Contacts of the helix formed by residues 226 - 238 (chain A) in PDB entry 2EZT
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 ALA 226 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223A ALA* 2.9 16.5 + - + +
225A LYS* 1.3 78.4 - - - +
227A GLY* 1.3 60.2 + - - +
228A LYS 3.2 2.7 - - - -
229A GLU* 3.2 12.0 + - + +
230A LEU* 2.8 31.4 + - - +
326A ALA 4.5 0.7 - - - -
327A GLN* 3.6 24.5 - - + +
330A LEU* 3.5 27.4 - - + -
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Residues in contact with GLY 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223A ALA 3.9 2.8 + - - -
224A ARG 4.6 1.6 + - - -
225A LYS 3.6 2.2 - - - -
226A ALA* 1.3 75.6 - - - +
228A LYS* 1.3 57.1 + - - +
230A LEU* 4.2 3.1 - - - -
231A GLU* 3.0 31.7 + - - +
250A ILE* 3.5 36.1 - - - +
251A VAL* 3.7 6.0 - - - +
409A PRO* 6.0 0.9 - - - -
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Residues in contact with LYS 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226A ALA 3.2 0.6 - - - -
227A GLY* 1.3 75.9 - - - +
229A GLU* 1.3 70.5 + - + +
231A GLU* 3.4 4.0 + - - +
232A GLN* 2.9 35.8 + - + +
334A LEU* 5.7 0.2 - - - -
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Residues in contact with GLU 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225A LYS 4.0 2.4 - - - +
226A ALA* 3.3 23.1 - - + +
228A LYS* 1.3 86.3 - - + +
230A LEU* 1.3 58.6 + - - +
232A GLN* 3.9 0.7 - - - +
233A LEU* 2.9 36.5 + - - +
327A GLN* 3.5 30.2 + - - +
330A LEU* 3.9 22.4 - - + +
331A ALA* 4.0 27.6 - - + +
334A LEU* 4.3 16.7 - - + +
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Residues in contact with LEU 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217A ILE* 3.9 21.1 - - + -
219A TYR* 3.7 52.9 - - + -
223A ALA* 4.0 9.4 - - + +
226A ALA 2.8 31.3 + - - +
227A GLY* 3.7 3.6 - - - +
229A GLU* 1.3 71.7 - - - +
231A GLU* 1.3 58.8 + - - +
233A LEU* 3.7 5.8 - - - +
234A SER* 3.0 28.9 + - - -
241A LEU* 3.7 11.4 - - + +
250A ILE* 4.0 12.3 - - + -
251A VAL* 3.9 8.1 - - + -
283A VAL* 4.9 0.9 - - + -
330A LEU* 3.7 24.5 - - + -
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Residues in contact with GLU 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227A GLY 3.0 17.3 + - - +
228A LYS* 4.0 3.8 - - - +
230A LEU* 1.3 76.9 - - - +
232A GLN* 1.3 58.3 + - - +
234A SER* 3.5 2.3 + - - -
235A LYS* 3.0 54.9 + - + +
241A LEU* 4.3 7.0 - - - -
251A VAL* 3.5 21.1 - - + +
252A ALA* 4.4 8.3 + - - +
255A TYR* 3.7 34.7 - - + +
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Residues in contact with GLN 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228A LYS* 2.9 22.1 + - + +
231A GLU* 1.3 73.0 - - - +
233A LEU* 1.3 60.8 + - - +
235A LYS* 4.0 22.9 + - - +
236A THR* 2.8 60.3 + - - +
334A LEU* 3.9 27.6 - - + -
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Residues in contact with LEU 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209A LEU* 5.7 1.8 - - + -
217A ILE* 4.4 17.0 - - + -
229A GLU 2.9 21.0 + - - +
230A LEU* 3.7 5.6 - - + +
232A GLN* 1.3 76.9 - - - +
234A SER* 1.3 56.7 + - - +
236A THR* 4.6 0.4 - - - -
237A LEU* 2.9 60.9 + - + +
281A LEU* 5.7 1.3 - - + -
330A LEU* 3.7 45.3 - - + +
333A ILE* 3.9 15.7 - - + -
334A LEU* 3.8 33.8 - - + +
337A VAL* 4.3 2.5 - - + -
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Residues in contact with SER 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217A ILE* 4.6 2.0 - - - +
230A LEU 3.0 18.3 + - - -
231A GLU 3.6 3.1 - - - -
233A LEU* 1.3 75.4 - - - +
235A LYS* 1.3 58.4 + - - +
238A LYS* 2.8 26.9 + - - -
239A ILE* 2.7 35.3 + - - +
241A LEU* 3.6 17.4 - - - +
255A TYR* 2.5 30.1 + - - -
257A ALA* 3.9 1.4 - - - +
346A TRP* 3.8 6.4 - - - -
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Residues in contact with LYS 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231A GLU* 3.0 46.2 + - + +
232A GLN* 3.8 23.5 + - - +
234A SER* 1.3 75.1 - - - +
236A THR* 1.3 52.9 + - - +
238A LYS* 2.7 37.9 + - - +
255A TYR* 3.5 27.4 - - + +
256A PRO* 6.0 0.2 - - - -
339A GLU* 4.5 1.2 - - - +
346A TRP* 4.7 5.3 - - + -
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Residues in contact with THR 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232A GLN* 2.8 47.7 + - - +
233A LEU 4.1 1.8 - - - -
235A LYS* 1.3 72.4 - - - +
237A LEU* 1.3 61.1 + - + +
238A LYS* 3.2 8.1 + - - -
334A LEU* 4.2 7.6 - - + +
337A VAL* 4.4 14.8 - - + +
338A SER* 3.6 32.3 - - - +
339A GLU* 3.7 14.3 + - - +
340A ARG 3.0 26.9 + - - -
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Residues in contact with LEU 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A THR* 5.8 0.2 - - + -
209A LEU* 4.5 10.3 - - + -
210A LEU* 3.5 31.0 - - + -
217A ILE* 5.7 0.2 - - + -
233A LEU* 2.9 42.1 + - + +
236A THR* 1.3 76.6 - - + +
238A LYS* 1.3 65.8 + - - +
239A ILE* 3.6 26.2 - - + -
333A ILE* 5.0 1.8 - - + -
337A VAL* 3.9 31.4 - - + -
338A SER 3.9 13.5 - - - +
340A ARG* 2.7 41.4 + - + +
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Residues in contact with LYS 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215A PRO* 5.1 0.7 - - - +
234A SER 2.8 9.9 + - - -
235A LYS 2.7 23.4 + - - +
236A THR 3.2 7.9 + - - -
237A LEU* 1.3 80.9 - - - +
239A ILE* 1.3 59.0 + - - +
240A PRO* 3.8 3.3 - - - +
339A GLU* 2.7 28.9 + - - -
340A ARG* 2.9 20.2 + - - +
341A GLU* 3.4 26.0 - - - +
342A SER* 3.8 10.8 - - - +
343A THR* 4.5 6.9 + - + +
345A TRP* 5.0 2.9 - - - -
346A TRP* 3.1 61.5 - - + +
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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