Contacts of the helix formed by residues 231 - 239 (chain C) in PDB entry 3IOT
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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116C ILE* 5.2 0.7 - - + -
210C TYR* 3.7 11.0 - - - +
214C GLU* 4.4 8.9 - - + +
227C ASN* 3.6 36.8 - - + +
228C GLY 3.2 6.7 + - - +
230C TRP* 1.3 78.6 - - - +
232C TRP* 1.3 65.7 + - + +
233C SER 3.4 1.1 - - - -
234C ASN* 3.4 18.6 + - - +
235C ILE* 3.2 24.5 + - + +
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Residues in contact with TRP 232 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114C SER* 5.9 0.6 - - - -
116C ILE* 4.6 6.3 - - + +
227C ASN 5.1 0.4 + - - -
228C GLY 3.5 20.2 + - - -
229C PRO* 3.4 33.6 - - + +
230C TRP 3.3 1.6 - - - -
231C ALA* 1.3 77.5 - - - +
233C SER* 1.3 67.4 + - - +
235C ILE* 3.1 25.3 + - + +
236C ASP* 3.0 19.5 + - - +
242C TYR* 4.0 10.3 - + - +
244C VAL* 3.8 28.0 - - + +
300C GLY* 5.4 4.9 - - - -
316C ARG* 3.4 66.0 - - + +
317C ILE* 3.9 18.2 - - + -
320C THR* 3.6 21.1 - - - -
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Residues in contact with SER 233 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229C PRO 4.8 0.4 + - - -
230C TRP 3.6 15.0 + - - -
232C TRP* 1.3 79.5 - - - +
234C ASN* 1.3 68.2 + - - -
235C ILE 3.4 0.2 + - - -
236C ASP* 3.5 17.3 + - - +
237C THR* 3.2 18.5 + - - -
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Residues in contact with ASN 234 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214C GLU* 3.4 26.1 + - + +
218C ASN* 4.1 13.8 - - - +
230C TRP 4.2 7.9 + - - -
231C ALA* 3.4 12.9 + - - +
232C TRP 3.2 0.8 - - - -
233C SER* 1.3 92.3 + - - +
235C ILE* 1.3 61.4 + - + +
237C THR* 3.4 10.1 + - - -
238C SER* 3.2 18.4 + - - -
419C GLN* 5.0 21.3 - - - +
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Residues in contact with ILE 235 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116C ILE* 4.0 37.0 - - + -
214C GLU* 6.3 0.7 - - + -
217C PHE* 3.9 17.7 - - + -
218C ASN* 3.7 19.3 - - - +
225C THR* 5.8 0.4 - - + -
231C ALA* 3.2 23.3 - - + +
232C TRP* 3.1 6.3 + - - +
234C ASN* 1.3 74.6 - - + +
236C ASP* 1.3 67.2 + - - +
237C THR 3.1 0.4 - - - -
238C SER* 2.7 32.4 + - - +
239C LYS 3.3 3.3 + - - -
240C VAL* 3.9 8.5 + - + +
242C TYR* 3.4 40.1 - - + -
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Residues in contact with ASP 236 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232C TRP* 3.0 20.2 + - - +
233C SER* 3.6 10.9 - - - +
235C ILE* 1.3 75.9 - - - +
237C THR* 1.3 60.1 + - - +
239C LYS* 3.2 28.1 + - - +
242C TYR* 2.6 31.7 + - - -
316C ARG* 4.2 8.2 + - - -
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Residues in contact with THR 237 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233C SER 3.2 13.4 + - - -
234C ASN* 3.4 11.3 + - - -
235C ILE 3.1 0.4 - - - -
236C ASP* 1.3 74.9 - - - +
238C SER* 1.3 63.3 + - - +
239C LYS* 3.0 17.5 + - - +
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Residues in contact with SER 238 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218C ASN* 3.4 36.9 + - - +
234C ASN 3.2 11.7 + - - -
235C ILE* 2.7 24.8 + - - +
237C THR* 1.3 75.5 - - - +
239C LYS* 1.3 66.5 + - - +
240C VAL* 3.3 23.9 + - - +
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Residues in contact with LYS 239 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235C ILE 3.3 0.8 + - - -
236C ASP* 3.2 20.9 + - - +
237C THR* 3.0 19.6 - - - +
238C SER* 1.3 80.9 + - - +
240C VAL* 1.3 62.0 + - - +
241C ASN 4.1 1.2 + - - -
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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