Contacts of the helix formed by residues 205 - 218 (chain B) in PDB entry 1OH7
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 205 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201B LEU 4.2 0.6 + - - -
202B TRP* 3.3 21.7 + - + +
203B GLU 3.5 1.9 - - - +
204B PHE* 1.3 76.1 - - - +
206B ILE* 1.3 86.6 + - - +
207B ASP* 2.9 36.4 + - - +
208B THR* 3.4 17.3 + - - +
209B ALA* 3.0 22.7 + - - +
235B CYS* 4.1 0.2 - - - -
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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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204B PHE 3.4 3.4 + - - -
205B GLU* 1.3 86.3 + - - +
207B ASP* 1.3 72.5 + - - +
209B ALA* 3.2 2.0 + - - +
210B ARG* 3.0 51.9 + - - +
231B PRO* 3.3 48.0 - - + +
234B LEU* 3.8 14.4 - - + -
235B CYS* 3.7 13.8 - - - +
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Residues in contact with ASP 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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205B GLU* 2.9 20.6 + - - +
206B ILE* 1.3 85.4 - - - +
208B THR* 1.3 64.1 + - - +
210B ARG* 4.2 13.8 + - - +
211B GLN* 3.3 25.9 + - - +
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Residues in contact with THR 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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202B TRP* 4.9 10.0 + - + +
203B GLU 6.1 1.3 - - - +
205B GLU* 3.4 23.9 + - - +
207B ASP* 1.3 75.9 - - - +
209B ALA* 1.3 57.2 + - - +
211B GLN* 3.3 10.3 + - - +
212B GLN* 2.9 46.3 + - - +
242B GLN* 5.2 13.7 - - + +
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Residues in contact with ALA 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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203B GLU 6.0 0.7 - - - +
204B PHE 5.6 0.7 - - - -
205B GLU 3.0 14.8 + - - +
206B ILE* 3.4 12.8 - - - +
207B ASP 3.2 0.4 - - - -
208B THR* 1.3 75.1 - - - +
210B ARG* 1.3 67.2 + - - +
211B GLN 3.2 0.2 + - - -
212B GLN* 3.2 3.5 + - - +
213B LEU* 3.0 31.1 + - - +
234B LEU* 3.6 31.0 - - + +
235B CYS* 4.2 4.0 - - - -
238B GLY* 4.0 17.0 - - - -
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Residues in contact with ARG 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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206B ILE* 3.0 43.3 + - + +
207B ASP* 4.2 13.9 + - - +
209B ALA* 1.3 75.6 - - - +
211B GLN* 1.3 56.2 + - - +
213B LEU* 4.0 5.2 - - - +
214B ASN* 2.6 46.7 + - - +
222B LEU* 4.7 7.6 - - + -
228B GLU* 2.8 49.8 + - - +
231B PRO* 4.3 11.7 - - - +
234B LEU* 3.6 22.7 - - + +
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Residues in contact with GLN 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 ASP 3.3 16.9 + - - +
208B THR* 3.9 8.4 - - - +
209B ALA 3.1 0.8 - - - -
210B ARG* 1.3 76.8 - - - +
212B GLN* 1.3 83.4 + - - +
214B ASN* 4.2 4.3 - - - +
215B LEU* 3.1 28.9 + - + +
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Residues in contact with GLN 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B THR* 2.9 39.6 + - - +
209B ALA* 3.7 4.9 - - - +
211B GLN* 1.3 90.1 + - - +
213B LEU* 1.3 53.0 + - + +
215B LEU* 3.1 18.2 + - - +
216B GLN* 2.7 34.0 + - - +
238B GLY* 5.2 6.3 - - - +
241B LEU* 4.3 14.5 - - + +
242B GLN* 4.9 19.8 - - + +
245B LYS* 4.5 23.2 + - - +
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Residues in contact with LEU 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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155B PHE* 3.8 22.9 - - + -
209B ALA 3.0 21.5 + - - +
210B ARG 4.0 2.7 - - - +
212B GLN* 1.3 77.2 - - - +
214B ASN* 1.3 56.7 + - - +
216B GLN* 3.2 2.6 + - - +
217B PHE* 3.0 50.8 + - + -
222B LEU* 4.3 8.5 - - + -
234B LEU* 3.3 46.7 - - + +
237B ALA* 3.9 17.3 - - + +
238B GLY* 4.6 2.7 - - - +
241B LEU* 3.6 24.2 - - + -
258B ILE* 4.9 4.9 - - + -
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Residues in contact with ASN 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 ARG* 2.6 35.2 + - - +
211B GLN* 4.2 5.1 - - - +
213B LEU* 1.3 72.4 - - - +
215B LEU* 1.3 60.7 + - - +
217B PHE 3.4 0.5 + - - -
218B GLY* 2.9 26.9 + - - -
219B THR* 2.7 46.2 + - - +
220B ARG 3.3 18.8 + - - +
221B ASP* 3.2 21.3 + - - +
222B LEU* 3.3 14.9 - - - +
228B GLU* 5.0 1.4 + - - -
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Residues in contact with LEU 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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211B GLN* 3.1 22.5 + - + +
212B GLN* 3.1 21.0 + - - +
214B ASN* 1.3 80.4 - - - +
216B GLN* 1.3 63.2 + - - +
217B PHE 3.4 0.5 + - - -
218B GLY* 3.5 7.3 + - - -
245B LYS* 5.3 9.0 - - - +
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Residues in contact with GLN 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 GLN 2.7 16.0 + - - +
213B LEU 3.2 8.0 + - - +
215B LEU* 1.3 74.6 - - - +
217B PHE* 1.3 70.6 + - + +
218B GLY 3.8 0.3 + - - -
241B LEU* 3.7 31.3 - - + +
245B LYS* 3.7 24.9 + - - +
251B THR* 5.8 1.7 - - - +
252B LEU* 2.9 32.9 + - - +
253B PRO* 4.7 3.2 - - - +
255B ILE* 2.8 32.9 + - + +
256B ARG* 5.4 0.3 - - - -
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Residues in contact with PHE 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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155B PHE* 3.8 20.4 - + - -
213B LEU* 3.0 37.9 + - + +
214B ASN 4.4 0.9 - - - +
216B GLN* 1.3 83.8 - - + +
218B GLY* 1.3 62.3 + - - +
219B THR* 3.3 10.9 + - + +
222B LEU* 4.1 7.6 - - + -
225B PHE* 3.9 30.8 - + + -
255B ILE* 3.5 21.8 - - + -
256B ARG* 3.3 25.5 - - - +
257B SER 3.3 30.3 - - - -
258B ILE* 4.1 19.7 - - + -
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Residues in contact with GLY 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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214B ASN 2.9 7.0 + - - -
215B LEU* 3.5 6.0 + - - -
216B GLN 3.5 3.6 + - - -
217B PHE* 1.3 77.0 - - - +
219B THR* 1.3 60.2 + - - +
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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