Contacts of the helix formed by residues 238 - 250 (chain D) in PDB entry 3FAA
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 GLU 238 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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215D ARG* 3.5 44.7 - - - +
216D PHE* 3.6 22.6 - - - +
234D PHE* 4.1 5.6 - - + -
235D SER* 2.6 21.8 + - - +
237D ARG* 1.3 91.8 + - + +
239D GLU* 1.3 63.1 + - - +
240D ARG* 3.2 4.5 + - - -
241D SER* 3.2 30.0 + - - +
242D TRP* 3.4 9.9 + - - +
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Residues in contact with GLU 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 SER* 3.3 16.2 + - - +
237D ARG 3.4 4.8 + - - +
238D GLU* 1.3 76.4 - - - +
240D ARG* 1.3 69.7 + - + +
242D TRP* 3.3 5.4 + - - +
243D PHE* 3.1 19.8 + - - +
276D LEU* 3.7 23.8 - - + -
173E GLU* 3.5 17.7 - - + +
174E GLY* 3.6 27.2 + - - +
225E ARG* 6.0 1.9 - - - -
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Residues in contact with ARG 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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237D ARG 5.2 2.6 + - - -
238D GLU* 3.2 1.5 - - - -
239D GLU* 1.3 85.6 - - + +
241D SER* 1.3 62.9 + - - +
243D PHE* 3.8 1.0 - - - +
244D ARG* 2.9 32.9 + - + +
174E GLY* 3.7 25.5 - - - +
176E THR* 4.3 18.0 - - + +
225E ARG 5.6 4.2 + - - -
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Residues in contact with SER 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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216D PHE* 5.2 5.1 - - - +
234D PHE* 4.1 15.5 - - - -
238D GLU* 3.2 29.6 + - - -
240D ARG* 1.3 77.6 - - - +
242D TRP* 1.3 57.8 + - - +
244D ARG* 3.7 5.1 - - - +
245D GLU* 2.9 34.2 + - - +
353D GLY* 4.3 10.9 - - - -
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Residues in contact with TRP 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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234D PHE* 3.8 33.1 - + + -
238D GLU 3.4 3.7 + - - +
239D GLU 3.3 10.1 + - - +
240D ARG 3.2 0.2 - - - -
241D SER* 1.3 78.5 - - - +
243D PHE* 1.3 86.7 + + - +
245D GLU* 3.0 3.8 + - - +
246D ALA* 2.8 28.6 + - + +
265D ALA* 4.6 7.6 - - + -
266D ASP* 3.9 24.7 - - - -
267D ASN* 3.9 22.9 - - + -
276D LEU* 3.5 42.6 - - + -
277D TRP 2.9 23.7 + - - +
278D LEU* 3.3 22.0 - - + +
172E SER* 4.2 17.9 - - - -
173E GLU* 3.8 22.2 - - + -
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Residues in contact with PHE 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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239D GLU 3.1 6.9 + - - +
240D ARG 3.8 3.4 - - - +
242D TRP* 1.3 89.3 - + - +
244D ARG* 1.3 61.3 + - + +
246D ALA* 3.1 5.4 + - + +
247D GLU* 2.7 67.3 + - + +
172E SER* 3.9 15.0 - - - -
173E GLU 3.3 26.5 - - - +
174E GLY 3.6 7.2 - - - -
175E THR* 3.3 39.5 - - + -
179E ASP* 3.4 24.9 - - + -
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Residues in contact with ARG 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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240D ARG* 2.9 22.8 + - + +
241D SER* 3.7 2.0 - - - +
243D PHE* 1.3 84.0 - - + +
245D GLU* 1.3 63.7 + - - +
247D GLU* 3.3 8.2 + - - +
248D ILE* 3.1 41.1 + - - +
