Contacts of the helix formed by residues 205 - 223 (chain D) in PDB entry 2Y0N
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 ASN 205 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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202D CYS* 3.8 11.4 + - - +
203D GLN 3.9 1.2 + - - -
204D THR* 1.3 73.6 - - - +
206D ILE* 1.3 60.6 + - - +
207D ILE* 3.3 6.5 + - - +
208D THR* 3.0 41.1 + - - +
209D ILE* 3.0 19.7 + - - +
448D SER 3.7 3.8 + - - +
449D TYR* 3.3 49.3 + - - +
450D ILE 4.7 1.3 - - - -
451D TYR 3.4 15.7 - - - +
452D GLY* 4.3 0.7 - - - -
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Residues in contact with ILE 206 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205D ASN* 1.3 72.9 - - - +
207D ILE* 1.3 66.5 + - - +
209D ILE* 3.6 5.7 - - - +
210D LEU* 2.9 44.8 + - + +
261D LEU 6.2 0.2 - - - -
262D ARG* 5.1 3.6 - - + -
265D PHE* 3.4 44.0 - - + -
448D SER* 3.4 20.1 + - - +
451D TYR 3.0 13.9 + - - +
452D GLY 3.3 30.1 - - - +
456D LEU* 3.7 28.7 - - + -
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Residues in contact with ILE 207 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440B GLU* 4.1 9.2 - - + +
441B PHE* 4.3 8.0 - - + -
205D ASN* 3.3 8.9 + - - +
206D ILE* 1.3 78.2 - - - +
208D THR* 1.3 60.0 + - + +
210D LEU* 3.8 5.1 - - - +
211D GLU* 3.0 46.2 + - + +
262D ARG* 3.8 23.8 - - + -
448D SER* 3.5 33.0 + - - +
449D TYR* 3.6 46.4 - - + +
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Residues in contact with THR 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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203D GLN 6.0 0.9 - - - +
204D THR* 3.6 12.5 + - - -
205D ASN* 3.0 39.2 + - - +
207D ILE* 1.3 79.1 - - + +
209D ILE* 1.3 64.1 + - - +
211D GLU* 3.2 16.6 + - - +
212D SER* 2.9 24.7 + - - -
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Residues in contact with ILE 209 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204D THR* 3.9 16.6 - - - +
205D ASN 3.0 22.0 + - - +
206D ILE* 3.3 12.8 + - + +
208D THR* 1.3 74.5 + - - +
210D LEU* 1.3 62.8 + - - +
212D SER* 3.2 8.9 + - - -
213D TYR* 3.1 20.3 + - - +
452D GLY 3.9 4.5 - - - -
453D ALA* 3.4 43.1 - - + +
456D LEU* 4.1 17.9 - - + -
487D PHE* 4.5 5.8 - - + -
490D PHE* 4.6 2.0 - - + -
491D LEU* 4.4 15.7 - - + -
498D PHE* 4.3 25.1 - - + -
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Residues in contact with LEU 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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441B PHE* 3.5 19.7 - - + -
206D ILE* 2.9 31.0 + - + +
207D ILE* 3.8 0.7 - - - +
209D ILE* 1.3 77.3 - - - +
211D GLU* 1.3 61.7 + - - +
213D TYR* 3.3 6.5 + - - +
214D VAL* 3.2 26.3 + - - +
258D VAL* 3.2 43.3 - - + +
261D LEU* 4.4 14.8 - - + -
262D ARG* 3.8 17.9 - - + +
456D LEU* 4.3 9.2 - - + -
487D PHE* 3.8 30.1 - - + -
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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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440B GLU* 3.6 20.1 - - - +
441B PHE* 4.3 14.6 - - + -
207D ILE* 3.0 35.0 + - - +
208D THR* 3.2 19.0 + - - +
210D LEU* 1.3 74.0 - - - +
212D SER* 1.3 63.5 + - - +
214D VAL* 3.7 7.4 + - - +
215D LYS* 3.4 35.8 + - - +
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Residues in contact with SER 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 THR 2.9 12.5 + - - -
209D ILE* 3.3 13.5 - - - -
211D GLU* 1.3 76.0 - - - +
213D TYR* 1.3 64.1 + - - +
215D LYS* 3.4 14.4 + - - +
216D HIS* 3.1 32.6 + - - +
490D PHE* 4.4 12.0 - - - -
498D PHE* 4.8 8.2 - - - -
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Residues in contact with TYR 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 ILE 3.1 6.8 + - - +
210D LEU* 3.3 7.4 + - - +
212D SER* 1.3 79.4 - - - +
214D VAL* 1.3 53.9 + - - +
216D HIS 3.2 6.4 + - - -
