Contacts of the helix formed by residues 200 - 211 (chain B) in PDB entry 1OIZ
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 PRO 200 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160B LEU* 4.1 9.0 - - + -
163B TRP* 3.7 28.7 - - + -
198B ASN 3.9 3.1 - - - +
199B GLU* 1.3 93.4 - - + +
201B VAL* 1.3 64.1 + - - +
202B ILE* 3.1 20.0 - - + +
203B PHE* 3.0 38.2 + - + +
204B HIS* 4.2 0.5 + - - -
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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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199B GLU 3.6 2.1 + - - -
200B PRO* 1.3 70.8 - - - +
202B ILE* 1.3 60.4 - - + +
203B PHE 3.2 0.2 - - - -
204B HIS* 3.1 35.8 + - + +
205B ALA* 3.2 11.8 + - - +
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Residues in contact with ILE 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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1276A TRT 5.6 4.3 - - + -
163B TRP* 6.3 0.2 - - - +
200B PRO* 3.1 19.4 + - + -
201B VAL* 1.3 78.8 - - + +
203B PHE* 1.3 73.0 + - + +
205B ALA* 3.8 11.0 - - + +
206B VAL* 3.0 31.6 + - + +
1275B TRT 3.7 44.9 - - - +
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Residues in contact with PHE 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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160B LEU* 3.6 18.4 - - + -
163B TRP* 4.2 24.7 - + - -
196B LEU* 3.5 28.5 - - + -
199B GLU* 3.9 14.4 - - + -
200B PRO* 3.0 45.5 + - + +
202B ILE* 1.3 80.2 - - + +
204B HIS* 1.3 57.5 + - - +
207B PHE* 2.9 33.1 + - - +
224B MET* 3.6 8.0 - - + +
1275B TRT 3.7 57.3 - + + -
1276B TRT 5.0 5.2 - - - -
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Residues in contact with HIS 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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199B GLU* 2.5 43.9 + - + +
200B PRO 4.3 4.0 - - - -
201B VAL* 3.1 24.1 + - + +
203B PHE* 1.3 74.8 - - + +
205B ALA* 1.3 59.2 + - - +
207B PHE* 4.0 1.8 - - - +
208B SER* 3.0 31.9 + - - -
224B MET* 3.7 25.2 - - + +
225B HIS 4.6 0.7 - - - -
226B GLY* 4.1 17.6 - - - -
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Residues in contact with ALA 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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1276A TRT 4.2 5.1 - - + +
201B VAL 3.2 9.7 + - - +
202B ILE* 3.9 17.3 - - + +
203B PHE 3.4 0.2 - - - -
204B HIS* 1.3 79.3 - - - +
206B VAL* 1.3 62.3 + - + +
208B SER* 2.8 22.4 + - - -
209B MET* 3.5 11.8 + - - +
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Residues in contact with VAL 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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1276A TRT 3.3 46.7 - - + -
202B ILE* 3.0 30.5 + - + +
203B PHE 3.9 0.2 - - - +
205B ALA* 1.3 73.4 - - + +
207B PHE* 1.3 66.6 + - - +
209B MET* 3.1 6.2 + - - +
210B ILE* 3.0 30.9 + - + +
1275B TRT 3.5 42.4 - - + +
1276B TRT 3.9 13.0 - - + -
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Residues in contact with PHE 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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203B PHE 2.9 19.7 + - - +
204B HIS 4.1 2.7 - - - +
206B VAL* 1.3 76.8 - - - +
208B SER* 1.3 58.5 + - - +
210B ILE* 3.9 6.1 - - + -
211B LYS* 2.9 67.9 + - + +
214B LEU* 3.7 25.1 - - + -
219B LYS 4.1 5.8 - - - -
222B ILE* 3.7 42.8 - - + -
224B MET* 3.7 28.5 - - + -
1275B TRT 3.9 18.4 - + + -
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Residues in contact with SER 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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173A PRO* 3.6 41.6 - - - +
204B HIS 3.0 17.3 + - - -
205B ALA* 2.8 19.3 + - - -
207B PHE* 1.3 80.0 - - - +
209B MET* 1.3 59.2 + - - +
211B LYS* 4.7 2.3 - - - +
212B PRO* 4.5 7.8 - - - +
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Residues in contact with MET 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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171A ILE* 3.1 31.2 - - + +
172A THR 4.2 1.3 - - - +
173A PRO* 3.6 35.0 - - - -
176A ALA* 3.8 7.3 - - + +
1276A TRT 3.3 77.1 - - + +
205B ALA 3.7 12.1 - - - +
206B VAL 3.1 7.4 + - - +
208B SER* 1.3 81.1 - - - +
210B ILE* 1.3 61.4 + - - +
211B LYS 3.6 0.2 - - - -
212B PRO* 3.6 8.7 - - - +
213B PHE* 3.6 16.1 - - - -
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Residues in contact with ILE 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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210A ILE* 4.2 35.0 - - + -
214A LEU* 6.1 0.4 - - + -
1274A TRT 5.5 0.9 - - + -
1276A TRT 3.8 33.0 - - + -
206B VAL* 3.0 27.5 + - + +
207B PHE* 3.9 7.6 - - + -
209B MET* 1.3 75.9 - - - +
211B LYS* 1.3 69.4 + - - +
212B PRO* 3.2 4.3 - - - -
213B PHE* 2.9 24.8 + - + +
214B LEU* 3.6 29.5 - - + +
1275B TRT 3.9 35.2 - - + -
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Residues in contact with LYS 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 PHE* 2.9 50.0 + - + +
208B SER* 5.2 1.8 - - - +
210B ILE* 1.3 76.9 - - - +
212B PRO* 1.3 70.2 - - + +
213B PHE 3.0 1.9 + - - -
214B LEU* 3.1 22.7 + - + +
219B LYS* 3.4 38.6 - - + +
220B GLU* 2.8 35.5 + - - +
222B ILE 6.0 0.2 - - - -
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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