Contacts of the helix formed by residues 231 - 239 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116A ILE* 5.2 0.4 - - + -
210A TYR* 3.7 9.6 - - - +
214A GLU* 4.4 8.5 - - + +
227A ASN* 3.6 37.7 - - + +
228A GLY 3.2 6.9 + - - +
230A TRP* 1.3 78.4 - - - +
232A TRP* 1.3 64.3 + - + +
233A SER 3.4 1.6 - - - -
234A ASN* 3.5 17.7 + - - +
235A ILE* 3.2 24.6 + - + +
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Residues in contact with TRP 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A SER* 5.7 0.7 - - - -
116A ILE* 4.6 11.0 - - + +
227A ASN 5.0 0.6 + - - -
228A GLY 3.5 19.9 + - - -
229A PRO* 3.4 33.0 - - + +
230A TRP 3.3 1.6 - - - -
231A ALA* 1.3 77.3 - - - +
233A SER* 1.3 66.5 + - - +
235A ILE* 3.1 19.8 + - + +
236A ASP* 3.0 20.4 + - - +
242A TYR* 3.7 11.8 + + - +
244A VAL* 3.8 27.6 - - + +
300A GLY* 5.4 5.4 - - - -
316A ARG* 3.5 64.4 - - + +
317A ILE* 3.9 18.2 - - + -
320A THR* 3.6 22.0 - - - -
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Residues in contact with SER 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229A PRO 4.9 0.2 + - - -
230A TRP 3.6 14.6 + - - -
232A TRP* 1.3 80.5 - - - +
234A ASN* 1.3 66.8 + - - -
236A ASP* 3.5 13.9 + - - +
237A THR* 3.1 24.5 + - - -
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Residues in contact with ASN 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A GLU* 3.4 26.3 + - - +
218A ASN* 4.1 12.9 - - - +
230A TRP 4.2 10.3 + - - -
231A ALA* 3.7 9.7 + - - +
232A TRP 3.2 0.6 - - - -
233A SER* 1.3 89.5 + - - +
235A ILE* 1.3 64.7 + - + +
237A THR* 3.4 10.2 + - - -
238A SER* 3.2 18.9 + - - -
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Residues in contact with ILE 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A ILE* 4.0 36.6 - - + -
214A GLU* 6.3 1.1 - - + -
217A PHE* 3.9 18.4 - - + -
218A ASN* 3.7 18.4 - - - +
225A THR* 5.8 0.2 - - + -
231A ALA* 3.2 23.6 - - + +
232A TRP* 3.1 6.6 + - + +
234A ASN* 1.3 73.9 - - + +
236A ASP* 1.3 65.9 + - - +
237A THR 3.1 0.2 - - - -
238A SER* 2.6 32.1 + - - +
239A LYS 3.2 3.6 + - - -
240A VAL* 3.9 7.9 + - + +
242A TYR* 3.5 40.1 - - + -
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Residues in contact with ASP 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232A TRP* 3.0 17.0 + - - +
233A SER* 3.6 15.9 - - - +
235A ILE* 1.3 76.2 - - - +
237A THR* 1.3 60.8 + - - +
239A LYS* 3.2 28.2 + - - +
242A TYR* 2.6 33.2 + - - -
316A ARG* 4.2 7.0 + - - -
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Residues in contact with THR 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A SER 3.1 13.7 + - - -
234A ASN* 3.4 11.2 + - - -
235A ILE 3.1 0.2 - - - -
236A ASP* 1.3 74.9 - - - +
238A SER* 1.3 63.0 + - - +
239A LYS* 3.0 16.8 + - - +
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Residues in contact with SER 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218A ASN* 3.5 35.5 + - - +
234A ASN 3.2 11.9 + - - -
235A ILE* 2.6 25.9 + - - +
237A THR* 1.3 74.7 - - - +
239A LYS* 1.3 66.3 + - - +
240A VAL* 3.3 24.1 + - - +
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Residues in contact with LYS 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235A ILE 3.2 0.4 + - - -
236A ASP* 3.2 19.9 + - - +
237A THR* 3.0 20.8 - - - +
238A SER* 1.3 80.5 + - - +
240A VAL* 1.3 62.6 + - - +
241A ASN 4.1 1.3 + - - -
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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