217D PHE* 2.8 57.8 + + + +
254D CYS* 3.5 26.7 - - - -
257D MET* 4.2 9.6 - - + -
258D VAL* 4.3 10.5 - - + -
483D HIS* 4.1 5.1 + + - -
486D LEU* 3.4 25.0 - - + +
487D PHE* 3.6 34.2 + + + -
490D PHE* 3.3 57.1 - + + -
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Residues in contact with VAL 214 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441B PHE* 4.6 11.4 - - + +
442B ASP* 5.7 2.0 - - - +
210D LEU 3.2 16.3 + - - +
211D GLU* 3.9 7.2 - - - +
212D SER 3.3 0.2 - - - -
213D TYR* 1.3 77.0 - - - +
215D LYS* 1.3 62.9 + - + +
217D PHE* 3.2 9.3 + - - +
218D ALA* 3.1 21.9 + - + +
251D VAL* 5.0 6.4 - - + +
254D CYS* 4.7 5.8 - - - -
255D LYS* 4.1 35.0 - - + -
258D VAL* 3.7 30.3 - - + -
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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 GLU* 3.4 24.2 + - - +
212D SER* 3.4 11.9 + - - +
213D TYR 3.3 0.2 - - - -
214D VAL* 1.3 77.6 - - + +
216D HIS* 1.3 70.2 + - + +
218D ALA* 3.0 8.6 + - - +
219D ILE* 2.9 35.6 + - + +
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Residues in contact with HIS 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 SER* 3.1 27.2 + - - +
213D TYR* 3.2 8.8 - - - +
215D LYS* 1.3 87.4 - - + +
217D PHE* 1.3 57.2 + - - +
219D ILE* 3.5 32.1 - - + +
220D ASN* 3.9 16.3 + - - +
490D PHE* 4.4 23.4 - + + -
494D TYR* 5.5 6.4 + + + +
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Residues in contact with PHE 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 TYR* 2.8 42.2 + + + +
214D VAL 3.4 5.8 - - - +
216D HIS* 1.3 77.7 - - - +
218D ALA* 1.3 63.6 + - - +
219D ILE 3.4 0.4 - - - -
220D ASN* 3.3 8.6 - - + +
221D ALA* 2.9 28.6 + - + +
248D GLU 3.4 26.9 - - - -
249D LYS* 4.2 7.6 - - - -
250D ASN 4.0 4.0 - - - -
251D VAL* 3.6 35.2 - - + -
254D CYS* 3.6 32.8 - - + -
483D HIS* 3.9 15.0 - + - -
486D LEU* 4.2 8.1 - - + -
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Residues in contact with ALA 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 VAL* 3.1 12.4 + - + +
215D LYS* 3.0 10.9 + - - +
217D PHE* 1.3 79.7 - - - +
219D ILE* 1.3 63.3 + - + +
221D ALA* 3.5 9.6 + - - +
222D ALA* 3.5 17.7 + - - +
251D VAL* 4.2 18.4 - - + -
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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* 2.9 21.8 + - + +
216D HIS* 3.5 41.5 - - + +
218D ALA* 1.3 73.0 - - + +
220D ASN* 1.3 66.4 + - - +
222D ALA* 3.3 19.3 + - - +
223D PHE* 3.8 31.8 + - + -
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Residues in contact with ASN 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 HIS 3.9 16.4 + - - +
217D PHE* 3.3 12.2 + - - +
219D ILE* 1.3 78.1 - - - +
221D ALA* 1.3 63.8 + - - +
222D ALA 3.3 0.7 + - - -
223D PHE* 3.0 37.3 + - - +
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Residues in contact with ALA 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 PHE* 2.9 23.9 + - + +
218D ALA* 3.6 11.7 - - - +
219D ILE 3.3 0.4 - - - -
220D ASN* 1.3 76.6 - - - +
222D ALA* 1.3 60.2 + - - +
223D PHE 3.3 5.6 + - - +
249D LYS* 4.6 27.8 - - + +
251D VAL* 5.7 3.8 - - + -
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Residues in contact with ALA 222 (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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218D ALA 3.5 8.7 + - - +
219D ILE* 3.3 13.6 + - - +
220D ASN 3.2 0.8 - - - -
221D ALA* 1.3 77.6 - - - +
223D PHE* 1.3 65.5 + - + +
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Residues in contact with PHE 223 (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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219D ILE* 3.8 36.5 + - + -
220D ASN* 3.0 29.6 + - - +
221D ALA* 3.7 5.9 - - - +
222D ALA* 1.3 84.2 - - + +
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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