Contacts of the helix formed by residues 207 - 221 (chain D) in PDB entry 1ORR
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 GLY 207 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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195D MET 5.4 1.1 - - - -
200D GLN* 3.7 25.8 - - - -
202D ALA* 3.1 9.9 - - - +
206D GLN* 1.3 78.0 - - - +
208D TRP* 1.3 56.2 + - - +
209D VAL 3.5 2.2 - - - -
210D GLY 3.3 2.4 + - - -
211D TRP* 2.7 35.8 + - - +
1501D CDP 3.1 13.3 + - - -
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Residues in contact with TRP 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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194D SER* 3.0 23.3 + - - -
207D GLY* 1.3 70.0 - - - +
209D VAL* 1.3 74.0 + - + +
211D TRP* 4.3 5.2 - - - -
212D PHE* 3.0 35.7 + + + -
237D ARG* 3.7 21.5 - - + +
239D VAL* 3.7 20.6 - - + -
274D LEU* 4.0 29.6 - - + -
275D SER 4.1 2.9 - - - -
276D LEU* 3.6 30.1 - - + -
279D LEU* 3.3 32.3 - - + -
1501D CDP 3.2 78.0 + - + +
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Residues in contact with VAL 209 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194D SER* 5.3 2.5 - - - -
195D MET 5.7 0.7 - - - +
196D TYR* 3.9 36.8 - - + -
207D GLY 3.5 0.6 - - - -
208D TRP* 1.3 95.8 - - + +
210D GLY* 1.3 64.0 + - - +
212D PHE* 3.5 1.7 + - - +
213D CYS* 3.0 33.1 + - - -
239D VAL* 3.8 33.0 - - + -
274D LEU* 5.5 0.2 - - + -
279D LEU* 4.1 15.3 - - + +
329D VAL* 4.0 19.7 - - + -
332D MET* 4.6 2.2 - - + -
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Residues in contact with GLY 210 (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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200D GLN* 4.3 6.8 + - - -
202D ALA* 3.6 12.7 - - - +
207D GLY 3.3 6.2 + - - -
208D TRP 3.2 0.2 - - - -
209D VAL* 1.3 79.1 - - - +
211D TRP* 1.3 64.3 - - - +
213D CYS* 3.1 5.4 + - - +
214D GLN* 3.0 22.5 + - - +
332D MET* 3.8 27.8 - - - +
336D THR* 4.7 2.6 + - - +
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Residues in contact with TRP 211 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202D ALA* 3.3 8.6 - - + +
203D THR* 3.3 29.6 - - - +
204D TYR* 3.5 36.7 - + + -
207D GLY 2.7 23.2 + - - +
208D TRP* 3.8 5.4 - - - +
209D VAL 3.3 0.2 - - - -
210D GLY* 1.3 73.5 - - - +
212D PHE* 1.3 82.8 + + - +
214D GLN* 2.8 33.4 - - + +
215D LYS* 2.8 50.0 + - + +
227D PHE* 5.5 4.0 - - + +
228D THR 5.1 1.6 + - - -
1501D CDP 3.3 25.8 + + + -
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Residues in contact with PHE 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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208D TRP* 3.0 39.2 + + + +
211D TRP* 1.3 89.1 - + - +
213D CYS* 1.4 60.2 + - - +
215D LYS* 3.0 16.0 - - + +
216D ALA* 2.8 26.5 + - - +
227D PHE* 3.7 24.9 - + - -
228D THR 3.9 7.0 - - - -
229D ILE* 4.4 0.4 - - + -
276D LEU* 3.5 28.7 - - + -
279D LEU* 4.0 16.2 - - + -
280D PHE* 3.8 25.4 - + + -
283D LEU* 5.0 3.0 - - + +
291D MET* 3.8 6.9 - - + +
1501D CDP 3.5 35.7 - + - -
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Residues in contact with CYS 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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209D VAL* 3.0 28.7 + - - +
210D GLY 3.1 9.1 + - - +
212D PHE* 1.4 72.7 - - - +
214D GLN* 1.3 56.0 + - - +
216D ALA* 2.8 12.9 + - - +
217D VAL* 2.8 34.1 + - - +
279D LEU* 5.7 0.9 - - - -
283D LEU* 4.3 16.4 - - - -
