Contacts of the helix formed by residues 202 - 217 (chain D) in PDB entry 3J82
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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286C ASP* 4.9 9.9 + - - +
39D ARG* 6.1 1.6 - - - -
190D MET* 4.9 0.5 - - - +
200D PHE 3.5 0.7 - - - +
201D THR* 1.4 86.7 - - + +
203D THR* 1.4 55.5 + - - +
204D ALA* 3.2 8.0 + - - +
205D GLU* 2.7 52.6 + - + +
206D ARG* 2.6 33.3 + - - +
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Residues in contact with THR 203 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39D ARG* 2.7 41.5 + - - +
62D ARG 5.1 2.8 + - - -
63D GLY 5.5 0.9 + - - -
65D LEU 4.3 2.9 + - - -
67D LEU* 4.9 23.5 - - + +
202D THR* 1.4 69.3 - - - +
204D ALA* 1.3 66.2 + - - +
205D GLU 3.1 0.2 - - - -
206D ARG* 2.7 35.5 - - + +
207D GLU* 3.3 10.2 + - - +
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Residues in contact with ALA 204 (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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286C ASP* 4.2 23.1 - - + +
287C VAL* 5.6 1.6 - - + -
288C ASP* 3.5 25.8 - - - +
62D ARG* 4.3 17.5 + - + +
63D GLY* 4.4 4.3 - - - +
202D THR* 3.2 7.4 + - - +
203D THR* 1.3 82.5 + - - +
205D GLU* 1.3 64.7 + - + +
207D GLU* 3.1 16.6 + - - +
208D ILE* 3.1 15.9 + - + +
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Residues in contact with GLU 205 (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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286C ASP* 6.1 0.4 - - - +
287C VAL* 4.7 19.0 - - + +
190D MET* 4.5 1.7 - - - +
199D SER 2.7 21.6 - - - +
200D PHE* 3.6 24.1 - - + -
201D THR* 2.7 30.2 + - - +
202D THR* 2.7 42.1 + - + +
204D ALA* 1.3 75.8 - - + +
206D ARG* 1.3 65.7 + - - +
208D ILE* 3.1 12.2 + - + +
209D VAL* 2.9 19.6 + - - +
242D LEU* 5.7 4.1 - - + +
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Residues in contact with ARG 206 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67D LEU* 5.3 4.3 - - - -
69D TYR* 5.1 11.0 + - - -
183D ARG* 3.9 10.7 + - - +
186D THR* 3.1 20.8 + - - +
187D ASP* 2.7 34.4 + - - -
190D MET* 3.2 31.5 - - + +
201D THR 5.7 0.2 - - - +
202D THR 2.6 10.8 + - - +
203D THR* 2.7 31.0 - - + +
205D GLU* 1.3 74.9 - - - +
207D GLU* 1.3 71.9 + - - +
209D VAL* 2.8 19.6 + - - +
210D ARG* 2.9 18.2 + - - +
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Residues in contact with GLU 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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59D GLN* 3.8 14.1 + - + +
62D ARG* 4.4 22.0 - - + +
67D LEU* 4.3 16.8 - - + +
69D TYR* 4.4 4.9 + - - -
203D THR 3.5 12.8 - - - +
204D ALA* 3.1 9.1 + - - +
206D ARG* 1.3 98.4 + - - +
208D ILE* 1.3 65.4 + - - +
210D ARG* 3.2 37.8 + - - +
211D ASP* 3.0 21.3 + - - +
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Residues in contact with ILE 208 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287C VAL* 3.7 14.4 - - + -
288C ASP* 3.1 26.9 - - - +
62D ARG* 3.9 9.4 - - - +
200D PHE* 4.4 3.6 - - + -
204D ALA 3.1 17.4 + - - +
205D GLU* 3.1 14.3 + - + +
207D GLU* 1.3 74.1 - - - +
209D VAL* 1.3 65.6 + - - +
211D ASP* 3.0 7.0 + - - +
212D ILE* 3.0 29.4 + - + +
240D TYR* 3.8 19.5 - - + +
242D LEU* 3.0 31.0 - - + -
243D PRO* 3.3 17.0 - - + -
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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
----------------------------------------------------------
186D THR* 3.5 22.2 - - - +
189D LEU* 3.8 17.1 - - + +
190D MET* 3.1 58.6 - - + +
193D LEU* 4.3 4.5 - - + -
200D PHE* 4.1 17.2 - - + -
205D GLU 2.9 7.1 + - - +
206D ARG 2.8 6.9 + - - +
208D ILE* 1.3 75.8 - - - +
