Contacts of the helix formed by residues 236 - 241 (chain C) in PDB entry 2PCB
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 TYR 236 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206C LEU* 4.0 13.9 - - + -
211C TRP* 3.6 31.8 + + - +
223C TRP* 3.7 55.4 - + + +
231C MET* 4.4 4.7 - - + -
232C LEU 3.0 12.1 + - - +
233C PRO 3.6 4.0 - - - +
235C ASP* 1.3 72.4 - - - +
237C SER* 1.3 56.9 + - - +
238C LEU 3.1 4.5 - - - -
239C ILE* 2.9 54.2 - - + +
240C GLN* 3.0 36.8 + - + -
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Residues in contact with SER 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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150C ASP* 3.9 4.4 - - - -
151C ALA* 3.3 33.6 + - - -
154C VAL* 4.9 2.8 - - - +
233C PRO 3.1 9.2 + - - -
234C THR* 2.7 22.9 + - - -
236C TYR* 1.3 70.7 - - - +
238C LEU* 1.3 58.4 + - - +
239C ILE 3.0 2.0 - - - -
240C GLN* 2.7 38.4 + - - +
241C ASP* 2.8 21.0 + - - +
244C TYR* 3.8 2.8 - - - -
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Residues in contact with LEU 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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154C VAL* 5.1 4.0 - - + -
168C VAL* 4.8 5.2 - - + -
169C VAL* 3.4 31.6 - - + +
172C MET* 3.6 38.8 - - + -
202C PHE* 4.3 11.9 - - + -
203C TYR* 5.3 0.7 - - + -
206C LEU* 4.3 6.7 - - + -
234C THR 4.4 6.1 - - - +
235C ASP 3.0 18.3 + - - +
237C SER* 1.3 79.4 + - - +
239C ILE* 1.3 57.2 + - - +
241C ASP 3.3 1.2 - - - +
244C TYR* 2.9 38.5 - - + +
245C LEU* 2.8 27.4 + - - -
248C VAL* 3.5 14.3 - - + +
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Residues in contact with ILE 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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206C LEU* 3.7 39.5 - - + +
207C LEU* 4.5 15.3 - - + +
211C TRP* 5.3 0.2 - - + -
236C TYR* 2.9 58.1 - - + +
238C LEU* 1.3 77.3 - - - +
240C GLN* 1.4 67.6 + - - +
241C ASP 3.1 6.6 - - - +
245C LEU* 3.9 31.8 - - + +
248C VAL* 4.5 8.7 - - + -
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Residues in contact with GLN 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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149C LYS 5.4 1.0 - - - +
150C ASP* 5.0 7.6 - - - +
151C ALA* 5.1 1.1 + - + -
223C TRP* 4.6 8.5 - - - +
233C PRO 4.5 2.9 - - - +
236C TYR* 3.0 44.3 + - + +
237C SER* 2.7 28.0 + - - +
239C ILE* 1.4 82.6 - - - +
241C ASP* 1.3 57.1 + - - +
242C PRO* 3.9 5.7 - - - +
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Residues in contact with ASP 241 (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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151C ALA* 3.6 23.4 - - + +
155C ARG* 3.5 34.6 + - - -
237C SER 2.8 13.8 + - - +
239C ILE 4.3 0.2 - - - -
240C GLN* 1.3 77.2 - - - +
242C PRO* 1.3 66.0 - - - +
243C LYS* 2.9 29.6 + - - +
244C TYR* 3.0 14.1 + - + -
245C LEU* 2.4 38.4 + - - +
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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