Contacts of the helix formed by residues 206 - 220 (chain D) in PDB entry 2OHI
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 LEU 206 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149D LEU* 3.3 35.9 - - + +
150D LEU* 3.7 20.2 - - + -
151D HIS* 3.5 33.0 - - + +
202D LEU 3.5 16.6 - - - +
203D ILE* 2.7 25.4 + - + +
205D PRO* 1.3 79.5 - - + +
207D SER* 1.3 52.6 + - - +
208D LYS 3.3 2.9 - - - -
209D LEU* 2.9 18.2 + - + +
210D VAL* 2.8 33.3 + - - +
319E TYR* 4.2 18.4 - - + +
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Residues in contact with SER 207 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199D TYR* 2.7 30.6 + - - -
203D ILE 3.2 1.0 + - - -
204D THR* 3.0 19.5 + - - -
205D PRO 3.3 1.4 - - - -
206D LEU* 1.3 77.3 - - - +
208D LYS* 1.3 62.1 + - - +
210D VAL* 3.2 18.8 + - - +
211D LEU* 3.4 6.9 + - - +
251D ALA* 3.6 18.8 - - - +
340D ARG* 4.5 6.9 - - - +
341D THR* 3.2 27.0 - - - +
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Residues in contact with LYS 208 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205D PRO 5.1 1.2 + - - +
206D LEU 3.3 0.8 - - - -
207D SER* 1.3 76.7 - - - +
209D LEU* 1.3 68.9 + - + +
211D LEU* 3.5 12.8 + - + +
212D LYS* 3.3 28.7 + - - +
251D ALA 5.9 0.4 - - - +
339D ASN* 5.4 1.2 + - - +
340D ARG* 3.6 55.1 - - + +
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Residues in contact with LEU 209 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148D PRO 5.2 1.1 - - - +
149D LEU* 4.3 35.0 - - + +
150D LEU* 4.0 19.9 - - + +
205D PRO 5.3 2.2 - - - +
206D LEU* 2.9 19.9 + - + +
208D LYS* 1.3 82.2 - - + +
210D VAL* 1.3 65.5 + - - +
212D LYS* 3.8 25.0 - - + +
213D LYS* 3.0 23.6 + - - +
340D ARG* 6.0 2.5 - - - +
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Residues in contact with VAL 210 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150D LEU* 3.9 14.6 - - + -
172D PHE* 6.1 0.2 - - + -
199D TYR* 4.3 2.5 - - - +
203D ILE* 3.4 30.1 - - + -
206D LEU 2.8 20.9 + - - +
207D SER* 3.2 10.9 + - - +
209D LEU* 1.3 76.3 - - - +
211D LEU* 1.3 63.9 + - - +
213D LYS* 3.0 9.8 + - + +
214D PHE* 3.0 48.2 + - + -
247D TYR* 4.4 16.2 - - + -
251D ALA* 4.6 10.1 - - + -
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Residues in contact with LEU 211 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207D SER 3.4 11.6 + - - +
208D LYS* 3.8 11.7 - - + +
209D LEU 3.3 0.2 - - - -
210D VAL* 1.3 76.6 - - + +
212D LYS* 1.3 60.9 + - + +
214D PHE* 3.0 43.1 + - + +
215D ASP* 3.2 17.2 + - - +
248D THR* 4.6 10.5 - - + -
251D ALA* 4.0 26.0 - - + +
252D THR* 3.7 29.6 - - + -
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Residues in contact with LYS 212 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208D LYS* 3.3 18.7 + - - +
209D LEU* 3.8 27.3 - - + +
210D VAL 3.2 0.4 - - - -
211D LEU* 1.3 75.3 - - + +
213D LYS* 1.3 57.2 + - - +
215D ASP* 3.5 11.1 + - - +
216D GLU* 3.1 27.5 + - - +
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Residues in contact with LYS 213 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131D THR* 5.4 0.2 + - - -
