Contacts of the helix formed by residues 224 - 237 (chain B) in PDB entry 3Q41
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 SER 224 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B SER* 4.5 1.6 + - - -
223B ALA* 1.3 76.6 - - - +
225B GLU* 1.3 64.3 + - - +
226B ASP* 3.4 6.6 + - - +
227B ASP* 3.1 34.4 + - - +
228B ALA* 2.8 31.2 + - - +
252B ARG* 3.8 22.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 225 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B PRO* 3.4 40.4 - - + +
101B HIS* 5.6 0.3 - - - -
144B TYR* 5.4 0.7 + - - -
224B SER* 1.3 78.3 - - - +
226B ASP* 1.3 64.7 + - - +
229B ALA* 3.1 23.7 + - - +
252B ARG* 3.5 42.8 + - + +
255B SER* 3.4 30.5 - - - +
256B GLY* 4.8 3.4 - - - -
257B ASN 4.6 5.2 - - - +
258B ALA* 3.4 13.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 226 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B SER* 3.2 6.3 + - - +
225B GLU* 1.3 83.9 + - - +
227B ASP* 1.3 57.1 + - - +
229B ALA* 3.4 8.3 - - - +
230B THR* 2.7 34.0 + - - -
233B ARG* 4.6 1.2 + - - -
257B ASN* 3.4 29.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 227 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B SER* 5.4 2.1 + - - -
197B PHE* 3.7 18.1 - - + -
199B PRO* 2.5 35.7 - - - +
200B GLY* 4.6 2.9 - - - -
201B THR 4.3 10.3 - - - +
204B VAL* 5.5 0.2 - - - +
223B ALA* 3.7 18.6 - - + -
224B SER* 3.1 23.3 + - - +
226B ASP* 1.3 77.5 - - - +
228B ALA* 1.3 66.5 + - - +
229B ALA 3.2 0.9 - - - -
230B THR* 3.3 6.4 + - - -
231B VAL* 3.1 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 228 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B LEU* 3.8 23.6 - - + -
223B ALA* 3.7 2.6 - - + +
224B SER 2.8 16.9 + - - +
225B GLU 3.8 3.8 - - - +
227B ASP* 1.3 75.4 - - - +
229B ALA* 1.3 59.0 + - - +
231B VAL* 3.1 3.9 + - - +
232B TYR* 2.9 53.2 + - + -
253B GLU* 3.9 20.6 - - + -
258B ALA* 3.9 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 229 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225B GLU 3.1 13.0 + - - +
226B ASP* 3.4 15.0 - - - +
227B ASP 3.2 0.2 - - - -
228B ALA* 1.3 79.4 - - - +
230B THR* 1.3 56.2 + - - +
232B TYR* 3.5 11.0 + - - +
233B ARG* 2.9 44.9 + - - +
257B ASN* 4.0 23.6 - - + +
258B ALA* 4.3 1.3 - - - +
261B TYR* 4.1 12.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 230 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B THR 3.8 12.2 + - - +
202B LYS* 3.7 32.1 - - + +
203B ASN 3.9 8.5 - - - +
204B VAL* 4.4 10.4 - - + +
226B ASP 2.7 22.8 + - - -
227B ASP* 3.8 8.6 + - - -
228B ALA 3.2 0.6 - - - -
229B ALA* 1.3 77.1 - - - +
231B VAL* 1.3 58.9 + - - +
233B ARG* 3.7 24.8 + - - +
234B ALA* 3.1 26.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 231 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B LEU* 4.7 8.1 - - + -
197B PHE* 5.0 10.1 - - + -
204B VAL* 4.2 24.7 - - + -
208B LEU* 3.7 17.8 - - + +
221B LEU* 3.8 38.6 - - + -
227B ASP 3.1 14.8 - - - +
228B ALA 3.1 8.5 + - - +
230B THR* 1.3 74.0 - - - +
232B TYR* 1.3 63.1 + - + +
234B ALA* 3.1 1.1 + - - -
235B ALA* 2.6 38.7 + - - +
247B TRP* 4.2 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 232 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B LEU* 3.7 20.0 - - + -
228B ALA* 2.9 28.4 + - + +
229B ALA* 3.7 6.3 - - - +
231B VAL* 1.3 75.7 - - + +
233B ARG* 1.3 63.1 + - - +
235B ALA* 3.7 5.0 - - - +
236B ALA* 3.1 26.2 + - - +
241B THR* 5.2 1.2 + - - -
247B TRP* 3.9 17.3 - + - -
249B VAL* 3.3 3.5 - - - +
253B GLU* 2.5 44.1 + - - +
258B ALA* 3.5 22.0 - - + -
261B TYR 3.3 18.3 - - - +
262B ALA* 3.7 9.9 - - + -
263B PRO* 3.6 17.6 - - + +
266B ILE* 3.3 31.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 233 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B LYS* 5.9 3.6 - - - +
226B ASP 4.6 1.0 + - - -
229B ALA* 2.9 24.4 + - - +
230B THR* 3.7 41.9 + - - +
232B TYR* 1.3 78.3 - - - +
234B ALA* 1.3 60.0 + - + +
236B ALA* 3.8 4.6 + - - +
237B MET* 3.5 18.2 + - - +
261B TYR* 4.0 44.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 234 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B ASN* 6.2 0.4 - - - -
204B VAL 4.8 10.3 - - - +
205B THR* 4.5 17.5 - - - +
208B LEU* 4.1 13.9 - - + -
230B THR* 3.1 19.7 + - + +
231B VAL* 3.9 2.5 - - - +
233B ARG* 1.3 74.6 - - - +
235B ALA* 1.3 64.2 + - - +
237B MET* 3.5 9.2 + - - +
238B LEU* 3.4 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 235 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B LEU* 3.8 6.0 - - + +
231B VAL 2.6 22.3 + - - +
232B TYR* 3.3 6.3 + - - +
234B ALA* 1.3 69.7 - - - +
236B ALA* 1.3 65.2 + - - +
238B LEU* 3.0 9.0 + - - -
239B ASN 3.1 0.2 + - - -
240B MET* 3.0 43.7 + - + +
241B THR* 4.7 2.9 - - - +
247B TRP* 3.7 32.5 - - + -
263B PRO* 6.4 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 236 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B TYR 3.1 17.0 + - - +
233B ARG* 4.0 4.9 - - - +
235B ALA* 1.3 76.4 - - - +
237B MET* 1.3 63.7 + - - +
238B LEU 3.0 1.1 + - - -
239B ASN* 3.2 11.4 + - - +
241B THR* 3.8 32.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 237 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B ARG 3.5 13.5 + - - +
234B ALA* 3.5 12.7 + - - +
235B ALA 3.2 0.8 - - - -
236B ALA* 1.3 79.2 - - - +
238B LEU* 1.3 69.2 + - + +
239B ASN 3.6 0.2 - - - -
----------------------------------------------------------
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