Contacts of the helix formed by residues 325 - 335 (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 ASP 325 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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194A LEU* 4.0 29.6 - - + +
195A PRO 3.0 17.0 + - - +
225A LYS* 4.3 12.5 + - - -
307A ILE* 4.3 5.8 - - - +
324A ALA* 1.3 68.9 - - - +
326A ALA* 1.3 56.5 + - - +
327A GLN* 3.3 11.5 + - - +
328A LYS* 2.9 42.6 + - + +
329A THR* 2.7 36.7 + - - -
1612A FAD 3.0 31.1 + - - -
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Residues in contact with ALA 326 (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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222A GLY 3.5 15.9 - - - +
223A ALA* 3.9 11.7 - - + -
226A ALA* 5.1 0.2 - - + -
283A VAL* 3.7 21.1 - - + -
305A ILE* 4.1 10.5 - - - -
324A ALA 3.4 0.2 + - - -
325A ASP* 1.3 70.8 - - - +
327A GLN* 1.3 60.8 + - - +
329A THR* 3.3 1.2 + - - -
330A LEU* 2.9 37.5 + - + +
1612A FAD 2.9 28.7 + - + +
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Residues in contact with GLN 327 (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* 3.4 49.9 + - + +
226A ALA* 3.6 19.0 - - + +
229A GLU* 3.5 22.9 + - - +
325A ASP* 3.3 12.2 + - - +
326A ALA* 1.3 76.0 - - - +
328A LYS* 1.3 67.1 + - - +
330A LEU* 3.8 0.5 - - - +
331A ALA* 2.8 36.9 + - - +
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Residues in contact with LYS 328 (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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194A LEU* 3.4 37.9 + - - +
195A PRO 4.2 6.7 - - - +
196A GLU* 3.3 36.0 + - - +
197A PRO* 3.9 15.6 - - + +
325A ASP* 2.9 31.4 + - + +
326A ALA 3.4 0.2 - - - -
327A GLN* 1.3 80.5 + - - +
329A THR* 1.3 61.9 + - - +
331A ALA* 3.8 4.5 - - - +
332A ALA* 3.1 23.7 + - - +
195B PRO* 4.9 5.5 - - - +
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Residues in contact with THR 329 (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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197A PRO* 3.6 7.9 - - - +
202A VAL* 3.9 22.9 - - + -
205A LEU* 5.1 0.9 - - + -
305A ILE* 3.4 37.6 - - + +
322A VAL* 4.1 7.6 - - + -
324A ALA* 3.5 19.9 - - - +
325A ASP 2.7 22.8 + - - -
326A ALA 3.8 3.4 - - - -
327A GLN 3.2 0.2 - - - -
328A LYS* 1.3 74.6 - - - +
330A LEU* 1.3 60.9 + - - +
332A ALA* 3.0 5.5 + - - +
333A ILE* 3.0 30.4 + - + +
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Residues in contact with LEU 330 (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* 5.1 1.1 - - + -
223A ALA* 4.6 2.2 - - + -
226A ALA* 3.5 25.1 - - + +
229A GLU* 3.9 15.4 - - + +
230A LEU* 3.7 29.6 - - + -
233A LEU* 3.7 25.1 - - + +
281A LEU* 4.3 22.2 - - + -
283A VAL* 4.2 20.6 - - + -
305A ILE* 4.5 6.5 - - + -
326A ALA 2.9 25.4 + - - +
327A GLN 4.0 1.1 - - - +
329A THR* 1.3 73.9 - - - +
331A ALA* 1.3 59.9 + - - +
333A ILE* 3.4 4.7 + - + +
334A LEU* 3.0 29.6 + - - +
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Residues in contact with ALA 331 (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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229A GLU* 4.0 21.0 - - + +
327A GLN* 2.8 24.6 + - - +
328A LYS* 3.8 6.3 - - - +
330A LEU* 1.3 75.7 - - - +
332A ALA* 1.3 62.4 + - - +
334A LEU* 3.3 6.1 + - - +
335A ALA* 3.1 25.1 + - - +
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Residues in contact with ALA 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A PRO* 4.4 12.8 - - + -
202A VAL* 4.1 13.2 - - + -
328A LYS 3.1 14.9 + - - +
329A THR 3.0 10.8 + - - +
331A ALA* 1.3 74.1 - - - +
333A ILE* 1.3 63.6 + - - +
335A ALA* 3.5 13.2 + - - +
336A GLN* 3.1 21.7 + - - +
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Residues in contact with ILE 333 (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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202A VAL* 3.7 15.5 - - + -
205A LEU* 3.4 26.2 - - + -
206A THR* 3.5 26.0 - - + +
209A LEU* 5.0 5.8 - - + -
233A LEU* 3.9 18.8 - - + -
237A LEU* 5.0 4.5 - - + -
281A LEU* 4.2 16.8 - - + -
305A ILE* 4.4 10.1 - - + -
329A THR* 3.0 20.5 + - + +
330A LEU* 3.7 15.0 - - + +
331A ALA 3.4 0.2 - - - -
332A ALA* 1.3 72.1 - - - +
334A LEU* 1.3 67.7 + - - +
336A GLN* 3.1 24.5 + - - +
337A VAL* 3.5 10.2 + - + +
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Residues in contact with LEU 334 (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* 6.6 0.4 - - + -
229A GLU* 4.3 23.1 - - + +
232A GLN* 3.9 38.6 - - + -
233A LEU* 3.8 28.5 - - + +
236A THR* 4.2 10.5 - - + +
330A LEU 3.0 16.4 + - - +
331A ALA* 3.3 5.6 + - - +
333A ILE* 1.3 77.6 - - - +
335A ALA* 1.3 60.5 + - - +
336A GLN 3.3 0.9 + - - -
337A VAL* 3.4 25.6 + - + +
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Residues in contact with ALA 335 (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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331A ALA 3.1 16.7 + - - +
332A ALA* 3.8 8.7 - - - +
333A ILE 3.2 0.4 - - - -
334A LEU* 1.3 75.1 - - - +
336A GLN* 1.3 58.4 + - - +
337A VAL 3.6 1.5 - - - +
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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