145D LEU* 4.4 5.4 - - - -
146D GLU 2.7 29.8 + - - -
147D THR* 3.8 24.6 - - + +
148D PRO* 4.6 6.1 - - - +
150D LEU* 4.6 18.2 - - + -
157D PHE* 4.6 11.2 - - + -
209D LEU 3.0 12.2 + - - +
210D VAL* 3.0 12.8 + - - +
212D LYS* 1.3 74.1 - - - +
214D PHE* 1.3 67.1 + - + +
216D GLU* 3.2 37.9 + - + +
217D VAL* 3.2 31.0 + - + +
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Residues in contact with PHE 214 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172D PHE* 4.3 22.0 - + - -
210D VAL* 3.0 34.3 + - + -
211D LEU* 3.2 28.3 - - + +
213D LYS* 1.3 77.4 - - + +
215D ASP* 1.3 66.0 + - - +
217D VAL* 3.2 9.7 + - + +
218D LYS* 3.2 23.7 + - - +
223D LEU* 4.5 18.4 - - + +
244D ILE* 4.1 25.8 - - + -
247D TYR* 4.3 9.0 - - + -
248D THR* 3.3 29.8 - - + -
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Residues in contact with ASP 215 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211D LEU* 3.2 19.2 + - - +
212D LYS* 3.9 11.6 - - - +
214D PHE* 1.3 76.5 - - - +
216D GLU* 1.3 56.2 + - - +
217D VAL 3.1 0.7 - - - -
218D LYS* 3.1 13.1 + - - +
219D GLU* 2.7 55.4 + - - +
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Residues in contact with GLU 216 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131D THR* 4.2 12.1 + - - +
145D LEU* 3.4 15.3 - - - +
212D LYS 3.1 18.8 + - - +
213D LYS* 3.2 40.5 + - + +
214D PHE 3.3 0.2 - - - -
215D ASP* 1.3 76.0 - - - +
217D VAL* 1.3 59.6 + - - +
219D GLU* 4.1 12.7 + - + +
220D LEU* 3.3 42.7 + - + +
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Residues in contact with VAL 217 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145D LEU* 3.6 30.5 - - + -
157D PHE* 5.7 3.4 - - + -
159D LEU* 5.9 3.4 - - + -
213D LYS* 3.2 16.7 + - + +
214D PHE* 3.2 11.3 + - + +
215D ASP 3.1 0.6 - - - -
216D GLU* 1.3 77.0 - - - +
218D LYS* 1.3 58.9 + - - +
220D LEU* 3.4 4.8 + - - -
221D GLY 3.1 8.5 + - - -
222D LEU* 3.0 41.3 + - + +
223D LEU* 3.4 38.1 - - + +
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Residues in contact with LYS 218 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214D PHE 3.2 15.3 + - - +
215D ASP* 3.1 14.3 + - - +
217D VAL* 1.3 77.6 - - - +
219D GLU* 1.3 58.7 + - + +
221D GLY* 2.9 21.0 + - - +
222D LEU 4.9 0.9 - - - +
223D LEU* 4.5 24.5 - - + +
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Residues in contact with GLU 219 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215D ASP* 2.7 41.2 + - - +
216D GLU* 4.1 12.0 + - + +
218D LYS* 1.3 72.3 - - + +
220D LEU* 1.3 62.3 + - + +
221D GLY 3.4 1.0 + - - -
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Residues in contact with LEU 220 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131D THR* 4.3 12.1 - - + -
132D GLY* 6.4 0.7 - - - -
145D LEU* 4.2 19.1 - - + -
216D GLU* 3.3 36.4 + - + +
217D VAL 3.4 1.5 + - - +
218D LYS 3.1 0.8 - - - -
219D GLU* 1.3 80.4 - - + +
221D GLY* 1.3 64.5 + - - +
222D LEU* 3.5 25.1 - - + +
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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