210D ARG* 1.3 69.9 + - - +
212D ILE* 2.9 18.6 + - - +
213D LYS* 2.9 12.7 + - + +
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Residues in contact with ARG 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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16D MET* 5.9 6.0 - - - +
59D GLN* 2.8 33.9 - - - +
186D THR* 4.2 8.5 - - + -
206D ARG* 2.9 14.5 + - - +
207D GLU* 3.4 29.0 + - - +
208D ILE 3.1 0.4 - - - -
209D VAL* 1.3 86.3 - - + +
211D ASP* 1.3 64.2 + - - +
213D LYS* 3.2 25.8 - - - +
214D GLU* 2.8 60.1 + - - +
401D ADP 4.8 7.0 - - + +
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Residues in contact with ASP 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 GLU 3.0 12.6 + - - +
208D ILE* 3.0 8.7 + - - +
210D ARG* 1.3 80.0 + - - +
212D ILE* 1.3 65.6 + - - +
214D GLU* 2.7 28.2 + - - +
215D LYS* 2.9 49.0 + - - +
240D TYR* 3.7 19.9 + - - +
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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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189D LEU* 5.0 4.9 - - + -
193D LEU* 4.2 12.6 - - + -
200D PHE* 4.1 14.6 - - + -
208D ILE* 3.1 28.5 - - + +
209D VAL* 2.9 16.7 + - - +
211D ASP* 1.3 76.1 - - - +
213D LYS* 1.3 62.7 + - - +
215D LYS* 4.4 0.8 - - - +
216D LEU* 2.7 44.7 + - + +
240D TYR* 3.9 30.7 - - + -
248D ILE* 4.2 11.2 - - + -
250D ILE* 3.5 31.4 - - + -
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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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182D GLY* 4.1 2.6 + - - -
185D LEU* 4.5 11.0 - - - -
186D THR* 2.9 37.2 - - + +
189D LEU* 4.0 12.5 - - + +
209D VAL 2.9 13.2 + - - +
210D ARG* 3.2 22.3 - - - +
212D ILE* 1.3 78.2 - - - +
214D GLU* 1.3 80.2 + - + +
217D CYS* 2.7 55.8 + - + +
257D CYS* 4.8 3.6 - - - -
306D TYR* 4.0 20.9 - - - +
401D ADP 2.4 39.2 + - - +
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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 ARG* 2.8 60.3 + - - +
211D ASP* 2.7 37.2 + - - +
213D LYS* 1.3 89.2 + - + +
215D LYS* 1.3 75.8 + - + +
217D CYS 4.3 4.0 + - - +
306D TYR* 6.0 0.5 - - - -
401D ADP 4.7 34.6 + - + +
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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 ASP* 2.9 40.1 + - - +
212D ILE* 4.4 0.9 - - - +
214D GLU* 1.3 90.8 + - + +
216D LEU* 1.3 66.3 + - + +
217D CYS 4.3 2.4 - - - +
240D TYR* 4.6 15.5 - - + -
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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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212D ILE* 2.7 29.9 + - + +
213D LYS* 4.6 0.2 - - - -
215D LYS* 1.3 82.1 - - + +
217D CYS* 1.3 64.4 + - - +
218D TYR* 3.7 1.7 + - - +
238D LYS* 4.5 11.9 - - + -
239D SER 4.7 2.9 - - - +
240D TYR* 4.6 14.4 - - + -
250D ILE* 3.0 47.8 - - + -
254D ARG* 2.9 71.0 + - + -
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Residues in contact with CYS 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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189D LEU* 3.3 34.3 - - - -
212D ILE 4.7 0.2 - - - -
213D LYS* 2.7 41.8 + - + +
214D GLU 4.6 2.9 - - - +
215D LYS 3.6 4.0 - - - +
216D LEU* 1.3 79.5 - - - +
218D TYR* 1.4 59.9 + - - +
250D ILE* 5.5 0.2 - - - -
254D ARG* 3.4 27.8 - - - +
257D CYS* 4.1 4.5 - - - -
258D PRO* 3.7 12.1 - - + -
306D TYR* 4.0 14.9 - - + -
307D PRO* 5.7 2.8 - - - +
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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
------------------------------------------------------------
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