +
258C LEU* 3.3 36.9 + - + +
261C TYR* 3.3 37.0 - - + +
283C PHE* 3.2 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 230 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168C LYS* 2.6 51.4 + - - +
169C ASP 5.1 0.7 + - - -
170C VAL* 3.6 27.6 - - + +
171C LEU* 5.8 0.7 - - - -
197C TYR* 4.3 12.1 + - - +
226C GLU* 3.1 28.5 + - - +
227C ARG* 2.8 20.0 + - - +
229C GLN* 1.3 75.3 - - - +
231C ILE* 1.3 63.9 + - + +
233C TYR* 2.8 14.6 + - - +
234C VAL* 3.0 24.3 + - + +
283C PHE* 4.7 0.2 - - - -
377C PHE* 4.5 12.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 231 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204C PHE* 4.5 8.1 - - + -
220C ILE* 4.3 10.3 - - + -
222C THR* 3.9 21.1 - - + -
227C ARG* 2.9 22.1 + - + +
228C ALA 3.5 6.7 - - - +
230C GLU* 1.3 72.2 - - + +
232C LEU* 1.3 61.5 + - - +
234C VAL* 3.2 7.5 + - - +
235C LEU* 2.9 38.7 + - + +
310C LEU* 3.6 28.9 - - + -
339C VAL* 3.6 22.9 - - + -
377C PHE* 3.4 35.4 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
228C ALA 3.0 18.6 + - - +
229C GLN* 3.1 10.1 + - - +
231C ILE* 1.3 75.2 - - - +
233C TYR* 1.3 57.4 + - - +
235C LEU* 3.2 17.1 + - + +
236C TYR* 3.0 23.2 + - - +
247C ILE* 4.2 0.7 - - + -
249C LEU* 4.4 13.7 - - + -
258C LEU* 3.9 22.0 - - + -
283C PHE 3.0 26.7 - - - +
285C PRO* 3.6 13.4 - - + +
288C LEU* 3.5 38.8 - - + -
310C LEU* 3.5 24.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 233 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169C ASP* 4.4 10.5 - - + -
170C VAL* 3.7 17.5 - - + -
229C GLN 3.0 4.6 + - - -
230C GLU 2.8 9.4 + - - +
232C LEU* 1.3 73.2 - - - +
234C VAL* 1.3 63.0 + - + +
235C LEU 3.0 4.5 - - - -
236C TYR* 3.1 1.9 + - - +
237C THR* 3.0 51.0 + - + +
271C GLU* 2.6 45.6 + - - +
272C VAL* 3.9 17.5 - - + +
275C HIS* 3.3 13.5 + + - -
282C PRO* 3.0 50.5 - - + -
283C PHE* 3.5 26.2 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 234 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170C VAL* 5.8 0.2 - - + -
197C TYR* 3.4 22.9 - - - +
201C VAL* 3.9 28.3 - - + -
204C PHE* 4.2 24.2 - - + -
205C LEU* 4.4 3.4 - - + +
230C GLU* 3.0 23.4 + - + +
231C ILE* 3.8 6.7 - - - +
233C TYR* 1.3 81.8 - - + +
235C LEU* 1.3 60.5 + - - +
237C THR* 3.9 7.2 - - - -
238C HIS* 3.2 27.8 - - + +
377C PHE* 4.6 11.0 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
204C PHE* 4.2 27.4 - - + -
205C LEU* 6.3 0.2 - - + -
208C LEU* 5.2 7.9 - - + -
231C ILE* 2.9 28.5 - - + +
232C LEU* 3.4 19.5 - - + +
233C TYR 3.0 0.4 - - - -
234C VAL* 1.3 80.0 - - - +
236C TYR* 1.3 59.4 + - - +
238C HIS 3.6 0.2 - - - -
239C GLY* 2.9 29.8 + - - -
242C LEU* 4.3 20.7 - - + +
247C ILE* 3.5 43.3 - - + +
285C PRO* 3.9 12.3 - - + +
308C VAL* 5.0 10.3 - - + -
310C LEU* 5.0 0.7 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
232C LEU 3.0 9.5 + - - +
233C TYR 3.1 4.2 + - - +
235C LEU* 1.3 74.4 - - - +
237C THR* 1.3 67.8 + - + +
238C HIS 3.0 9.3 + - - -
239C GLY* 3.4 8.5 + - - -
240C HIS 5.0 0.9 + - - -
275C HIS* 4.1 13.5 - + - -
280C LYS* 3.6 31.2 + - + +
281C ASN 3.8 11.9 - - - -
282C PRO* 3.4 43.7 - - + +
284C ARG 3.8 10.8 - - - -
285C PRO* 3.7 26.9 - - + +
286C ALA 4.8 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 237 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233C TYR* 3.0 53.5 + - + +
234C VAL* 3.9 3.5 - - - -
236C TYR* 1.3 77.6 - - + +
238C HIS* 1.3 84.5 + - - +
240C HIS* 4.5 7.0 + - - -
271C GLU* 4.9 2.4 + - - +
275C HIS* 3.9 21.3 - - + +
----------------------------------------------------------
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