Contacts of the helix formed by residues 198 - 205 (chain B) in PDB entry 2B9R
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 198 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196B GLU* 2.9 23.2 + - + +
197B TRP* 1.3 72.3 - - - +
199B PRO* 1.3 64.3 - - + +
200B THR* 2.8 16.0 - - - -
201B LEU* 2.5 50.1 + - - +
202B GLN* 3.0 8.4 + - - +
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Residues in contact with PRO 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197B TRP 3.7 2.9 - - - +
198B THR* 1.3 87.8 - - + +
200B THR* 1.3 55.1 + - - +
202B GLN* 3.1 25.5 + - + +
203B HIS* 2.7 35.0 + - - +
209B GLU* 5.2 2.7 - - - +
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Residues in contact with THR 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148B ILE* 5.3 0.2 - - - +
149B GLY* 6.2 4.5 - - - -
198B THR* 3.9 14.4 - - - -
199B PRO* 1.3 79.7 - - - +
201B LEU* 1.3 65.5 + - + +
203B HIS* 3.5 5.2 + - - -
204B TYR* 3.3 39.7 + - + +
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Residues in contact with LEU 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145B ALA* 4.6 0.9 - - + +
148B ILE* 3.7 35.4 - - + +
149B GLY* 5.6 4.3 - - - +
185B PHE* 3.8 18.8 - - + -
189B LEU* 3.8 21.8 - - + -
197B TRP* 3.4 44.2 - - + -
198B THR* 2.5 36.7 + - - +
200B THR* 1.3 76.1 - - + +
202B GLN* 1.3 54.7 + - - +
204B TYR* 3.3 2.1 + - - +
205B LEU* 3.0 36.6 + - + +
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Residues in contact with GLN 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197B TRP* 3.6 9.4 - - - +
198B THR 3.0 5.8 + - - +
199B PRO* 3.1 36.6 + - + +
201B LEU* 1.3 76.3 - - - +
203B HIS* 1.3 59.0 + - - +
205B LEU 4.3 1.1 - - - +
206B SER* 2.8 34.4 + - - +
207B TYR 3.1 17.7 - - - +
208B THR* 3.4 11.1 - - - +
209B GLU* 2.4 61.8 + - - +
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Residues in contact with HIS 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199B PRO 2.7 19.4 + - - +
200B THR* 3.6 9.9 - - - +
202B GLN* 1.3 77.0 - - - +
204B TYR* 1.3 83.9 + + + +
205B LEU 3.4 0.5 + - - -
206B SER* 3.8 9.0 + - - -
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Residues in contact with TYR 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B TYR* 4.2 5.5 - - - -
144B ARG* 3.0 41.2 + - - +
148B ILE* 3.8 36.1 - - + -
200B THR* 3.3 32.3 + - + +
201B LEU 3.9 0.4 - - - +
203B HIS* 1.3 101.8 - + + +
205B LEU* 1.3 68.2 + - - +
206B SER 3.6 0.4 - - - -
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Residues in contact with LEU 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B TYR* 3.6 38.4 + - + +
141B PHE* 5.7 1.3 - - + +
144B ARG* 3.9 18.6 - - + +
145B ALA* 4.0 18.4 - - + -
148B ILE* 3.9 20.6 - - + -
182B ALA* 5.1 6.5 - - + -
197B TRP* 3.7 32.8 - - + -
201B LEU* 3.0 16.4 + - + +
202B GLN 3.8 0.7 - - - -
204B TYR* 1.3 89.7 - - - +
206B SER* 1.3 69.6 + - - +
207B TYR* 2.7 23.2 + - + -
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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