Contacts of the helix formed by residues 233 - 237 (chain C) in PDB entry 2R2N
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 233 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197C VAL* 4.4 1.6 - - + -
199C ASN* 3.5 28.1 + - - +
200C GLY 3.3 23.6 - - - -
202C ASN* 3.8 8.4 + - + -
231C ASP 3.2 0.8 - - - -
232C PRO* 1.3 88.8 - - + +
234C TYR* 1.3 63.9 + - - +
235C PHE 3.1 3.4 - - - +
236C LEU* 2.9 26.9 + - + -
237C GLN* 4.0 0.7 + - - +
263C LYS* 3.5 41.3 - - + -
352C ALA* 4.4 0.3 - - - +
353C GLY* 3.9 26.5 - - - +
354C MET* 4.2 16.4 - - + -
355C PHE* 3.6 21.5 - + - -
426C PMP 2.7 33.1 + + + -
428C KYN 5.2 0.3 + - - -
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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
----------------------------------------------------------
94C LEU* 4.3 10.9 + - + +
95C HIS* 3.6 24.1 + + - -
199C ASN* 3.9 4.3 - - - +
231C ASP* 3.1 32.1 + - - +
232C PRO 3.4 1.0 - - - -
233C TYR* 1.3 78.2 - - - +
235C PHE* 1.3 89.9 + + + +
236C LEU 3.2 2.5 + - - -
237C GLN* 2.9 47.1 + - - +
242C ARG* 2.9 45.5 + - + +
243C VAL 4.2 8.4 + - - -
245C THR* 3.4 20.4 - - + +
257C ARG* 3.1 27.1 - - - +
259C ASP* 4.6 2.0 - - - +
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Residues in contact with PHE 235 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C LEU* 4.2 8.3 - - + -
91C GLN* 5.9 1.1 - - - -
94C LEU* 3.8 27.6 - - + -
95C HIS* 6.1 0.4 - + - -
231C ASP 6.0 0.2 - - - -
232C PRO 4.8 3.7 + - - +
233C TYR* 3.1 1.4 - - - +
234C TYR* 1.3 100.6 - + + +
236C LEU* 1.3 70.0 + - - +
237C GLN 3.8 1.6 - - - -
242C ARG* 5.2 3.1 - - - +
259C ASP* 4.4 12.8 - - + -
260C SER 4.8 11.2 - - - -
261C PHE* 5.3 2.7 - + - -
264C ILE* 3.7 34.5 - - + +
273C PHE* 5.2 7.6 - + - -
315C PHE* 3.5 31.0 - + - -
316C MET* 4.3 8.7 - - + -
319C VAL* 3.6 28.9 - - + +
323C ILE* 3.5 16.4 - - - +
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Residues in contact with LEU 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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233C TYR* 2.9 19.7 + - + +
235C PHE* 1.3 90.5 - - - +
237C GLN* 1.3 62.4 + - - +
238C PHE* 3.7 8.2 + - - -
263C LYS* 4.1 14.4 - - + +
264C ILE* 3.9 9.6 - - + -
322C VAL* 3.6 31.2 - - + -
323C ILE* 4.0 11.7 - - + +
326C TYR* 4.2 18.6 - - + -
352C ALA* 3.3 1.6 - - - -
353C GLY* 3.0 39.1 + - - +
354C MET* 3.7 30.1 - - + -
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Residues in contact with GLN 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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199C ASN* 3.2 34.8 + - + +
207C SER* 5.6 0.2 - - - +
233C TYR 4.1 4.3 - - - +
234C TYR* 2.9 46.7 - - - +
235C PHE 3.8 1.6 - - - -
236C LEU* 1.3 75.1 - - - +
238C PHE* 1.3 64.6 + - - +
239C ASN* 3.4 18.8 + - + +
240C LYS* 4.5 0.3 + - - -
241C PHE 4.6 1.0 + - - -
242C ARG* 3.4 16.8 - - + +
243C VAL* 3.3 32.8 + - - +
323C ILE* 3.6 22.5 - - + +
351C ALA 4.6 1.3 - - - +
352C ALA* 3.7 9.2 - - + -
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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