Contacts of the helix formed by residues 202 - 219 (chain D) in PDB entry 2ORE
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 THR 202 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200D SER* 3.2 16.9 + - - +
201D PHE* 1.3 74.4 - - - +
203D LEU* 1.3 64.5 + - - +
204D GLU* 3.5 21.6 + - - +
205D GLN* 3.0 29.5 + - - +
206D GLN* 3.0 23.7 + - - +
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Residues in contact with LEU 203 (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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186D PRO* 3.5 33.9 - - + -
202D THR* 1.3 71.4 - - - +
204D GLU* 1.3 75.6 + - - +
206D GLN* 3.1 16.6 + - + +
207D ALA* 3.2 13.0 + - - +
232D LEU* 4.0 14.8 - - + -
236D TRP* 3.5 34.1 + - + -
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Residues in contact with GLU 204 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202D THR* 3.1 22.9 - - - +
203D LEU* 1.3 88.5 + - - +
205D GLN* 1.3 58.9 + - + +
207D ALA* 3.5 6.0 + - - +
208D HIS* 3.1 24.3 + - - +
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Residues in contact with GLN 205 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164D SER* 4.8 1.6 + - - -
165D TYR* 3.3 40.6 + - - +
200D SER 3.8 4.7 - - - +
201D PHE* 3.6 26.0 - - + -
202D THR* 3.0 35.7 + - - +
204D GLU* 1.3 73.9 - - + +
206D GLN* 1.3 67.8 + - - +
207D ALA 3.1 2.0 - - - -
208D HIS* 3.5 2.8 - - - +
209D LEU* 3.0 24.8 + - - +
301D SAH 4.0 10.3 + - - -
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Residues in contact with GLN 206 (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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182D PRO* 4.3 3.6 - - - +
183D PRO 2.9 26.1 + - - -
184D TYR 4.0 0.8 + - - -
185D ALA* 3.7 22.2 - - - +
186D PRO* 4.8 1.2 - - - +
201D PHE* 3.2 24.0 - - + +
202D THR 3.0 18.6 + - - +
203D LEU* 3.1 16.1 + - + +
205D GLN* 1.3 77.7 - - - +
207D ALA* 1.3 60.8 + - - +
209D LEU* 3.5 15.1 + - - +
210D ALA* 3.6 7.1 + - - +
227D ASN* 3.7 14.9 + - - +
236D TRP* 3.3 34.1 - - + -
237D TYR* 4.0 12.3 + - - -
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Residues in contact with ALA 207 (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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203D LEU 3.2 5.6 + - - +
204D GLU* 3.7 9.2 - - - +
205D GLN 3.1 0.4 - - - -
206D GLN* 1.3 76.8 - - - +
208D HIS* 1.3 64.6 + - - +
209D LEU 3.1 2.0 - - - -
210D ALA* 3.0 6.8 + - - +
211D GLU* 2.9 24.7 + - - +
236D TRP* 3.5 33.6 - - + +
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Residues in contact with HIS 208 (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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165D TYR* 2.7 33.5 + + - +
166D ALA* 4.2 11.0 - - + +
204D GLU 3.1 14.8 + - - +
205D GLN* 3.1 9.6 + - - +
207D ALA* 1.3 75.8 - - - +
209D LEU* 1.3 57.2 + - - +
211D GLU* 3.2 18.3 + - + +
212D ILE* 2.8 52.6 + - + +
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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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35D PHE* 4.1 12.8 - - + -
165D TYR* 4.1 16.1 - - + -
169D MET* 3.2 40.8 - - + +
180D CYS* 3.9 15.9 - - + -
182D PRO* 3.9 33.9 - - + -
201D PHE* 5.1 4.0 - - + -
205D GLN 3.0 10.8 + - - +
206D GLN* 3.6 11.0 - - - +
207D ALA 3.1 0.2 - - - -
208D HIS* 1.3 75.1 - - - +
210D ALA* 1.3 60.4 + - - +
212D ILE* 3.2 7.3 + - - +
213D ALA* 2.9 26.3 + - - +
225D ILE* 4.3 14.8 - - + -
237D TYR* 4.6 5.8 - - - +
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Residues in contact with ALA 210 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206D GLN 3.6 2.7 + - - +
207D ALA* 3.0 8.8 + - - +
209D LEU* 1.3 76.2 - - - +
211D GLU* 1.3 60.7 + - - +
213D ALA* 3.0 9.2 + - - +
214D GLU* 2.9 34.7 + - - +
225D ILE* 4.5 0.9 - - - -
236D TRP* 3.5 31.6 - - + +
237D TYR* 3.7 25.7 - - + -
268D TYR* 4.0 5.0 + - - +
