Contacts of the helix formed by residues 204 - 214 (chain B) in PDB entry 2PKG
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 GLU 204 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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167B ARG* 2.6 48.2 + - - +
168B GLN 5.1 0.2 + - - -
171B ARG* 2.7 35.4 + - - +
196B LEU* 5.4 0.2 - - + -
200B ASN* 2.7 33.1 + - - +
203B SER* 1.3 84.6 + - - +
205B ILE* 1.3 65.9 + - + +
207B PRO* 3.3 11.8 - - - +
208B MET* 3.2 29.7 + - + +
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Residues in contact with ILE 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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189B LEU* 4.5 13.9 - - + -
192B PHE* 4.1 13.7 - - + -
193B ALA* 4.1 24.2 - - + -
196B LEU* 3.4 34.5 - - + -
200B ASN 3.3 0.4 + - - -
201B VAL* 3.1 25.1 + - + +
204B GLU* 1.3 73.8 - - - +
206B ILE* 1.3 60.9 + - - +
208B MET* 2.8 23.2 + - + +
209B PHE* 2.6 33.9 + - + -
231B ILE* 3.6 28.7 - - + -
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Residues in contact with ILE 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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201B VAL* 3.1 14.5 + - + +
202B LYS* 3.4 11.4 - - - +
205B ILE* 1.3 76.2 - - - +
207B PRO* 1.3 60.2 - - + +
209B PHE* 3.4 14.1 - - + +
210B SER* 2.7 40.4 + - - -
231B ILE* 3.8 29.2 - - + -
235B LEU* 4.1 9.2 - - + -
243B LEU* 3.6 57.7 - - + +
244B VAL* 4.7 3.4 - - + -
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Residues in contact with PRO 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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202B LYS 3.7 5.2 - - - +
203B SER* 3.3 21.8 - - - +
204B GLU* 3.3 18.2 - - - +
206B ILE* 1.3 96.4 - - + +
208B MET* 1.3 61.3 + - + +
210B SER* 3.3 6.5 + - - -
211B ASN* 3.0 30.9 + - - +
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Residues in contact with MET 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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167B ARG* 4.8 13.7 - - + +
170B PHE* 3.7 30.5 - - + -
171B ARG* 3.9 28.5 - - + +
174B CYS* 3.8 21.0 - - + +
189B LEU* 4.2 8.5 - - + -
192B PHE* 4.8 4.9 - - + -
196B LEU* 5.5 0.4 - - + -
204B GLU* 3.2 27.4 - - + +
205B ILE* 2.8 32.0 + - + +
207B PRO* 1.3 70.7 - - + +
209B PHE* 1.3 67.7 + - - +
211B ASN* 3.3 6.8 + - - +
212B LEU* 3.0 28.7 + - - +
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Residues in contact with PHE 209 (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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189B LEU* 3.6 17.7 - - + +
205B ILE 2.6 20.1 + - - +
206B ILE* 3.4 19.5 - - + +
208B MET* 1.3 72.1 - - - +
210B SER* 1.3 64.8 + - - +
212B LEU* 3.0 5.2 + - - +
213B ALA* 2.9 19.2 + - - +
224B ALA* 3.6 33.2 - - + -
227B ALA* 4.6 1.1 - - + -
228B CYS* 3.7 31.4 - - + -
231B ILE* 3.5 31.6 - - + -
243B LEU 4.8 0.9 - - - -
244B VAL* 4.7 15.7 - - + -
247B THR* 3.4 38.4 - - + -
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Residues in contact with SER 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B ILE* 2.7 24.2 + - - -
207B PRO* 3.4 8.1 - - - -
209B PHE* 1.3 79.9 - - - +
211B ASN* 1.3 69.4 + - - +
213B ALA* 3.1 15.2 + - - +
214B SER* 3.1 16.7 + - - -
247B THR* 4.2 14.0 + - - -
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Residues in contact with ASN 211 (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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207B PRO 3.0 19.9 + - - +
208B MET* 3.3 6.6 + - - +
210B SER* 1.3 83.2 + - - +
212B LEU* 1.3 64.1 + - + +
214B SER* 3.4 8.9 + - - -
215B ASP* 3.2 19.9 + - - +
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Residues in contact with LEU 212 (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 CYS* 3.9 42.6 - - + +
182B ARG* 4.3 14.4 - - + +
186B ALA* 3.9 19.7 - - + -
189B LEU* 3.7 29.4 - - + -
208B MET 3.0 12.1 + - - +
209B PHE* 3.0 8.8 + - - +
211B ASN* 1.3 72.5 - - + +
213B ALA* 1.3 62.5 + - - +
214B SER 3.0 6.0 + - - -
215B ASP* 3.1 19.4 + - + +
220B VAL* 3.7 25.1 - - + +
221B ARG* 3.5 12.0 + - - -
224B ALA* 3.8 10.9 - - + +
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Residues in contact with ALA 213 (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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209B PHE* 2.9 12.5 + - + +
210B SER 3.1 9.1 + - - +
212B LEU* 1.3 75.5 - - - +
214B SER* 1.3 57.6 + - - +
215B ASP 3.6 0.2 - - - -
221B ARG* 3.1 20.8 - - - +
224B ALA* 3.2 22.8 - - + +
247B THR* 3.4 33.2 - - + -
250B GLN* 6.0 2.1 - - - +
251B ALA* 6.5 0.4 - - + -
254B ASP* 4.6 3.5 - - - +
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Residues in contact with SER 214 (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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210B SER* 3.1 15.8 + - - -
211B ASN* 3.5 9.2 + - - -
212B LEU 3.0 0.6 - - - -
213B ALA* 1.3 80.9 - - - +
215B ASP* 1.3 68.6 + - - +
216B GLU* 3.5 1.2 + - - -
221B ARG* 3.5 6.7 - - - +
250B GLN* 6.4 1.3 - - - -
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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