Contacts of the helix formed by residues 226 - 234 (chain B) in PDB entry 3JXI
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 THR 226 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B ILE 4.5 7.2 - - - -
214B ASN* 3.6 31.2 - - + +
215B SER 4.2 4.5 - - - -
216B PRO* 4.6 2.2 - - + -
217B PHE* 4.0 7.7 - - - -
224B GLY 3.8 9.9 - - - +
225B GLN* 1.3 80.5 - - - +
227B ALA* 1.3 65.4 + - - +
228B LEU* 3.5 16.3 + - - +
229B HIS* 3.0 28.4 + - - +
230B ILE* 3.4 12.8 + - - +
249B ASP* 5.1 0.7 + - + -
252B ALA* 3.8 21.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 227 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B LEU* 3.4 39.9 - - + -
182B PRO* 4.8 9.1 - - + +
185B LEU* 3.7 14.8 - - + +
213B ILE* 3.9 11.1 + - + +
215B SER 4.9 2.0 + - - -
217B PHE* 4.5 1.8 - - - -
226B THR* 1.3 72.8 - - - +
228B LEU* 1.3 57.3 + - - +
230B ILE* 3.3 10.6 + - - +
231B ALA* 2.9 28.1 + - - +
243B LEU* 3.8 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 228 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B ILE* 5.1 1.2 + - - +
214B ASN* 6.1 0.2 - - - +
226B THR* 3.1 10.7 + - - +
227B ALA* 1.3 77.4 - - - +
229B HIS* 1.3 64.7 + - - +
231B ALA* 3.4 1.1 + - - +
232B ILE* 3.0 38.5 + - + +
240B VAL* 4.0 42.8 - - + +
243B LEU* 3.9 14.5 - - + +
244B VAL* 4.1 7.6 - - + -
248B ALA* 3.9 20.2 - - + -
249B ASP 3.5 24.2 - - - +
250B VAL* 4.0 14.1 - - + -
274B PRO* 4.0 19.1 - - + -
290B LEU* 4.9 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 229 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B GLY 4.2 2.9 - - - -
225B GLN* 3.8 10.3 - - + +
226B THR* 3.0 32.6 + - - +
228B LEU* 1.3 77.8 - - - +
230B ILE* 1.3 59.0 + - + +
232B ILE* 3.3 2.8 + - - -
233B GLU* 2.9 27.0 + - - +
252B ALA* 3.2 34.3 + - + -
253B GLN 4.1 0.7 - - - -
254B ALA* 3.7 25.0 - - + +
270B PHE* 4.3 6.5 - + + -
272B GLU 2.8 25.8 + - - -
274B PRO* 4.0 16.0 - - + +
277B LEU* 3.4 28.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 230 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B PRO* 3.5 33.9 - - + +
185B LEU* 3.8 19.5 - - + -
186B LEU* 3.6 31.4 - - + -
217B PHE* 3.4 34.5 - - + -
225B GLN* 5.5 2.7 - - - +
226B THR 3.8 5.6 - - - +
227B ALA* 3.3 6.5 + - - +
228B LEU 3.3 0.2 - - - -
229B HIS* 1.3 73.8 - - + +
231B ALA* 1.3 58.4 + - - +
233B GLU* 3.2 6.4 + - - +
234B ARG* 2.8 42.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 231 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B LEU* 4.4 14.1 - - + +
227B ALA 2.9 17.7 + - - +
228B LEU* 3.6 5.6 - - - +
230B ILE* 1.3 75.4 - - - +
232B ILE* 1.3 59.7 + - - +
234B ARG* 3.8 0.8 + - - -
235B ARG 3.4 2.3 + - - -
236B CYS* 3.1 36.1 + - - +
239B TYR* 4.4 2.9 - - + -
240B VAL* 3.8 23.4 - - + +
243B LEU* 3.8 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 232 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B LEU* 3.0 27.0 + - + +
229B HIS* 3.6 3.6 - - - +
231B ALA* 1.3 75.4 - - - +
233B GLU* 1.3 65.5 + - - +
235B ARG* 2.9 8.1 + - - +
240B VAL* 3.8 19.7 - - + -
274B PRO* 3.4 40.6 - - + +
277B LEU* 3.8 11.4 - - + -
278B ALA* 3.8 28.9 - - + +
283B GLN* 2.7 37.4 + - - +
286B ILE* 4.0 15.9 - - + -
290B LEU* 4.2 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 233 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B HIS 2.9 17.9 + - - +
230B ILE* 3.8 6.9 - - - +
232B ILE* 1.3 78.9 - - - +
234B ARG* 1.3 80.9 + - - +
235B ARG* 3.3 14.7 + - - +
277B LEU* 4.1 20.6 - - + +
281B THR* 5.4 8.5 - - + +
283B GLN* 4.8 1.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 234 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B LEU 4.1 11.7 - - - +
186B LEU* 3.8 42.8 + - - +
188B LEU* 4.6 8.1 - - + +
230B ILE* 2.8 32.9 + - + +
233B GLU* 1.3 87.3 + - - +
235B ARG* 1.3 72.7 + - - +
236B CYS* 3.4 20.9 + - - -
----------------------------------------------------------
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