Contacts of the helix formed by residues 239 - 252 (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 ASP 239 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183D ASP* 3.1 13.7 + - - +
237D TRP* 4.1 9.1 - - - -
238D THR* 1.3 77.3 + - - +
240D PRO* 1.4 66.5 - - - +
241D MET* 3.8 10.0 + - - +
242D LYS* 3.2 46.3 + - + +
243D ILE 4.1 2.1 + - - -
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Residues in contact with PRO 240 (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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226D ILE* 3.7 36.3 - - + +
227D GLN 3.3 29.2 - - - +
228D MET 3.8 0.4 - - - +
229D ILE* 3.8 23.6 - - + +
237D TRP* 4.1 8.3 - - + +
238D THR 3.3 11.9 - - - +
239D ASP* 1.4 86.2 - - - +
241D MET* 1.3 63.8 + - + +
243D ILE* 3.2 22.0 - - - +
244D ILE* 3.3 11.5 + - + +
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Residues in contact with MET 241 (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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223D LEU* 5.0 12.1 - - + -
226D ILE* 4.4 16.6 - - + -
239D ASP* 3.2 8.6 - - - +
240D PRO* 1.3 81.2 - - + +
242D LYS* 1.3 61.6 + - - +
244D ILE* 3.7 33.8 - - + +
245D GLU* 3.1 50.7 + - + +
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Residues in contact with LYS 242 (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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183D ASP* 5.3 2.2 - - - +
188D GLU* 3.0 32.4 + - - -
191D LEU* 5.2 5.4 - - + -
192D MET* 3.9 26.2 - - + +
237D TRP* 4.4 15.7 - - + -
239D ASP* 3.2 35.5 + - + +
241D MET* 1.3 78.8 - - - +
243D ILE* 1.3 57.5 + - - +
245D GLU* 3.7 6.3 + - - +
246D ALA* 3.2 23.6 + - - +
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Residues in contact with ILE 243 (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* 3.8 25.1 - - + +
192D MET* 4.6 2.2 - - + -
195D ALA* 3.9 16.2 - - + -
229D ILE* 3.8 20.2 - - + -
237D TRP* 3.4 54.1 - - + -
239D ASP 4.1 0.8 + - - -
240D PRO 3.2 13.0 + - - +
242D LYS* 1.3 77.0 - - - +
244D ILE* 1.3 64.1 + - - +
246D ALA* 3.1 12.1 + - + +
247D TYR* 2.8 47.6 + - + -
250D TRP* 4.4 0.9 - - + -
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Residues in contact with ILE 244 (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* 4.6 11.7 - - + -
214D PHE* 4.1 20.9 - - + -
223D LEU* 4.9 18.4 - - + -
226D ILE* 4.3 16.4 - - + -
229D ILE* 3.9 22.0 - - + -
240D PRO* 3.3 19.0 + - + +
241D MET* 3.7 34.1 - - + +
242D LYS 3.4 0.2 - - - -
243D ILE* 1.3 77.3 - - + +
245D GLU* 1.3 57.7 + - + +
247D TYR* 3.3 6.6 + - - +
248D THR* 3.0 35.8 + - - +
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Residues in contact with GLU 245 (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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241D MET* 3.1 41.4 + - + +
242D LYS* 3.9 6.3 - - - +
244D ILE* 1.3 73.5 - - + +
246D ALA* 1.3 64.6 + - - +
248D THR* 3.5 8.0 + - - -
249D GLY* 3.0 20.1 + - - -
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Residues in contact with ALA 246 (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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192D MET* 3.9 23.8 - - + -
242D LYS 3.2 15.2 + - - +
243D ILE* 3.1 11.9 + - + +
245D GLU* 1.3 74.2 - - - +
247D TYR* 1.3 58.0 + - - +
249D GLY* 3.3 3.2 + - - -
250D TRP* 3.0 54.5 + - + -
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Residues in contact with TYR 247 (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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171D ALA* 4.9 3.8 - - + -
172D PHE* 2.9 51.9 + + + -
173D GLY 4.2 1.8 + - - -
195D ALA* 4.8 2.8 + - + -
198D PHE* 4.3 7.6 - - - -
199D TYR* 3.6 37.5 + + + -
203D ILE* 3.8 24.4 - - + +
210D VAL* 4.4 14.6 - - + -
214D PHE* 4.3 11.9 - - + -
243D ILE* 2.8 45.5 + - + +
244D ILE 3.6 4.0 - - - +
246D ALA* 1.3 70.5 - - - +
248D THR* 1.3 55.5 + - - +
250D TRP* 3.2 18.8 + + - +
251D ALA* 2.8 39.2 + - - +
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Residues in contact with THR 248 (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* 4.6 13.7 - - + -
214D PHE* 3.3 22.5 - - + -
244D ILE* 3.0 22.7 + - - +
245D GLU* 3.6 8.5 - - - -
247D TYR* 1.3 76.1 - - - +
249D GLY* 1.3 55.0 + - - +
251D ALA* 3.5 0.7 + - - -
252D THR* 2.6 43.0 + - + +
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Residues in contact with GLY 249 (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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245D GLU 3.0 15.0 + - - -
246D ALA* 3.7 3.6 - - - -
248D THR* 1.3 76.9 - - - +
250D TRP* 1.3 60.0 + - - +
252D THR* 3.4 1.5 + - - -
253D GLY 3.0 9.0 + - - -
254D MET* 2.9 50.3 + - - -
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Residues in contact with TRP 250 (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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192D MET* 4.3 9.6 - - + -
195D ALA* 3.6 24.0 - - + -
196D ARG* 3.5 39.7 - - + -
199D TYR* 3.5 41.9 - + + -
243D ILE* 4.4 2.0 - - + -
246D ALA* 3.0 39.8 + - + +
247D TYR* 3.2 19.3 + + - +
249D GLY* 1.3 77.5 - - - +
251D ALA* 1.3 62.1 + - - +
252D THR 3.4 0.5 + - - -
253D GLY* 3.5 9.0 + - - -
254D MET 5.1 0.2 - - - +
255D VAL 6.3 1.1 - - - -
306D LEU* 3.9 31.4 - - + +
307D GLU* 2.7 29.7 + - - -
341D THR* 3.6 16.1 + - - +
344D ARG* 5.4 0.2 + - - -
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Residues in contact with ALA 251 (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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199D TYR* 3.1 20.6 + - - +
207D SER* 3.6 31.5 - - - +
208D LYS* 5.7 0.5 - - - +
210D VAL* 4.6 4.7 - - + -
211D LEU* 4.0 24.9 - - + +
247D TYR 2.8 19.7 + - - +
248D THR 4.1 0.4 - - - +
250D TRP* 1.3 72.5 - - - +
252D THR* 1.3 60.3 + - - +
253D GLY 3.5 0.2 - - - -
340D ARG 4.2 3.6 - - - +
341D THR* 4.0 14.0 - - - -
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Residues in contact with THR 252 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211D LEU* 3.7 28.7 - - + -
248D THR* 2.6 30.7 + - + +
249D GLY* 3.4 6.9 + - - -
251D ALA* 1.3 75.0 - - - +
253D GLY* 1.3 62.7 + - - +
254D MET* 3.3 25.0 - - - +
341D THR 3.7 12.2 - - - +
342D LEU* 5.4 0.3 - - - +
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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