Contacts of the helix formed by residues 294 - 306 (chain E) in PDB entry 2X86
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 294 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171E TYR* 3.6 1.2 + - - -
211E PHE 5.5 0.7 - - - -
237E THR* 5.3 0.4 - - - -
239E ARG* 3.4 30.7 - - - +
241E GLU* 4.2 7.0 - - - -
292E PHE 3.4 1.7 + - - +
293E LYS* 1.3 75.2 - - - +
295E VAL* 1.3 59.5 + - - +
296E ALA* 3.5 9.7 + - - +
297E GLU* 2.7 39.6 + - - +
298E GLY* 2.8 27.4 + - - -
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Residues in contact with VAL 295 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171E TYR* 3.8 8.5 - - - +
211E PHE* 3.6 44.9 + - + +
241E GLU* 3.1 33.3 + - + +
245E ALA* 4.0 10.5 - - + +
246E VAL* 3.7 33.4 - - + +
249E ALA* 4.5 2.2 - - + -
294E THR* 1.3 72.6 - - - +
296E ALA* 1.3 67.6 + - - +
299E VAL* 2.9 38.0 + - + +
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Residues in contact with ALA 296 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241E GLU* 5.1 1.8 + - - -
249E ALA* 4.3 13.3 - - + +
294E THR* 3.3 9.0 + - - +
295E VAL* 1.3 81.7 - - - +
297E GLU* 1.3 54.5 + - + +
300E THR* 2.5 36.4 + - - +
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Residues in contact with GLU 297 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292E PHE 4.2 1.6 - - - +
293E LYS* 3.3 21.0 - - + -
294E THR* 2.7 45.7 + - - +
296E ALA* 1.3 80.2 - - + +
298E GLY* 1.3 64.5 + - - +
300E THR* 3.3 6.5 + - - -
301E GLU* 3.0 24.8 + - - +
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Residues in contact with GLY 298 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171E TYR* 3.2 22.4 - - - -
213E TYR* 3.7 17.9 - - - -
293E LYS* 4.2 8.6 - - - +
294E THR 2.8 14.4 + - - -
297E GLU* 1.3 75.0 - - - +
299E VAL* 1.3 54.9 + - - +
301E GLU* 3.3 6.1 + - - +
302E TYR* 2.9 30.1 + - - +
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Residues in contact with VAL 299 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171E TYR* 3.6 23.7 + - + -
185E ALA* 4.7 4.5 - - + -
246E VAL* 4.2 15.9 - - + +
249E ALA* 3.7 18.4 - - + -
250E THR* 3.4 28.3 - - - +
295E VAL* 2.9 39.2 + - + +
298E GLY* 1.3 70.8 - - - -
300E THR* 1.3 58.4 + - - +
302E TYR* 3.3 5.3 + - - +
303E MET* 2.8 46.2 + - + +
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Residues in contact with THR 300 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249E ALA* 3.8 24.7 - - + +
252E ALA* 5.6 2.2 - - + -
253E TYR* 4.3 22.4 - - + +
296E ALA 2.5 26.6 + - - +
297E GLU* 3.3 8.0 + - - -
299E VAL* 1.3 78.3 - - - +
301E GLU* 1.3 61.1 + - - +
303E MET* 3.1 6.3 + - - +
304E ALA* 3.0 23.7 + - - +
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Residues in contact with GLU 301 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213E TYR* 3.3 23.8 + - - +
293E LYS* 2.9 39.4 + - - +
297E GLU 3.0 18.5 + - - +
298E GLY 3.6 4.3 - - - +
300E THR* 1.3 76.5 - - - +
302E TYR* 1.3 62.9 + - - +
304E ALA* 3.4 8.0 + - + +
305E TRP* 3.1 20.7 + - + +
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Residues in contact with TYR 302 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171E TYR* 4.0 11.0 - + - -
172E GLY* 3.0 35.3 + - - -
173E PRO* 3.3 21.9 - - + +
174E ARG 5.2 0.2 + - - -
175E GLU* 2.6 34.2 + - - +
183E SER* 3.9 8.7 - - - -
185E ALA* 4.0 14.6 - - + -
186E PHE* 3.3 19.9 - - - -
213E TYR* 4.1 11.6 - - + -
298E GLY 2.9 16.7 + - - +
299E VAL* 3.4 5.8 - - - +
301E GLU* 1.3 74.6 - - - +
303E MET* 1.3 62.4 + - + +
305E TRP* 3.1 6.5 + + - +
306E LEU* 2.8 55.9 + - + +
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Residues in contact with MET 303 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185E ALA* 3.6 33.9 - - + +
189E ASN* 3.6 28.5 - - + +
250E THR* 3.6 27.6 - - + +
253E TYR* 3.5 37.4 + - + -
254E HIS* 3.9 8.5 - - - -
299E VAL* 2.8 37.5 + - + +
300E THR* 3.1 4.2 + - - +
302E TYR* 1.3 75.4 - - + +
304E ALA* 1.3 61.1 + - - +
306E LEU* 3.3 10.6 + - + -
307E ASN* 2.6 29.2 + - - +
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Residues in contact with ALA 304 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253E TYR* 3.4 21.4 + - + +
300E THR 3.0 12.0 + - - +
301E GLU* 3.5 11.2 - - + +
303E MET* 1.3 77.6 - - - +
305E TRP* 1.3 62.3 + - - +
307E ASN 3.1 21.3 + - - -
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Residues in contact with TRP 305 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173E PRO* 3.6 49.0 - - + +
174E ARG* 4.0 30.7 - - + +
213E TYR* 5.6 0.9 - - - +
301E GLU* 3.1 9.8 + - + +
302E TYR* 3.1 8.8 + + - +
304E ALA* 1.3 79.6 - - - +
306E LEU* 1.3 87.4 + - + +
307E ASN* 3.1 3.3 + - - +
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Residues in contact with LEU 306 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186E PHE* 4.1 24.0 - - + -
189E ASN* 3.5 38.9 + - + +
193E ASN* 5.1 1.2 + - - -
302E TYR* 2.8 53.9 + - + +
303E MET* 4.1 13.0 - - + -
304E ALA 3.2 0.4 - - - -
305E TRP* 1.3 91.7 - - + +
307E ASN* 1.3 75.7 + - - +
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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