Contacts of the helix formed by residues 230 - 234 (chain C) in PDB entry 2J9F
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 THR 230 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A PRO* 3.5 24.1 + - - +
11A GLY* 3.6 2.3 - - - -
193C GLU* 3.7 22.7 - - + +
221C ASN* 3.8 3.1 - - - +
223C GLY* 3.2 32.4 + - - +
229C PRO* 1.3 72.5 - - - +
231C SER* 1.3 63.2 + - - +
233C GLN* 3.0 17.3 + - - -
234C TYR* 3.2 49.2 + - + +
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Residues in contact with SER 231 (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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210A THR* 4.8 0.7 - - - -
229C PRO* 3.0 18.8 + - - +
230C THR* 1.3 80.8 + - - +
232C GLU* 1.3 62.9 + - - +
234C TYR 3.8 4.8 - - - +
235C ARG* 2.9 40.2 + - - +
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Residues in contact with GLU 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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210A THR* 4.0 14.4 - - - -
49B ALA* 5.1 0.9 - - - +
61B ARG* 4.2 20.4 + - - -
71B ASN* 2.7 47.4 + - + +
72B THR 4.1 3.1 - - - +
73B PRO* 3.8 19.8 - - - +
228C THR* 3.8 8.5 - - + +
229C PRO* 2.9 29.5 + - + +
231C SER* 1.3 87.2 + - - +
233C GLN* 1.3 60.3 + - - +
234C TYR 3.7 0.7 - - - -
235C ARG* 5.0 4.3 - - - +
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Residues in contact with GLN 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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206A ASN* 3.0 24.6 + - - -
210A THR* 3.8 3.0 - - - +
72B THR 5.1 0.4 + - - -
73B PRO* 3.4 6.8 - - - +
74B LEU* 2.8 27.3 + - - +
193C GLU* 3.8 19.3 + - + +
194C GLY* 3.8 10.5 - - - +
197C SER* 2.7 26.7 + - - +
225C ALA* 3.6 28.3 - - - +
228C THR* 3.9 14.9 + - - +
229C PRO 3.4 2.8 + - - +
230C THR* 3.0 21.5 + - + +
232C GLU* 1.3 81.0 - - - +
234C TYR* 1.3 68.7 + - + +
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Residues in contact with TYR 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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11A GLY* 2.5 33.3 + - - -
206A ASN* 3.5 7.4 - - - +
210A THR* 3.4 11.0 - - - +
246A TYR* 6.2 1.1 - - - -
193C GLU* 4.1 7.9 - - + -
221C ASN* 2.9 16.1 + - - -
230C THR* 3.2 39.6 + - + +
231C SER* 3.8 4.3 - - - +
233C GLN* 1.3 87.0 - - + +
235C ARG* 1.3 72.3 + - - +
236C GLY* 3.5 18.6 - - - +
238C GLY* 3.4 23.8 - - - +
239C ILE* 3.8 16.4 - - + -
242C ARG* 3.2 32.3 - - - +
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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