Contacts of the helix formed by residues 234 - 246 (chain D) in PDB entry 3ITX
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 ASP 234 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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235B TRP* 2.8 31.0 + - - -
262B THR* 6.0 1.2 - - - +
267B ILE* 4.9 2.6 - - - +
220D HIS* 3.4 21.0 - - + +
232D VAL 3.7 0.4 - - - -
233D GLN* 1.3 98.9 + - + +
235D TRP* 1.3 65.8 + - + +
236D GLY 3.0 12.3 + - - -
237D THR* 3.1 10.6 + - - -
238D ASN 3.0 20.1 + - - -
258D HIS* 6.2 0.9 - - - +
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Residues in contact with TRP 235 (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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233B GLN* 4.2 5.4 - - - -
234B ASP* 2.7 28.8 + - - -
235B TRP* 6.3 0.2 - - - -
236B GLY* 3.6 19.2 - - - -
237B THR* 3.4 26.9 - - - -
240B LEU* 3.9 16.8 - - + -
220D HIS* 3.7 23.8 - - + +
234D ASP* 1.3 78.3 - - + +
236D GLY* 1.3 64.3 + - - +
238D ASN* 3.6 3.8 - - - +
239D TYR* 2.8 32.4 + + + +
258D HIS* 5.7 0.2 + - - -
267D ILE* 3.6 47.1 - - + +
270D ARG* 3.6 32.3 - - + -
271D LEU* 3.9 29.6 - - + +
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Residues in contact with GLY 236 (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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235B TRP* 3.7 18.1 - - - -
236B GLY* 4.1 21.5 - - - -
239B TYR* 6.0 0.2 - - - -
234D ASP* 3.0 7.9 + - - -
235D TRP* 1.3 82.4 - - - +
237D THR* 1.3 64.1 + - - +
239D TYR* 3.2 7.6 + - - +
240D LEU* 3.2 24.9 + - - +
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Residues in contact with THR 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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235B TRP* 3.4 7.1 - - - -
270B ARG* 3.1 20.6 + - - +
196D PHE* 3.6 27.6 - - + -
231D VAL 3.5 20.6 - - - +
232D VAL* 4.1 3.4 - - - -
233D GLN* 2.6 29.9 + - - -
234D ASP* 3.1 8.0 + - - -
236D GLY* 1.3 75.3 - - - +
238D ASN* 1.3 62.7 + - - +
240D LEU* 3.2 9.1 + - - +
241D ILE* 3.0 28.0 + - + +
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Residues in contact with ASN 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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218D SER* 2.5 50.7 + - - -
220D HIS* 3.0 34.3 + - + +
232D VAL* 4.4 3.8 - - + +
234D ASP 3.0 17.9 + - - +
235D TRP* 3.6 6.1 - - - +
237D THR* 1.3 77.7 - - - +
239D TYR* 1.3 62.5 + - - +
241D ILE* 3.2 8.7 + - - +
242D ALA 3.0 19.4 + - - -
251D CYS* 3.3 27.3 - - + +
252D LEU 3.8 2.0 + - - -
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Residues in contact with TYR 239 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B TYR* 4.4 22.0 - + - -
240B LEU* 3.4 32.5 - - + +
235D TRP* 2.8 29.6 + + + +
236D GLY* 3.2 7.2 + - - +
238D ASN* 1.3 75.0 - - - +
240D LEU* 1.3 63.2 + - + +
242D ALA* 3.3 0.6 + - - -
243D GLN* 2.8 65.6 + - + +
251D CYS* 3.8 8.0 - - - -
271D LEU* 4.6 7.6 - - + -
274D PHE* 3.9 32.2 - - + +
276D LYS* 3.9 26.5 - - + -
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Residues in contact with LEU 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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235B TRP* 4.0 28.7 - - + -
239B TYR* 3.4 45.3 - - + +
270B ARG* 4.6 3.8 - - - -
274B PHE* 3.6 44.2 - - + -
196D PHE* 4.3 11.0 - - + -
200D LEU* 5.2 0.2 - - - -
236D GLY 3.2 9.4 + - - +
237D THR* 3.2 9.8 + - - +
239D TYR* 1.3 81.0 - - + +
241D ILE* 1.3 56.2 + - - +
243D GLN* 4.0 3.4 - - + +
244D THR* 2.6 37.6 + - - -
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Residues in contact with ILE 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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196D PHE* 3.4 24.7 - - + -
199D TYR* 3.2 41.1 - - + +
200D LEU* 4.0 9.4 - - + -
218D SER* 3.8 14.8 - - - +
232D VAL* 3.8 24.2 - - + -
237D THR* 3.0 20.8 + - + +
238D ASN* 3.4 10.1 - - - +
239D TYR 3.1 0.2 - - - -
240D LEU* 1.3 73.8 - - - +
242D ALA* 1.3 62.1 + - - +
244D THR* 3.1 2.3 + - - -
245D LEU* 2.8 57.2 + - + +
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Residues in contact with ALA 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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218D SER* 5.0 1.3 - - - +
238D ASN 3.0 11.9 + - - +
239D TYR 3.9 1.8 - - - +
241D ILE* 1.3 80.4 - - - +
243D GLN* 1.3 63.0 + - - +
246D GLY 3.3 17.8 + - - +
249D ALA* 3.5 31.5 - - - +
250D GLN* 3.9 4.3 - - - +
251D CYS* 3.8 16.8 - - - -
276D LYS* 3.2 28.6 + - + -
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Residues in contact with GLN 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 TYR* 2.8 56.2 + - + +
240D LEU* 4.0 4.7 - - + +
242D ALA* 1.3 73.8 - - - +
244D THR* 1.3 63.2 + - - +
246D GLY* 4.0 6.2 + - - -
274D PHE 5.0 2.8 - - - +
276D LYS* 3.7 20.8 + - - +
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Residues in contact with THR 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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274B PHE* 4.7 15.1 - - - -
200D LEU* 4.5 24.8 - - + +
240D LEU* 2.6 24.0 + - - -
241D ILE* 3.6 4.9 - - - -
243D GLN* 1.3 80.7 - - - +
245D LEU* 1.3 67.7 + - + +
246D GLY* 3.6 0.3 + - - -
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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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200D LEU* 4.0 10.8 - - + +
203D MET* 3.7 24.0 - - + +
204D ALA* 3.7 35.2 - - + +
207D TYR* 3.6 27.5 - - + -
216D LEU* 4.0 19.7 - - + -
218D SER* 5.7 0.7 - - - +
241D ILE* 2.8 43.1 + - + +
244D THR* 1.3 80.7 - - + +
246D GLY* 1.3 58.5 + - - +
249D ALA* 3.6 18.6 - - + -
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Residues in contact with GLY 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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207D TYR* 3.4 5.4 - - - -
242D ALA 3.3 5.2 + - - +
243D GLN 4.0 4.9 + - - -
244D THR 3.5 2.7 - - - -
245D LEU* 1.3 81.4 - - - +
247D PRO* 1.3 71.1 - - - +
248D LYS 3.1 3.4 - - - -
249D ALA 2.9 19.0 + - - -
276D LYS* 3.0 16.5 + - - -
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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