Contacts of the helix formed by residues 232 - 240 (chain C) in PDB entry 3Q29
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 232 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117C ILE* 4.9 3.1 - - + -
211C TYR* 3.9 6.7 - - - +
215C GLU* 5.0 8.6 - - + +
228C ASN* 3.5 35.9 - - + +
229C GLY 3.0 13.0 + - - +
231C TRP* 1.3 78.9 - - - +
233C TRP* 1.3 66.4 + - + +
234C SER 3.2 3.8 + - - -
235C ASN* 3.4 13.0 + - - +
236C ILE* 3.2 20.1 + - + +
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Residues in contact with TRP 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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115C SER* 5.5 1.3 - - - -
117C ILE* 3.8 25.9 - - + +
228C ASN 5.1 0.6 + - - -
229C GLY 3.6 13.8 + - - -
230C PRO* 3.2 33.9 + - + +
232C ALA* 1.3 78.5 - - - +
234C SER* 1.3 58.1 + - - +
236C ILE* 3.1 8.6 + - + +
237C ASP* 2.8 32.3 + - - +
243C TYR* 3.6 14.8 - + - +
245C VAL* 3.9 14.3 - - + +
299C PRO* 3.6 20.4 - - + -
315C ASP* 4.2 2.9 - - - -
317C ARG* 3.4 72.2 - - + +
318C ILE* 3.8 16.6 - - + -
321C THR* 3.5 25.6 - - - -
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Residues in contact with SER 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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231C TRP 4.0 1.0 + - - -
232C ALA 3.2 0.6 - - - -
233C TRP* 1.3 78.5 - - - +
235C ASN* 1.3 62.7 + - - +
237C ASP* 3.3 15.4 + - - +
238C THR* 3.1 24.1 + - - -
296C LYS 4.4 5.0 + - - -
297C ASP 3.0 26.9 + - - -
298C LYS* 3.6 18.7 - - - +
299C PRO* 4.0 12.3 - - - +
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Residues in contact with ASN 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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215C GLU* 2.9 31.2 + - - +
219C ASN* 3.7 11.9 - - - +
231C TRP 5.8 1.1 + - - -
232C ALA* 3.4 8.4 + - - +
233C TRP 3.3 0.4 - - - -
234C SER* 1.3 77.5 + - - +
236C ILE* 1.3 58.2 + - - +
238C THR* 3.4 10.6 + - - +
239C SER* 3.1 24.9 + - - -
298C LYS* 4.1 24.9 + - - +
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Residues in contact with ILE 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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117C ILE* 3.8 37.7 - - + -
218C PHE* 3.8 21.5 - - + -
219C ASN* 3.5 18.2 - - - +
226C THR* 5.3 2.2 - - + -
232C ALA* 3.2 20.9 - - + +
233C TRP* 3.1 11.4 + - - +
235C ASN* 1.3 74.7 - - - +
237C ASP* 1.3 66.3 - - - +
238C THR 3.1 0.2 - - - -
239C SER* 2.8 29.6 + - - +
240C LYS* 3.3 4.0 + - - -
241C VAL* 4.0 8.0 + - + +
243C TYR* 3.3 33.2 - - + -
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Residues in contact with ASP 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 TRP 2.8 18.8 + - - +
234C SER* 3.3 15.5 + - - +
236C ILE* 1.3 74.6 - - - +
238C THR* 1.3 61.4 + - - +
240C LYS* 3.2 27.1 + - - +
243C TYR* 2.6 32.1 + - - -
317C ARG* 3.9 11.7 + - - -
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Residues in contact with THR 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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234C SER* 3.1 12.6 + - - -
235C ASN* 3.5 13.9 + - - -
236C ILE 3.1 0.4 - - - -
237C ASP* 1.3 78.1 - - - +
239C SER* 1.3 60.8 + - - +
240C LYS* 3.2 21.6 + - - +
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Residues in contact with SER 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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219C ASN* 3.2 31.9 - - - +
235C ASN 3.1 12.8 + - - -
236C ILE* 2.8 20.3 + - - +
238C THR* 1.3 75.5 - - - +
240C LYS* 1.3 68.9 - - - +
241C VAL* 3.0 26.3 + - - +
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Residues in contact with LYS 240 (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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236C ILE 3.3 1.3 + - - -
237C ASP 3.2 20.5 + - - +
238C THR* 3.2 20.5 + - - +
239C SER* 1.3 81.9 + - - +
241C VAL* 1.3 64.9 + - - +
242C ASN* 3.5 2.4 + - - +
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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