Contacts of the helix formed by residues 223 - 235 (chain B) in PDB entry 1OZG
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 223 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B MET* 2.7 30.3 + - - +
218B ALA* 4.4 9.0 - - - +
220B GLN* 3.0 16.7 + - - +
222B GLU* 1.3 89.9 + - - +
224B SER* 1.3 57.1 + - - +
225B LYS 3.3 2.2 + - - -
226B ALA* 3.4 1.9 + - - -
227B LEU* 2.8 34.6 + - + +
323B ASP* 5.9 0.3 - - - -
324B ILE* 3.5 30.5 + - + +
325B ALA* 3.2 29.1 + - - +
328B LEU* 5.1 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 224 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B ALA 5.5 1.1 - - - -
220B GLN 3.5 5.0 + - - -
221B PRO* 3.4 22.3 + - - -
223B ASN* 1.3 76.6 - - - +
225B LYS* 1.3 65.5 + - - +
227B LEU* 3.7 7.6 - - - +
228B ARG* 3.1 24.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 225 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B PRO 4.8 1.9 + - - +
222B GLU 5.2 1.9 + - - +
223B ASN 3.3 0.4 - - - -
224B SER* 1.3 78.2 - - - +
226B ALA* 1.3 60.2 + - - +
228B ARG* 3.4 12.6 + - - +
229B ARG* 2.8 48.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 226 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222B GLU 5.4 0.4 + - - -
223B ASN 3.4 6.3 + - - +
225B LYS* 1.3 75.5 - - - +
227B LEU* 1.3 55.0 + - - +
229B ARG* 3.1 15.2 + - - +
230B LEU* 2.8 35.9 + - - +
325B ALA* 3.4 41.5 - - + +
328B LEU* 4.0 13.1 - - + +
329B ASN* 3.6 13.9 - - - +
332B ALA* 5.5 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 227 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B LEU* 4.0 37.5 - - + -
218B ALA* 3.5 27.6 - - + +
223B ASN* 2.8 22.8 + - + +
224B SER* 3.7 6.5 - - - +
226B ALA* 1.3 71.8 - - - +
228B ARG* 1.3 63.9 + - - +
230B LEU* 2.9 7.5 + - + +
231B LEU* 2.9 48.7 + - + +
247B ALA* 4.3 11.4 - - + +
248B VAL* 4.3 6.3 - - + -
281B ILE* 4.6 7.0 - - + -
328B LEU* 4.1 20.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 228 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B SER 3.1 16.0 + - - +
225B LYS* 3.5 8.7 + - - +
227B LEU* 1.3 78.6 - - - +
229B ARG* 1.3 77.9 - - - +
231B LEU* 3.8 8.1 - - - +
232B GLU* 2.8 73.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 229 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225B LYS* 2.8 38.4 + - - +
226B ALA* 3.3 9.5 - - - +
228B ARG* 1.3 92.0 - - - +
230B LEU* 1.3 58.5 + - - +
232B GLU* 4.1 2.3 - - - +
233B THR* 2.6 36.7 + - - +
329B ASN* 2.6 37.7 + - - +
332B ALA* 4.4 14.6 - - + -
333B GLN* 6.1 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 230 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B PHE* 3.8 34.5 - - + -
226B ALA 2.8 16.1 + - - +
227B LEU* 3.4 11.2 - - + +
229B ARG* 1.3 72.9 - - - +
231B LEU* 1.3 63.6 + - + +
233B THR* 3.4 1.7 + - - -
234B SER* 3.0 26.9 + - - -
281B ILE* 4.3 6.3 - - + -
328B LEU* 3.8 37.7 - - + +
331B LEU* 4.2 13.2 - - + -
332B ALA* 4.0 22.6 - - - +
335B ILE* 3.7 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 231 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B PHE* 3.6 22.9 - - + -
214B LEU* 6.0 0.2 - - + -
227B LEU* 2.9 38.6 + - + +
228B ARG* 3.9 6.5 - - - +
230B LEU* 1.3 76.7 - - + +
232B GLU* 1.3 57.3 + - - +
234B SER* 4.2 2.5 - - - -
235B HIS* 2.7 37.3 + - - +
236B ILE 4.2 3.8 - - - +
238B VAL* 3.2 33.7 - - + -
248B VAL* 3.8 29.6 - - + -
253B PHE* 3.6 21.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 232 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B ARG* 2.8 59.9 + - + +
229B ARG 4.1 2.9 - - - +
231B LEU* 1.3 77.5 - - - +
233B THR* 1.3 58.8 + - - +
235B HIS* 3.4 10.2 - - - +
253B PHE* 5.2 1.1 - - - -
338B ARG* 3.0 47.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 233 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B ARG* 2.6 27.3 + - - +
230B LEU 3.8 3.8 - - - -
231B LEU 3.2 0.8 - - - -
232B GLU* 1.3 80.0 - - - +
234B SER* 1.3 57.8 + - - +
332B ALA* 3.6 31.6 - - - +
335B ILE* 3.9 24.7 - - + +
336B ASP 5.8 0.8 - - - -
337B HIS 4.3 0.5 - - - -
338B ARG* 3.2 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 234 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B ILE* 5.6 0.4 - - - -
212B PHE* 3.9 8.5 - - - -
230B LEU 3.0 13.7 + - - -
231B LEU* 4.0 0.9 + - - -
233B THR* 1.3 77.6 - - - +
235B HIS* 1.3 68.1 + - - +
236B ILE* 3.1 36.0 + - - +
335B ILE* 3.6 27.5 - - - +
337B HIS 4.6 0.9 - - - -
338B ARG* 4.1 2.7 - - - +
339B LEU* 2.8 30.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 235 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B LEU 2.7 32.9 + - - -
232B GLU* 3.4 17.9 + - - +
234B SER* 1.3 74.0 + - - +
236B ILE* 1.3 59.7 + - - +
237B PRO 3.8 0.2 - - - -
253B PHE* 3.9 18.5 - + - -
255B ARG* 2.7 53.9 + - - +
338B ARG* 3.0 55.3 + - + +
----------------------------------------------------------
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