Contacts of the helix formed by residues 231 - 239 (chain N) in PDB entry 3O3U
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 N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210N TYR* 3.8 8.1 - - - +
214N GLU* 4.8 8.8 - - + +
227N ASN* 3.6 34.5 - - + +
228N GLY 3.0 13.6 + - - +
229N PRO 3.0 1.2 - - - -
230N TRP* 1.3 79.8 - - - +
232N TRP* 1.3 67.3 + - + +
233N SER 3.3 2.0 + - - -
234N ASN* 3.4 13.3 + - - +
235N ILE* 3.4 23.1 + - + +
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Residues in contact with TRP 232 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114N SER* 6.0 0.4 - - - -
116N ILE* 4.1 18.5 - - + +
227N ASN 5.3 0.6 + - - -
228N GLY 3.8 11.1 + - - -
229N PRO* 3.1 35.2 + - + +
231N ALA* 1.3 79.5 - - - +
233N SER* 1.3 63.1 + - - +
235N ILE* 3.1 7.6 + - + +
236N ASP* 2.9 26.5 + - - +
242N TYR* 3.6 10.2 + + - +
244N VAL* 3.8 22.8 - - + +
298N PRO* 3.7 23.6 - - + -
300N GLY* 5.2 1.3 - - - -
314N ASP* 4.7 0.2 - - - -
316N ARG* 3.5 74.9 - - + +
317N ILE* 3.9 18.6 - - + -
320N THR* 3.4 22.2 - - - -
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Residues in contact with SER 233 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230N TRP 4.0 0.3 + - - -
231N ALA 3.3 0.2 - - - -
232N TRP* 1.3 78.4 - - - +
234N ASN* 1.3 63.4 + - - +
236N ASP* 3.2 13.5 + - - +
237N THR* 3.1 25.8 + - - -
295N LYS 5.3 2.9 - - - -
296N ASP 3.3 14.7 + - - -
297N LYS* 2.9 35.9 + - - +
298N PRO* 4.0 14.9 - - - +
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Residues in contact with ASN 234 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214N GLU* 3.0 32.9 + - - +
218N ASN* 3.7 12.4 + - - +
230N TRP 5.8 1.0 + - - -
231N ALA* 3.4 6.6 + - - +
232N TRP 3.3 0.2 - - - -
233N SER* 1.3 78.5 + - - +
235N ILE* 1.3 62.6 + - - +
237N THR* 3.4 9.6 + - - -
238N SER* 3.1 21.8 + - - -
297N LYS* 2.8 30.2 + - - +
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Residues in contact with ILE 235 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116N ILE* 3.8 38.8 - - + -
217N PHE* 3.9 20.0 - - + -
218N ASN* 3.5 18.6 - - - +
225N THR* 5.3 1.8 - - + -
231N ALA* 3.4 19.5 - - + +
232N TRP* 3.1 10.0 + - - +
234N ASN* 1.3 73.2 - - - +
236N ASP* 1.3 67.1 + - - +
238N SER* 2.7 28.8 + - - +
239N LYS* 3.3 4.5 + - - -
240N VAL* 3.8 9.1 + - + +
242N TYR* 3.2 36.3 - - + -
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Residues in contact with ASP 236 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232N TRP 2.9 15.3 + - - +
233N SER* 3.3 15.3 - - - +
235N ILE* 1.3 76.1 - - - +
237N THR* 1.3 61.9 + - - +
239N LYS* 3.2 25.5 + - - +
240N VAL 5.8 0.2 - - - -
242N TYR* 2.7 32.7 + - - -
298N PRO* 6.1 0.5 - - - +
316N ARG* 4.1 10.7 + - - -
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Residues in contact with THR 237 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233N SER 3.1 13.8 + - - -
234N ASN* 3.6 13.6 + - - -
236N ASP* 1.3 76.7 - - - +
238N SER* 1.3 61.6 + - - +
239N LYS* 3.3 13.9 + - - +
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Residues in contact with SER 238 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218N ASN* 3.3 34.1 - - - +
234N ASN 3.1 11.6 + - - -
235N ILE* 2.7 22.6 + - - -
237N THR* 1.3 75.3 - - - +
239N LYS* 1.3 66.6 + - - +
240N VAL* 3.1 21.7 + - - +
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Residues in contact with LYS 239 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235N ILE 3.3 1.2 + - - -
236N ASP* 3.2 20.2 + - - +
237N THR* 3.2 11.3 - - - +
238N SER* 1.3 81.9 + - - +
240N VAL* 1.3 66.4 + - - +
241N ASN* 3.3 3.3 + - - +
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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