Contacts of the helix formed by residues 236 - 253 (chain D) in PDB entry 2CEA
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 236 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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235D VAL* 1.3 76.0 - - - +
237D VAL* 1.3 64.8 + - - +
238D GLY 3.3 2.0 - - - -
239D ALA* 3.1 19.2 + - - +
240D ALA* 3.1 13.0 + - - +
243D ARG* 5.0 1.7 + - - -
279D GLU* 3.2 14.0 + - - -
282D GLN* 4.3 10.9 + - - -
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Residues in contact with VAL 237 (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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233D LEU* 3.5 21.5 - - + -
234D PHE* 3.5 34.2 + - + +
235D VAL 3.3 3.1 - - - +
236D GLY* 1.3 76.2 - - - +
238D GLY* 1.3 62.4 + - - +
240D ALA* 3.0 10.4 + - + +
241D ARG* 2.9 45.5 + - + +
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Residues in contact with GLY 238 (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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230D PHE* 4.1 3.8 - - - -
233D LEU* 3.2 25.2 - - - +
234D PHE 4.5 0.4 + - - -
236D GLY 3.2 1.2 + - - -
237D VAL* 1.3 77.9 - - - +
239D ALA* 1.3 62.5 + - - +
241D ARG* 3.2 6.6 + - - +
242D VAL* 3.0 29.4 + - - +
279D GLU* 4.9 2.2 + - - -
283D THR* 4.2 20.2 - - - -
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Residues in contact with ALA 239 (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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236D GLY* 3.1 13.0 + - - +
238D GLY* 1.3 74.8 - - - +
240D ALA* 1.3 58.3 + - - +
242D VAL* 3.1 5.3 + - - +
243D ARG* 2.9 49.2 + - - +
279D GLU* 5.6 0.4 + - - -
282D GLN* 4.8 17.9 - - + +
283D THR* 4.5 5.6 + - - +
286D GLN* 3.6 24.0 - - + +
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Residues in contact with ALA 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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236D GLY 3.1 7.8 + - - +
237D VAL* 3.0 13.1 + - + +
239D ALA* 1.3 78.6 - - - +
241D ARG* 1.3 53.1 + - + +
243D ARG* 3.3 21.5 + - - +
244D ASP* 2.7 35.4 + - - +
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Residues in contact with ARG 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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150D TYR* 3.6 34.1 + - + -
229D ASP* 3.2 24.7 + - - +
230D PHE* 4.1 18.8 - - + -
233D LEU* 3.8 27.3 - - - +
237D VAL* 2.9 44.2 + - + +
238D GLY* 3.3 9.6 - - - +
239D ALA 3.1 0.2 - - - -
240D ALA* 1.3 74.5 - - + +
242D VAL* 1.3 55.7 + - - +
244D ASP* 3.2 6.8 + - - +
245D LEU* 2.7 36.3 + - - +
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Residues in contact with VAL 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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230D PHE* 3.7 22.4 - - + -
238D GLY 3.0 16.8 + - - +
239D ALA* 3.1 6.3 + - - +
241D ARG* 1.3 74.2 - - - +
243D ARG* 1.3 63.5 + - - +
245D LEU* 3.4 7.5 + - + +
246D PHE* 3.2 35.7 + - + +
283D THR* 4.1 18.8 - - + +
286D GLN* 3.8 4.7 - - + -
287D LEU* 3.7 34.5 - - + +
290D GLU* 3.8 14.7 - - + +
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Residues in contact with ARG 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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236D GLY 5.0 1.6 + - - -
239D ALA* 2.9 24.9 + - - +
240D ALA* 3.3 30.6 - - - +
242D VAL* 1.3 77.3 - - - +
244D ASP* 1.3 61.3 + - - +
246D PHE* 3.5 2.1 + - - +
247D ALA* 3.0 22.7 + - - +
286D GLN* 2.6 40.3 + - - +
290D GLU* 4.6 17.5 - - - +
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Residues in contact with ASP 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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150D TYR* 3.6 22.8 + - + -
240D ALA 2.7 20.5 + - - +
241D ARG* 3.4 7.9 - - - +
243D ARG* 1.3 71.0 - - - +
245D LEU* 1.3 68.0 + - - +
247D ALA* 2.9 9.7 + - - +
248D GLN* 2.9 44.8 + - - +
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Residues in contact with LEU 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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150D TYR* 4.0 27.6 - - + -
