Contacts of the helix formed by residues 206 - 216 (chain B) in PDB entry 5ITZ
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 206 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171B VAL* 4.4 8.1 - - - +
172B MET 3.2 23.2 + - - +
174B SER* 3.9 13.0 - - - +
177B VAL* 3.7 18.8 - - + +
204B ILE 3.4 2.4 + - - -
205B ASP* 1.3 70.3 - - - +
207B GLU* 1.3 56.0 + - - +
209B LEU* 3.4 13.7 - - - +
210B TYR* 2.9 31.7 + - - +
227B LEU* 4.2 2.6 - - - +
501B GDP 2.9 69.2 + - - -
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Residues in contact with GLU 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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174B SER* 2.8 32.4 + - - +
175B PRO* 4.8 3.8 - - - +
176B LYS* 3.1 35.1 + - - +
205B ASP* 3.0 14.3 + - - +
206B ASN* 1.3 79.2 - - - +
208B ALA* 1.3 61.4 + - - +
210B TYR* 3.5 4.0 + - - +
211B ASP* 3.0 34.3 + - - +
304B ALA* 3.5 18.6 - - + -
390B ARG* 3.5 29.0 + - - +
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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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205B ASP 2.8 13.8 + - - +
207B GLU* 1.3 73.0 - - - +
209B LEU* 1.3 57.8 + - - +
211B ASP* 3.2 6.9 + - - +
212B ILE* 2.8 38.3 + - + +
301B MET 3.6 12.3 - - - +
302B MET 3.6 26.7 - - - -
303B ALA 3.7 0.4 - - - -
304B ALA* 3.6 23.8 - - - +
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Residues in contact with LEU 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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204B ILE* 3.9 17.0 - - + -
205B ASP 2.9 17.9 + - - +
206B ASN* 3.4 26.9 - - - +
208B ALA* 1.3 76.5 - - - +
210B TYR* 1.3 62.2 + - - +
212B ILE* 3.5 1.8 + - - +
213B CYS* 3.1 29.5 + - - -
227B LEU* 3.7 27.4 - - + +
230B LEU* 3.9 17.4 - - + +
231B VAL* 3.5 27.1 - - + -
302B MET* 3.8 33.4 - - + -
501B GDP 3.9 2.2 - - - +
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Residues in contact with TYR 210 (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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176B LYS* 3.8 52.0 - - + -
177B VAL* 3.8 16.6 - - + -
206B ASN 2.9 17.8 + - - +
207B GLU 3.8 3.1 - - - +
209B LEU* 1.3 73.2 - - - +
211B ASP* 1.3 63.0 + - - +
213B CYS* 3.3 1.8 + - - +
214B PHE* 2.7 76.4 + + + +
220B THR 4.9 1.7 + - - -
222B PRO* 3.6 30.3 - - + +
227B LEU* 3.8 8.7 - - + +
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Residues in contact with ASP 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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176B LYS* 2.9 32.5 + - - +
207B GLU* 3.0 29.9 + - - +
208B ALA* 3.2 7.3 + - - +
210B TYR* 1.3 78.3 - - - +
212B ILE* 1.3 61.2 + - + +
214B PHE* 4.6 2.3 - - - +
215B ARG* 2.7 70.1 + - - +
216B THR* 4.9 0.2 + - - -
304B ALA* 4.9 2.8 - - - +
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Residues in contact with ILE 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* 2.8 21.9 + - + +
209B LEU 3.8 3.6 - - - +
211B ASP* 1.3 76.6 - - + +
213B CYS* 1.3 59.9 + - - +
216B THR* 2.8 36.7 + - - -
217B LEU* 2.9 13.7 + - + -
230B LEU* 3.6 19.7 - - + -
275B LEU* 4.1 24.2 - - + -
299B LYS* 3.4 22.0 - - - +
300B ASN 4.6 0.2 - - - -
301B MET 3.5 23.3 - - - +
302B MET* 4.0 28.5 - - + -
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Residues in contact with CYS 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 LEU 3.1 20.4 + - - +
210B TYR 3.7 2.2 - - - +
212B ILE* 1.3 79.4 - - - +
214B PHE* 1.3 61.6 + - - +
217B LEU* 3.3 20.6 + - - +
218B LYS 3.2 8.7 + - - -
219B LEU* 3.0 28.5 + - + +
222B PRO* 3.8 16.6 - - + -
226B ASP* 3.8 29.8 - - - -
227B LEU* 3.7 15.9 - - - -
230B LEU* 3.9 11.9 - - - -
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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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210B TYR* 2.7 55.9 + + + +
211B ASP* 4.1 2.2 - - - +
213B CYS* 1.3 76.6 - - - +
215B ARG* 1.3 80.0 + - + +
218B LYS* 3.7 13.5 - - - +
219B LEU 3.4 21.7 + - - +
220B THR* 3.8 22.7 - - + -
222B PRO* 4.4 2.7 - - + +
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Residues in contact with ARG 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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176B LYS* 3.7 12.7 - - - +
211B ASP* 2.7 56.5 + - - +
214B PHE* 1.3 92.2 - - + +
216B THR* 1.3 66.3 + - - +
218B LYS* 3.8 10.7 + - - +
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Residues in contact with THR 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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211B ASP 3.7 0.2 + - - -
212B ILE* 2.8 29.8 + - - -
215B ARG* 1.3 78.1 - - - +
217B LEU* 1.3 68.7 + - + +
218B LYS* 3.6 2.4 + - - +
275B LEU* 4.1 22.9 - - + -
299B LYS* 4.4 23.6 + - + +
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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