Contacts of the helix formed by residues 229 - 237 (chain B) in PDB entry 1OIZ
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 TYR 229 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197B ILE* 3.7 13.9 - - + -
198B ASN* 3.6 26.7 + - - -
225B HIS* 3.5 24.7 - - + -
226B GLY 3.5 13.7 - - - +
227B ASN 3.3 14.1 + - - -
228B ASN* 1.3 74.1 - - - +
230B LYS* 1.3 112.3 + - + +
231B GLN 3.4 2.2 - - - -
232B SER* 3.2 9.3 + - - -
233B LEU* 2.8 49.8 + - + +
244B GLU 3.3 10.6 + - - -
245B TYR* 3.3 22.9 - + - -
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Residues in contact with LYS 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228B ASN* 3.6 7.3 - - - +
229B TYR* 1.3 110.1 + - + +
231B GLN* 1.3 58.6 + - - +
233B LEU* 3.9 1.3 - - - +
234B LEU* 2.9 43.8 + - + +
243B LEU 4.7 1.2 + - - -
244B GLU 2.9 28.7 + - - -
245B TYR 3.7 12.1 - - - +
246B GLY* 3.6 16.4 - - - +
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Residues in contact with GLN 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B ASN* 5.2 3.5 + - - +
229B TYR 3.4 0.4 - - - -
230B LYS* 1.3 80.3 - - - +
232B SER* 1.3 62.4 + - - +
234B LEU* 3.5 17.7 + - - +
235B GLN* 3.2 46.4 + - - +
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Residues in contact with SER 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225B HIS* 2.8 36.1 + - - +
228B ASN 4.4 3.7 + - - -
229B TYR* 3.2 13.7 + - - -
231B GLN* 1.3 78.3 - - - +
233B LEU* 1.3 60.5 + - - +
235B GLN* 3.4 21.3 + - - +
236B HIS* 3.1 22.0 - - - -
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Residues in contact with LEU 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157B ILE* 4.1 11.9 - - + -
195B HIS* 4.4 4.9 - - + -
197B ILE* 4.1 18.2 - - + -
225B HIS* 3.9 23.3 - - + +
229B TYR* 2.8 45.3 + - + +
230B LYS 3.9 2.0 - - - +
232B SER* 1.3 77.7 + - - +
234B LEU* 1.3 58.5 + - - +
236B HIS* 3.1 3.7 + - - -
237B PHE* 3.0 55.6 + - + +
241B LEU* 3.8 27.4 - - + -
245B TYR* 4.2 9.0 - - + +
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Residues in contact with LEU 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230B LYS* 2.9 35.5 + - + +
231B GLN* 3.9 20.6 - - - +
232B SER 3.3 0.2 - - - -
233B LEU* 1.3 76.1 - - - +
235B GLN* 1.3 62.5 + - - +
237B PHE 3.8 8.5 - - - +
238B PRO* 3.2 31.3 - - + +
239B ASP 5.4 2.7 - - - +
241B LEU* 3.9 20.9 - - + -
245B TYR 4.4 3.6 - - - +
246B GLY* 3.7 29.6 - - - +
247B GLY* 4.3 6.5 - - - -
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Residues in contact with GLN 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B PRO* 5.5 1.4 - - - +
231B GLN* 3.2 33.3 + - - +
232B SER* 3.5 17.5 - - - +
233B LEU 3.2 0.8 - - - -
234B LEU* 1.3 79.2 - - - +
236B HIS* 1.3 63.2 + - + +
238B PRO* 3.8 8.8 - - - +
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Residues in contact with HIS 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B ASP* 4.2 2.6 - - - +
109B PRO* 3.7 13.7 - - - +
155B LYS* 6.3 1.2 - - - -
195B HIS* 3.5 25.7 + + - +
223B HIS* 3.9 26.4 - + - -
225B HIS* 3.9 12.4 + - - -
232B SER* 3.1 24.4 - - - -
233B LEU 3.1 7.4 + - - +
235B GLN* 1.3 81.3 - - + +
237B PHE* 1.3 85.5 + - + +
238B PRO* 3.4 5.6 - - - +
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Residues in contact with PHE 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B ASP* 3.9 18.2 - - + -
114B VAL* 3.9 20.6 - - + -
155B LYS* 3.8 26.5 - - + -
157B ILE* 3.6 23.1 - - + -
195B HIS* 3.5 31.0 - + - -
233B LEU* 3.0 34.9 + - + +
234B LEU* 3.5 6.9 - - - +
235B GLN 3.4 0.2 - - - -
236B HIS* 1.3 97.0 - - + +
238B PRO* 1.3 65.9 - - - +
239B ASP 3.6 1.6 + - - -
240B ILE* 3.7 15.0 + - + +
241B LEU* 3.6 37.0 + - + +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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