223D PHE* 4.8 10.0 - - + -
225D ILE* 3.5 39.9 - - + -
230D PHE* 5.4 5.8 - - + -
241D ARG 2.7 21.6 + - - +
242D VAL* 3.6 9.2 - - + +
243D ARG 3.4 0.2 - - - -
244D ASP* 1.3 74.7 + - - +
246D PHE* 1.3 85.4 + - + +
248D GLN* 3.2 4.7 + - - +
249D ALA* 2.9 23.9 + - - +
257D VAL* 4.1 23.7 - - + +
259D ILE* 4.9 8.1 - - + -
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Residues in contact with PHE 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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242D VAL* 3.2 23.0 + - + +
243D ARG 4.2 0.4 - - - +
245D LEU* 1.3 101.8 - - + +
247D ALA* 1.3 65.7 + - - +
249D ALA* 3.5 11.7 - - + +
250D LYS* 3.0 38.1 + - - +
257D VAL* 5.2 3.1 - - + -
259D ILE* 5.2 1.6 - - + -
287D LEU* 4.0 17.0 - - + -
290D GLU* 3.6 38.6 - - + +
291D MET* 3.2 36.8 - - + -
294D PHE* 3.8 24.5 - + + -
300D ILE* 5.4 3.1 - - + -
302D VAL* 4.0 15.7 - - + -
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Residues in contact with ALA 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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243D ARG 3.0 14.6 + - - +
244D ASP* 2.9 14.2 + - - +
246D PHE* 1.3 80.0 - - - +
248D GLN* 1.3 67.5 + - - +
250D LYS* 3.5 8.3 + - - +
251D ALA* 3.4 19.2 + - - +
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Residues in contact with GLN 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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150D TYR* 3.4 31.8 - - + +
223D PHE* 4.3 11.4 - - + -
244D ASP* 2.9 38.0 + - - +
245D LEU 3.5 6.3 - - - +
247D ALA* 1.3 80.7 - - - +
249D ALA* 1.3 64.6 - - - +
251D ALA* 3.2 7.2 + - - +
252D HIS* 2.9 41.6 + - - +
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Residues in contact with ALA 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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223D PHE* 4.2 12.1 - - + -
245D LEU 2.9 13.3 + - - +
246D PHE* 3.5 16.8 - - + +
247D ALA 3.2 0.2 - - - -
248D GLN* 1.3 77.6 - - - +
250D LYS* 1.3 62.3 + - - +
252D HIS 3.2 1.7 + - - -
253D ALA* 3.0 20.8 + - - +
255D CYS* 3.6 12.5 - - - -
257D VAL* 4.0 25.6 - - + -
300D ILE* 4.1 15.8 - - + +
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Residues in contact with LYS 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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246D PHE* 3.0 26.6 + - + +
247D ALA* 4.0 7.2 - - - +
248D GLN 3.3 0.2 - - - -
249D ALA* 1.3 76.3 - - - +
251D ALA* 1.3 60.5 + - - +
252D HIS 3.5 0.5 + - - -
253D ALA* 3.7 14.1 + - - +
290D GLU* 5.0 8.5 + - - +
293D GLY 4.3 15.4 + - - -
294D PHE* 3.8 25.0 - - + +
295D ASP 5.6 0.4 - - - +
298D GLU* 4.8 7.2 - - + +
300D ILE* 4.0 17.5 - - + -
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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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247D ALA 3.4 11.7 + - - +
248D GLN* 3.5 16.6 - - - +
249D ALA 3.1 0.6 - - - -
250D LYS* 1.3 80.9 - - - +
252D HIS* 1.3 66.6 + - + +
253D ALA 3.5 0.8 - - - +
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Residues in contact with HIS 252 (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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150D TYR 5.3 1.8 - - - -
151D LYS* 6.5 0.2 - - + -
152D PRO* 3.6 29.2 - - + +
221D PRO* 4.1 19.2 - - + +
223D PHE* 3.9 22.5 - + + -
248D GLN* 2.9 40.3 + - + +
249D ALA 3.2 3.3 + - - +
251D ALA* 1.3 85.4 - - + +
253D ALA* 1.3 67.4 + - - +
254D PRO* 3.0 12.9 - - - +
255D CYS* 4.5 1.1 - - + -
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Residues in contact with ALA 253 (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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249D ALA 3.0 12.2 + - - +
250D LYS 3.7 11.2 + - - +
251D ALA 3.5 1.9 - - - +
252D HIS* 1.3 79.8 - - - +
254D PRO* 1.3 66.9 - - + +
255D CYS 4.0 1.3 - - - +
298D GLU* 3.2 47.3 - - + +
300D ILE* 4.2 9.0 - - + -
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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