Contacts of the helix formed by residues 202 - 211 (chain H) in PDB entry 2R9R
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 PHE 202 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203H HIS* 1.3 87.5 + + + +
204H THR* 3.3 5.5 + - - +
205H TYR* 3.5 20.0 + + - +
206H SER* 3.2 26.6 + - - -
273H THR* 5.6 0.7 - - - -
276H ASN 4.3 5.2 - - - -
277H LYS* 3.9 50.7 - - + -
278H SER* 3.5 16.4 - - - -
279H VAL* 3.6 36.4 - - + +
282H PHE* 3.7 24.0 - + + -
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Residues in contact with HIS 203 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202H PHE* 1.3 99.4 - + + +
204H THR* 1.3 60.6 + - - +
206H SER* 3.5 6.9 + - - -
207H GLN* 3.2 29.0 + - - +
213H GLN* 5.9 4.8 - - + +
277H LYS* 5.5 8.6 + - - -
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Residues in contact with THR 204 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202H PHE 3.3 3.0 + - - +
203H HIS* 1.3 78.1 - - - +
205H TYR* 1.3 60.9 + - - +
207H GLN* 3.8 14.1 + - - +
208H SER* 2.9 43.1 + - - +
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Residues in contact with TYR 205 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202H PHE* 3.5 23.6 + + - +
203H HIS 3.4 0.2 - - - -
204H THR* 1.3 80.4 - - - +
206H SER* 1.3 58.0 + - - +
208H SER* 4.1 4.6 - - - -
209H THR* 2.8 26.9 + - - -
279H VAL* 4.8 11.9 - - + -
282H PHE* 3.8 27.4 - + - -
283H GLN* 3.9 31.9 - - + +
286H ARG* 3.0 42.4 + - - -
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Residues in contact with SER 206 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202H PHE* 3.2 21.8 + - - -
203H HIS* 3.5 11.4 + - - -
205H TYR* 1.3 75.3 - - - +
207H GLN* 1.3 63.1 + - - +
208H SER 3.2 0.2 - - - -
210H ILE* 2.9 42.3 + - - +
273H THR* 5.4 1.3 - - - -
282H PHE* 3.5 34.8 - - - -
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Residues in contact with GLN 207 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191H GLU 5.6 1.7 - - - +
203H HIS 3.2 16.4 + - - +
204H THR* 3.8 16.6 + - - +
205H TYR 3.4 0.2 - - - -
206H SER* 1.3 82.9 + - - +
208H SER* 1.3 59.6 + - - +
211H GLY* 2.9 30.1 + - - +
212H TYR* 3.6 22.9 - - - +
213H GLN* 3.7 21.2 + - + +
220H ASP* 3.4 21.6 + - - -
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Residues in contact with SER 208 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189H ARG* 5.4 7.6 + - - +
204H THR* 2.9 28.7 + - - +
205H TYR* 4.1 6.3 - - - -
206H SER 3.2 0.2 - - - -
207H GLN* 1.3 80.1 + - - +
209H THR* 1.3 57.5 + - - +
286H ARG* 6.0 0.7 - - - -
293H ARG* 3.1 20.1 + - - -
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Residues in contact with THR 209 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205H TYR 2.8 21.4 + - - -
206H SER 3.4 4.6 + - - -
207H GLN 3.3 0.4 - - - -
208H SER* 1.3 79.0 - - - +
210H ILE* 1.3 59.6 + - - +
282H PHE* 3.8 8.7 - - + -
286H ARG* 3.0 40.2 + - + +
289H VAL* 3.9 19.2 - - + +
290H GLN* 3.6 32.6 - - + +
293H ARG* 3.2 26.9 + - - +
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Residues in contact with ILE 210 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206H SER* 2.9 23.3 + - - +
209H THR* 1.3 75.1 - - - +
211H GLY* 1.3 58.6 + - - +
212H TYR* 3.5 42.4 - - + +
214H GLN* 3.7 11.2 - - + +
269H THR* 3.6 17.9 - - + +
273H THR* 3.4 32.8 - - + -
282H PHE* 4.5 4.5 - - + -
289H VAL* 3.7 22.2 - - + -
293H ARG* 3.2 23.3 + - - +
296H ARG* 3.6 9.2 + - - -
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Residues in contact with GLY 211 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183H GLU* 3.2 35.9 - - - +
207H GLN* 2.9 16.4 + - - +
208H SER 4.8 0.4 - - - -
209H THR 3.5 1.4 - - - -
210H ILE* 1.3 78.2 - - - +
212H TYR* 1.3 61.4 + - - +
222H PHE* 4.5 6.1 - - - +
293H ARG* 3.4 17.9 - - - -
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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