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Residues in contact with GLU 211 (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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207D ALA* 2.9 13.0 + - - +
208D HIS* 3.2 24.9 + - + +
210D ALA* 1.3 77.9 - - - +
212D ILE* 1.3 62.4 + - + +
214D GLU* 3.3 18.7 - - - +
215D GLY* 3.1 16.3 + - - -
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Residues in contact with ILE 212 (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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165D TYR* 3.9 13.9 - - + -
166D ALA* 3.9 27.6 - - + +
169D MET* 4.0 29.6 - - + -
208D HIS* 2.8 47.2 + - + +
209D LEU* 3.5 6.5 - - - +
210D ALA 3.2 0.2 - - - -
211D GLU* 1.3 74.6 - - + +
213D ALA* 1.3 63.9 + - - +
215D GLY* 2.9 3.9 + - - +
216D LEU* 2.9 30.0 + - + +
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Residues in contact with ALA 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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169D MET* 4.5 3.8 - - + +
209D LEU 2.9 13.6 + - - +
210D ALA 3.2 9.6 - - - +
212D ILE* 1.3 74.9 - - - +
214D GLU* 1.3 63.4 + - - +
215D GLY 3.2 0.2 + - - -
216D LEU* 3.2 3.1 + - - +
217D VAL* 3.0 27.0 + - - +
223D VAL* 4.2 20.0 - - + +
225D ILE* 4.1 10.1 - - + -
268D TYR* 3.7 33.8 - - + -
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Residues in contact with GLU 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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210D ALA* 2.9 15.6 + - - +
211D GLU* 3.3 18.9 - - - +
212D ILE 3.2 0.2 - - - -
213D ALA* 1.3 75.9 - - - +
215D GLY* 1.3 59.8 + - - +
217D VAL* 3.0 25.8 - - + +
218D GLU* 3.6 7.6 + - - +
236D TRP 4.3 13.5 - - - +
238D GLN* 5.3 2.1 - - - +
239D ARG* 3.2 48.4 + - + +
268D TYR* 4.1 9.3 + - + -
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Residues in contact with GLY 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 GLU 3.1 9.6 + - - -
212D ILE* 2.9 8.2 + - - -
214D GLU* 1.3 76.2 - - - +
216D LEU* 1.3 64.3 + - - +
218D GLU* 3.2 19.2 + - - +
219D ARG* 3.6 9.9 + - - +
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Residues in contact with LEU 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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169D MET* 3.8 40.4 - - + +
170D ALA* 5.6 0.7 - - - -
172D ALA* 4.7 2.2 - - + -
178D VAL* 3.8 18.6 - - + -
212D ILE* 2.9 22.8 + - + +
213D ALA 3.2 5.1 + - - +
215D GLY* 1.3 69.0 - - - +
217D VAL* 1.3 58.7 + - - +
219D ARG* 2.8 59.3 + - - +
221D ILE* 3.1 34.0 + - + +
223D VAL* 3.7 21.3 - - + -
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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
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213D ALA 3.0 15.2 + - - +
214D GLU* 3.0 29.2 - - + +
216D LEU* 1.3 76.8 - - - +
218D GLU* 1.3 58.5 + - + +
220D HIS* 3.1 18.5 + - - -
221D ILE 3.1 11.2 + - - +
223D VAL* 5.1 0.2 - - - +
268D TYR* 3.6 45.8 - - + +
269D LYS 3.9 4.0 - - - +
270D PRO* 3.8 22.2 - - + +
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Residues in contact with GLU 218 (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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214D GLU 4.1 7.3 - - - +
215D GLY* 3.2 12.0 + - - +
216D LEU 3.0 1.0 - - - -
217D VAL* 1.3 78.6 - - + +
219D ARG* 1.3 59.1 + - + +
220D HIS* 2.9 27.2 + - - -
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Residues in contact with ARG 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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169D MET 4.7 2.8 + - - -
170D ALA* 5.2 6.9 + - - +
172D ALA 3.5 19.2 + - - -
173D ASP* 5.5 1.2 - - - +
174D ASP* 4.4 11.7 - - - +
215D GLY 3.6 6.4 + - - +
216D LEU* 2.8 42.0 + - - +
218D GLU* 1.3 77.5 - - + +
220D HIS* 1.3 71.6 + - - +
221D ILE* 3.2 20.6 + - + +
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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