329D VAL* 4.3 6.1 - - - -
332D MET* 3.7 23.1 - - + -
333D TYR* 3.9 18.0 - - - -
336D THR* 3.7 21.8 - - - +
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Residues in contact with GLN 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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202D ALA* 5.8 3.1 - - + +
210D GLY 3.0 11.9 + - - +
211D TRP* 2.8 27.1 - - + +
213D CYS* 1.3 73.4 - - - +
215D LYS* 1.3 69.9 + - - +
216D ALA 2.9 1.6 - - - -
217D VAL* 2.9 10.1 + - - +
218D GLU* 2.8 56.7 + - - +
336D THR* 2.9 25.8 - - + +
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Residues in contact with LYS 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 TRP* 2.8 62.3 + - + +
212D PHE* 3.0 28.9 - - + +
214D GLN* 1.3 80.3 - - - +
216D ALA* 1.3 65.0 + - - +
218D GLU* 3.5 30.6 + - + +
219D ILE* 3.1 29.0 + - - +
227D PHE* 3.7 48.9 - - + -
291D MET* 4.4 2.0 - - + -
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Residues in contact with ALA 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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212D PHE 2.8 11.3 + - - +
213D CYS* 2.8 18.0 + - - +
215D LYS* 1.3 82.6 - - - +
217D VAL* 1.3 62.0 + - - +
219D ILE* 3.4 3.9 + - - +
220D LYS* 3.4 21.1 + - - +
283D LEU* 4.2 13.2 - - + -
287D CYS* 4.9 4.3 - - + -
289D ILE* 4.9 4.3 - - + +
291D MET* 4.3 17.9 - - - -
333D TYR* 3.7 18.6 + - + -
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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 CYS 2.8 8.9 + - - +
214D GLN* 2.9 14.1 + - - +
216D ALA* 1.3 77.2 - - - +
218D GLU* 1.3 65.2 + - + +
219D ILE 3.2 0.5 + - - -
220D LYS* 3.5 1.0 + - - +
221D ASN* 3.2 39.8 + - - +
333D TYR* 3.4 28.5 - - + +
336D THR* 3.4 31.4 - - + +
337D SER* 3.6 27.8 - - - +
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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 GLN* 2.8 48.4 + - - +
215D LYS* 3.5 31.9 + - + +
216D ALA 3.3 0.2 - - - -
217D VAL* 1.3 75.5 - - + +
219D ILE* 1.3 62.7 + - + +
221D ASN* 3.5 17.9 - - - +
223D ILE* 3.6 18.1 - - - +
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Residues in contact with ILE 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 LYS 3.1 21.1 - - - +
216D ALA* 3.4 5.8 + - - +
217D VAL 3.2 0.4 - - - -
218D GLU* 1.3 73.6 - - + +
220D LYS* 1.3 56.6 + - - +
221D ASN 2.8 3.4 - - - -
222D GLY* 2.3 46.1 + - - +
223D ILE 3.8 15.5 - - - +
226D PRO* 6.4 1.6 - - + -
227D PHE* 4.5 17.0 - - + -
289D ILE* 3.9 24.7 - - + -
290D ASP 4.7 12.3 - - - +
291D MET* 4.3 19.1 - - - -
292D ARG 5.1 2.2 - - - +
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Residues in contact with LYS 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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216D ALA 3.4 11.3 + - - +
217D VAL 3.9 1.8 - - - +
219D ILE* 1.3 82.7 - - - +
221D ASN* 1.3 69.6 + - - +
222D GLY* 2.6 13.0 + - - -
287D CYS* 6.1 1.1 - - + +
289D ILE* 3.6 25.8 - - + -
333D TYR* 3.9 24.2 + - - +
337D SER* 5.2 8.1 + - - -
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Residues in contact with ASN 221 (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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217D VAL* 3.2 29.9 + - - +
218D GLU* 3.5 9.5 - - - +
219D ILE 2.7 4.5 + - - -
220D LYS* 1.3 97.3 - - - +
222D GLY* 1.4 52.4 + - - +
223D ILE* 3.0 11.8 + - - +
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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