Contacts of the helix formed by residues 197 - 208 (chain B) in PDB entry 2PWY
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 ASN 197 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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195B LEU 4.3 0.3 - - - +
196B PRO* 1.3 91.6 - - - +
198B ILE* 1.3 65.6 + - - +
199B THR* 3.5 18.8 - - - +
200B GLN* 3.0 42.7 + - + +
201B VAL* 3.2 13.0 + - - +
245B PHE* 4.0 2.9 - - - -
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Residues in contact with ILE 198 (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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226A TRP* 4.0 33.2 - - + -
228A VAL* 6.1 0.9 - - + -
197B ASN* 1.3 72.5 - - - +
199B THR* 1.3 65.8 + - + +
201B VAL* 3.2 23.7 + - + +
202B LEU* 2.9 50.7 + - + +
218B VAL* 4.8 1.6 - - + -
245B PHE* 3.6 38.5 - - + -
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Residues in contact with THR 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 ASN* 3.5 16.1 - - - +
198B ILE* 1.3 82.5 - - + +
200B GLN* 1.3 59.1 + - - +
202B LEU* 3.4 12.1 + - + +
203B GLU* 3.0 30.5 + - - +
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Residues in contact with GLN 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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171B LEU 5.2 0.2 - - - -
172B MET* 3.0 36.4 + - - +
175B TRP* 3.6 19.9 - - + -
195B LEU* 3.7 27.5 - - + +
196B PRO* 3.3 15.0 - - - +
197B ASN* 3.0 50.9 + - + +
199B THR* 1.3 76.3 - - - +
201B VAL* 1.3 61.3 + - - +
203B GLU* 3.3 0.6 + - - -
204B LEU* 2.8 31.4 + - - +
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Residues in contact with VAL 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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228A VAL* 5.4 2.2 - - + -
195B LEU* 3.9 14.4 - - + -
197B ASN 3.2 10.7 + - - +
198B ILE* 3.2 18.3 + - + +
200B GLN* 1.3 77.2 - - - +
202B LEU* 1.3 62.3 + - + +
204B LEU* 3.2 1.9 + - - +
205B VAL* 3.0 36.1 + - + +
218B VAL* 3.9 26.2 - - + -
245B PHE* 3.6 35.0 - - + -
247B VAL* 3.8 24.0 - - + +
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Residues in contact with LEU 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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228A VAL* 4.5 8.3 - - + -
230A LEU* 3.6 33.3 - - + +
233A ALA* 3.9 21.3 - - + -
198B ILE* 2.9 40.7 + - + +
199B THR* 3.8 11.2 - - + +
200B GLN 3.3 0.2 - - - -
201B VAL* 1.3 78.2 - - + +
203B GLU* 1.3 56.1 + - - +
205B VAL* 3.7 5.3 - - - +
206B ARG* 3.0 29.6 + - - +
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Residues in contact with GLU 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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175B TRP* 3.4 50.8 + - + -
199B THR 3.0 18.3 + - - +
200B GLN* 3.7 4.7 - - - +
202B LEU* 1.3 76.5 - - - +
204B LEU* 1.3 57.6 + - - +
206B ARG* 3.4 6.3 + - + +
207B ALA* 2.9 29.0 + - + +
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Residues in contact with LEU 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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174B PRO* 4.0 7.9 - - + -
175B TRP* 3.8 25.0 - - + +
178B LEU* 4.0 32.5 - - + -
191B LEU* 5.0 1.8 - - + -
193B ALA* 3.7 29.6 - - + -
195B LEU* 3.9 14.8 - - + -
200B GLN 2.8 20.5 + - - +
201B VAL 3.6 4.5 - - - +
203B GLU* 1.3 71.8 - - - +
205B VAL* 1.3 57.6 + - - +
207B ALA* 3.3 2.2 + - - +
208B ALA* 2.8 32.2 + - - +
247B VAL* 4.1 19.5 - - + -
249B LEU* 4.4 13.7 - - + -
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Residues in contact with VAL 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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228A VAL* 4.2 12.1 - - + +
230A LEU* 4.0 23.3 - - + +
201B VAL* 3.0 31.1 + - + +
202B LEU* 3.7 6.3 - - - +
203B GLU 3.3 0.2 - - - -
204B LEU* 1.3 75.1 - - - +
206B ARG* 1.3 62.0 + - - +
208B ALA* 3.4 14.9 + - - +
209B GLU* 3.5 15.2 + - + +
215B LEU* 3.8 43.5 - - + -
218B VAL* 4.7 0.9 - - + -
247B VAL* 4.6 7.2 - - + -
249B LEU* 5.7 1.8 - - - -
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Residues in contact with ARG 206 (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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230A LEU* 4.2 11.9 - - + -
202B LEU 3.0 16.5 + - - +
203B GLU* 3.8 6.1 - - + +
205B VAL* 1.3 75.5 - - - +
207B ALA* 1.3 63.1 + - - +
209B GLU* 3.1 38.0 + - - +
210B ALA* 4.4 0.5 + - - +
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Residues in contact with ALA 207 (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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175B TRP* 3.5 29.6 - - + +
178B LEU* 3.8 8.1 - - + -
203B GLU* 2.9 19.2 + - + +
204B LEU 3.7 2.9 - - - +
206B ARG* 1.3 76.2 - - - +
208B ALA* 1.3 57.3 + - - +
209B GLU 3.1 0.2 - - - -
210B ALA* 3.1 21.9 + - - +
211B HIS* 3.3 14.5 + - + +
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Residues in contact with ALA 208 (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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178B LEU* 3.8 11.8 - - + +
204B LEU 2.8 17.5 + - - +
205B VAL* 3.6 7.9 - - - +
206B ARG 3.2 0.4 - - - -
207B ALA* 1.3 73.0 - - - +
209B GLU* 1.3 63.2 + - - +
210B ALA 3.1 0.4 - - - -
211B HIS* 3.1 25.3 + - - +
213B PHE* 4.2 14.3 + - + +
249B LEU* 4.1 35.2 - - + -
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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