Contacts of the helix formed by residues 231 - 238 (chain B) in PDB entry 3IO6
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 ALA 231 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210B TYR* 3.9 7.6 - - - +
214B GLU* 4.2 11.0 - - + +
227B ASN* 3.7 31.2 - - + +
228B GLY 3.1 14.1 + - - +
230B TRP* 1.3 82.0 - - - +
232B TRP* 1.3 67.9 + - + +
233B SER 3.3 0.2 - - - -
234B ASN* 3.0 20.6 + - - +
235B ILE* 3.5 20.4 + - + +
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Residues in contact with TRP 232 (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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114B SER* 5.2 0.8 - - - -
116B ILE* 4.1 14.9 - - + +
227B ASN 5.1 0.6 + - - -
228B GLY 3.8 13.8 + - - -
229B PRO* 3.4 34.7 - - + +
230B TRP 3.3 0.8 - - - -
231B ALA* 1.3 76.7 - - - +
233B SER* 1.3 59.2 + - - +
235B ILE* 3.1 8.9 + - + +
236B ASP* 2.8 35.2 + - - +
242B TYR* 3.9 16.9 + + - +
244B VAL* 3.7 25.0 - - + +
300B GLY* 5.9 2.9 - - - -
314B ASP* 4.7 0.4 - - - -
316B ARG* 3.4 63.0 - - + +
317B ILE* 3.8 20.6 - - + -
320B THR* 3.6 22.0 - - - -
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Residues in contact with SER 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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229B PRO 4.8 0.2 + - - -
230B TRP 3.6 14.3 + - - -
232B TRP* 1.3 78.4 - - - +
234B ASN* 1.3 70.7 + - - +
236B ASP* 3.5 11.1 + - - +
237B THR* 2.9 25.3 + - - -
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Residues in contact with ASN 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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214B GLU* 3.1 32.9 - - - +
218B ASN* 3.4 17.0 - - - +
230B TRP 5.4 0.9 - - - +
231B ALA* 3.0 7.4 + - - +
233B SER* 1.3 89.7 + - - +
235B ILE* 1.3 58.1 + - + +
237B THR* 3.5 12.3 + - - +
238B SER* 3.2 19.4 + - - -
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Residues in contact with ILE 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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116B ILE* 4.2 25.8 - - + -
214B GLU* 5.5 2.7 - - + +
217B PHE* 4.0 27.1 - - + -
218B ASN* 3.5 16.8 - - - +
225B THR* 5.4 2.2 - - + -
227B ASN* 6.1 0.2 - - + -
231B ALA* 3.7 20.6 - - + +
232B TRP* 3.1 7.2 + - - +
234B ASN* 1.3 75.8 - - + +
236B ASP* 1.3 65.4 + - - +
237B THR 3.2 0.4 - - - -
238B SER* 3.0 22.5 + - - +
239B LYS* 3.6 6.6 + - - -
240B VAL* 3.8 14.4 + - + +
242B TYR* 3.5 40.1 - - + -
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Residues in contact with ASP 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B TRP* 2.8 26.4 + - - +
233B SER* 3.7 11.1 - - - +
235B ILE* 1.3 77.2 - - - +
237B THR* 1.3 60.4 + - - +
239B LYS* 3.8 17.7 + - - +
242B TYR* 3.3 25.9 + - - -
316B ARG* 4.2 8.9 + - - -
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Residues in contact with THR 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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233B SER 2.9 15.8 + - - -
234B ASN* 3.5 16.4 + - - +
235B ILE 3.2 0.2 - - - -
236B ASP* 1.3 74.1 - - - +
238B SER* 1.3 57.9 + - - +
239B LYS* 3.0 23.8 + - - +
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Residues in contact with SER 238 (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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218B ASN* 3.4 33.8 + - - +
234B ASN 3.2 7.2 + - - -
235B ILE* 3.0 23.2 + - - -
237B THR* 1.3 77.0 - - - +
239B LYS* 1.3 65.9 + - - +
240B VAL* 3.1 18.9 + - - +
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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