353D GLY 3.6 26.4 + - - +
354D LEU 4.6 0.8 + - - -
355D ALA 3.0 19.6 + - - -
357D ARG* 4.7 2.8 - - - +
366D ASP* 2.6 41.6 + - - +
367D ILE* 3.0 30.4 - - - +
179E ASP* 3.2 25.6 + - - +
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Residues in contact with GLU 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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232D LYS* 2.7 32.7 + - - -
234D PHE* 3.8 7.8 - - - -
241D SER* 2.9 17.9 + - - +
242D TRP 3.6 2.5 - - - +
244D ARG* 1.3 76.3 - - - +
246D ALA* 1.3 64.3 + - - +
247D GLU 3.2 0.3 + - - -
248D ILE* 3.3 1.7 + - - +
249D TYR* 3.1 45.6 + - + -
278D LEU* 4.0 14.6 - - + -
351D ASP* 3.6 13.8 - - - +
352D LEU 3.9 12.1 - - - +
353D GLY* 3.7 24.0 + - - +
601D 55F 3.6 21.1 + - - +
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Residues in contact with ALA 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 TRP* 2.8 27.4 + - + +
243D PHE* 3.4 8.3 - - + +
245D GLU* 1.3 72.7 - - - +
247D GLU* 1.3 65.2 + - - +
249D TYR* 3.5 1.7 + - - +
250D GLN* 3.1 32.8 + - - +
262D PHE* 4.7 7.0 - - - -
265D ALA* 4.2 15.0 - - + -
278D LEU* 3.9 23.5 - - + +
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Residues in contact with GLU 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 PHE* 2.7 49.8 + - + +
244D ARG* 3.4 10.8 - - - +
246D ALA* 1.3 72.1 - - - +
248D ILE* 1.3 68.5 + - + +
250D GLN* 3.1 25.8 + - - +
251D THR* 3.9 2.3 + - - -
357D ARG* 3.1 34.4 + - - +
179E ASP* 3.9 6.6 - - - +
183E ASP* 2.9 29.5 - - - +
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Residues in contact with ILE 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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244D ARG* 3.1 57.4 + - - +
245D GLU 3.9 4.5 - - - +
247D GLU* 1.3 83.5 - - + +
249D TYR* 1.3 62.9 + - - +
251D THR* 2.8 28.2 + - - +
254D LEU* 3.1 9.8 - - + +
329D ILE* 4.5 11.2 - - + -
352D LEU* 3.5 40.4 - - + +
355D ALA* 4.0 16.4 - - + +
357D ARG* 4.4 17.7 - - + +
366D ASP* 4.2 7.6 - - - +
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Residues in contact with TYR 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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245D GLU* 3.1 55.8 + - + +
246D ALA 3.9 3.1 - - - +
247D GLU 3.3 0.2 - - - -
248D ILE* 1.3 76.0 - - - +
250D GLN* 1.3 57.9 + - - +
251D THR 3.1 5.5 + - - +
254D LEU* 3.9 20.7 - - + +
259D ILE* 4.6 6.2 - - + +
260D LEU* 3.4 33.4 - - + +
262D PHE* 3.5 45.5 - + + +
278D LEU* 5.6 0.2 - - + -
349D ILE 4.5 0.2 + - - -
350D ALA* 3.6 11.3 - - - -
351D ASP 3.4 21.8 + - - -
352D LEU* 4.0 25.6 - - + +
601D 55F 3.7 16.8 - - + +
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Residues in contact with GLN 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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192D GLY* 6.0 5.5 - - - -
195D LEU* 4.5 9.7 - - - +
198D GLN* 3.2 36.6 + - - +
246D ALA* 3.1 28.4 - - - +
247D GLU* 3.1 12.5 + - - +
248D ILE 3.1 0.6 - - - -
249D TYR* 1.3 74.9 - - - +
251D THR* 1.3 57.6 + - - +
252D VAL 4.1 0.9 + - - -
262D PHE* 3.6 22.7 - - + -
265D ALA* 4.5 4.5 - - - +
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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