Contacts of the helix formed by residues 215 - 225 (chain B) in PDB entry 3REO
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 GLY 215 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212B GLY 3.2 3.9 + - - -
213B GLY 3.1 5.3 - - - -
214B THR* 1.3 78.1 - - - +
216B ALA* 1.3 66.2 + - - +
217B VAL 3.2 2.9 - - - -
218B ALA* 3.2 4.1 + - - +
219B SER* 2.9 24.6 + - - -
232B ASN* 3.5 28.7 - - - -
245B PHE* 3.6 9.3 - - - -
248B VAL* 5.2 0.4 - - - -
250B HIS* 4.1 3.4 - - - -
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Residues in contact with ALA 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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184B SER* 3.3 32.3 - - - +
187B SER* 5.8 0.7 - - - -
188B THR* 3.5 20.2 - - + +
212B GLY 4.4 1.4 + - - -
214B THR* 3.5 3.2 - - - +
215B GLY* 1.3 76.9 - - - +
217B VAL* 1.3 63.4 + - + +
219B SER* 2.7 23.1 + - - -
220B MET* 3.1 16.4 + - - +
245B PHE* 4.0 10.2 - - + -
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Residues in contact with VAL 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B SER* 3.7 26.2 - - - +
191B MET* 3.2 35.7 - - + -
209B ASP* 3.6 15.0 + - - +
212B GLY 4.9 2.7 + - - +
215B GLY* 3.2 0.8 - - - -
216B ALA* 1.3 77.7 - - - +
218B ALA* 1.3 65.8 + - - +
220B MET* 3.1 7.1 + - - +
221B ILE* 3.1 34.6 + - + +
266B PHE* 3.5 26.0 - - + -
268B LYS* 4.5 7.6 - - + -
370B SAH 5.2 4.0 - - - +
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Residues in contact with ALA 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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207B ILE* 6.1 1.6 - - + -
209B ASP* 4.1 16.3 + - + -
215B GLY* 3.2 9.8 + - - +
217B VAL* 1.3 79.1 - - - +
219B SER* 1.3 63.2 + - - +
221B ILE* 3.2 10.5 + - - +
222B VAL* 3.0 26.9 + - - +
230B ALA* 4.4 11.0 - - + -
231B ILE 4.8 1.6 - - - +
232B ASN* 4.4 14.1 - - + -
248B VAL* 4.0 24.2 - - + -
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Residues in contact with SER 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B GLY 2.9 9.2 + - - -
216B ALA* 2.7 23.6 + - - +
218B ALA* 1.3 77.7 - - - +
220B MET* 1.3 58.8 + - - +
222B VAL* 3.7 2.7 + - - +
223B ALA* 3.0 27.7 + - - +
245B PHE* 3.5 44.9 - - - -
246B SER 5.3 1.9 - - - +
248B VAL* 3.7 8.9 - - - +
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Residues in contact with MET 220 (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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188B THR* 3.7 42.2 - - + +
191B MET* 4.0 12.3 - - + +
192B LYS* 3.6 39.7 - - + +
195B LEU* 3.9 16.2 - - + +
216B ALA* 3.1 18.1 + - + +
217B VAL* 3.1 7.5 + - - +
219B SER* 1.3 79.0 + - - +
221B ILE* 1.3 63.5 + - - +
223B ALA* 3.5 6.6 + - - +
224B LYS* 3.1 23.0 + - - +
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Residues in contact with ILE 221 (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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191B MET* 4.5 3.1 - - + -
195B LEU* 4.5 8.3 - - + -
201B PHE* 3.6 54.7 - - + -
207B ILE* 4.2 22.0 - - + -
209B ASP* 6.0 0.9 - - + -
217B VAL* 3.1 32.8 + - + +
218B ALA* 3.6 9.4 - - - +
220B MET* 1.3 73.8 - - - +
222B VAL* 1.3 59.2 + - - +
224B LYS* 3.1 3.9 + - - -
225B TYR* 2.9 32.9 + - + +
228B ILE* 4.0 27.6 - - + -
266B PHE* 4.8 2.5 - - + -
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Residues in contact with VAL 222 (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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218B ALA 3.0 12.0 + - - +
219B SER* 3.9 4.7 - - - +
221B ILE* 1.3 72.2 - - - +
223B ALA* 1.3 65.7 + - - +
225B TYR 3.0 6.9 - - - +
226B PRO* 3.0 46.1 - - + +
228B ILE* 3.7 11.9 - - + +
230B ALA* 3.2 35.0 - - + -
246B SER 3.7 21.3 - - - +
247B GLY* 3.7 18.8 - - - +
248B VAL* 4.1 3.8 - - + -
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Residues in contact with ALA 223 (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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219B SER 3.0 19.7 + - - +
220B MET* 3.7 8.5 - - - +
221B ILE 3.3 0.4 - - - -
222B VAL* 1.3 75.8 - - - +
224B LYS* 1.3 61.8 + - - +
226B PRO* 3.9 11.1 - - - +
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Residues in contact with LYS 224 (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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195B LEU* 2.7 46.5 + - + +
196B GLU* 4.4 7.5 + - - +
198B TYR 5.3 0.4 - - - -
199B ASN* 5.9 1.6 - - - -
202B GLU* 4.9 3.4 - - - -
220B MET 3.1 12.7 + - - +
221B ILE 3.1 8.5 + - - +
223B ALA* 1.3 77.7 - - - +
225B TYR* 1.3 101.0 + - + +
226B PRO* 3.7 6.5 - - - +
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Residues in contact with TYR 225 (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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195B LEU* 4.7 2.2 - - + -
198B TYR 4.3 11.4 + - - -
199B ASN* 4.4 1.9 + - - -
201B PHE* 3.8 30.9 - + + +
202B GLU* 3.1 60.7 + - + +
203B GLY 5.3 0.9 - - - -
221B ILE* 2.9 20.3 + - + +
222B VAL 3.0 3.3 - - - +
224B LYS* 1.3 115.2 - - + +
226B PRO* 1.3 68.7 - - - +
227B SER 3.1 3.4 - - - +
228B ILE* 2.9 35.4 + - + +
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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