Contacts of the helix formed by residues 210 - 218 (chain B) in PDB entry 3GG0
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 ASP 210 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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206B ILE* 3.9 10.5 - - + -
207B ALA* 3.0 20.2 + - + +
209B GLU* 1.3 108.6 - - - +
211B ARG* 1.3 56.8 + - - +
212B TYR 3.5 2.0 - - - -
213B ARG* 2.7 40.3 + - - +
214B PHE* 3.0 29.7 + - + +
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Residues in contact with ARG 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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203B PHE* 2.6 55.3 + - + +
204B ALA* 3.6 18.4 + - - +
206B ILE* 3.0 23.8 + - + +
207B ALA 3.1 6.4 + - - +
208B ALA* 3.5 40.0 + - - +
209B GLU 3.6 0.2 - - - -
210B ASP* 1.3 75.5 - - - +
212B TYR* 1.3 65.6 + - + +
214B PHE* 3.3 2.0 + - - +
215B ASP* 2.8 30.9 + - - +
241B LEU* 6.2 2.7 - - + -
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Residues in contact with TYR 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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208B ALA 5.1 0.6 + - - -
209B GLU 5.4 1.5 + - - +
210B ASP 3.5 0.6 - - - -
211B ARG* 1.3 79.4 - - + +
213B ARG* 1.3 63.2 + - - +
215B ASP* 3.2 3.8 + - - +
216B LEU* 3.2 19.6 + - - +
241B LEU* 4.1 22.7 - - + -
243B GLY* 3.7 21.8 + - - +
244B SER* 3.5 38.0 - - - +
247B HIS* 3.4 38.7 + + + -
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Residues in contact with ARG 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 GLU 5.9 0.4 - - - +
210B ASP* 2.7 45.9 + - - +
211B ARG 3.3 0.2 - - - -
212B TYR* 1.3 77.7 - - - +
214B PHE* 1.3 57.8 + - - +
216B LEU* 3.3 5.7 + - - +
217B GLU* 2.9 60.4 + - + +
248B HIS* 5.1 16.6 - - + -
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Residues in contact with PHE 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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168B PRO* 4.4 17.7 - - + -
169B CYS* 4.1 16.6 - - + -
191B ILE* 4.0 12.1 - - + -
202B MET* 3.6 46.0 - - + -
203B PHE* 4.4 12.6 - + - -
206B ILE* 3.7 36.1 - - + -
210B ASP* 3.0 19.2 + - + +
211B ARG 3.6 4.0 - - - +
212B TYR 3.3 0.2 - - - -
213B ARG* 1.3 77.6 - - - +
215B ASP* 1.3 57.7 + - - +
217B GLU* 4.7 5.8 - - + -
218B SER* 2.8 38.0 + - - -
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Residues in contact with ASP 215 (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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203B PHE* 3.4 17.5 - - + -
211B ARG 2.8 16.7 + - - +
212B TYR 3.2 1.3 + - - +
214B PHE* 1.3 76.2 - - - +
216B LEU* 1.3 58.4 + - - +
218B SER* 2.7 19.6 + - - -
219B LYS* 2.8 43.3 + - - +
240B LEU* 3.6 6.4 - - - +
241B LEU* 3.1 22.6 + - + +
244B SER* 2.7 28.9 + - - +
501B C2E 2.8 25.6 + - - -
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Residues in contact with LEU 216 (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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212B TYR 3.2 10.3 + - - +
213B ARG* 3.8 7.0 - - - +
215B ASP* 1.3 80.7 - - - +
217B GLU* 1.3 61.9 + - + +
219B LYS* 3.3 17.2 + - - +
240B LEU* 4.0 12.8 - - + -
244B SER 4.1 11.4 - - - +
245B LEU* 4.2 6.3 - - + -
248B HIS* 3.5 41.1 - - + +
251B ALA* 3.9 22.4 - - + -
254B TRP* 3.3 30.5 - - + -
255B LEU* 3.8 35.0 - - + -
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Residues in contact with GLU 217 (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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213B ARG* 2.9 52.8 + - + +
214B PHE* 4.2 5.2 + - + +
216B LEU* 1.3 77.0 - - + +
218B SER* 1.3 62.9 + - - +
219B LYS 3.1 2.6 + - - -
220B ALA* 3.6 16.6 + - - +
221B TYR* 4.1 8.7 - - - -
248B HIS* 4.8 7.3 + - - +
254B TRP* 3.6 33.1 + - + -
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Residues in contact with SER 218 (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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169B CYS* 3.6 25.6 - - - -
171B PHE* 3.1 18.4 - - - -
191B ILE* 3.8 16.9 - - - +
214B PHE* 2.8 20.5 + - - -
215B ASP* 2.7 26.2 + - - -
217B GLU* 1.3 77.5 - - - +
219B LYS* 1.3 67.9 + - - +
220B ALA 3.1 1.3 - - - -
221B TYR* 3.0 23.7 + - - +
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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