Contacts of the helix formed by residues 282 - 293 (chain A) in PDB entry 2ZC1
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 GLN 282 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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246A SER* 3.9 14.6 - - - +
247A SER 3.4 14.6 - - - +
248A ARG 2.9 24.5 - - - +
249A ASP* 3.4 13.5 - - - +
250A ALA* 3.9 18.6 - - - +
251A ILE* 4.3 9.0 - - + +
277A THR* 4.4 1.1 - - - -
281A GLN* 1.3 82.7 + - - +
283A GLY* 1.3 66.0 + - - +
284A PRO 3.4 2.2 - - - -
285A GLN* 3.2 41.8 + - + +
286A GLN* 2.8 26.2 + - - +
313A TYR* 3.4 3.6 + - - -
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Residues in contact with GLY 283 (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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277A THR* 4.1 3.8 - - - +
281A GLN 3.3 1.2 + - - -
282A GLN* 1.3 71.8 - - - +
284A PRO* 1.3 67.8 - - - +
286A GLN* 3.3 2.6 + - - +
287A ALA* 3.1 22.3 + - - +
302A ILE* 4.0 22.1 - - - +
305A MET* 4.2 1.8 - - - -
313A TYR* 2.8 22.9 + - - -
317A THR* 3.7 12.4 - - - +
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Residues in contact with PRO 284 (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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283A GLY* 1.3 90.7 - - - +
285A GLN* 1.3 69.3 + - - +
287A ALA* 3.2 4.0 + - + +
288A GLU* 2.9 31.7 + - - +
313A TYR* 3.4 26.2 - - + +
316A GLU* 3.7 44.6 - - + +
317A THR* 3.4 22.7 - - - +
320A HIS* 3.8 7.0 + - - +
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Residues in contact with GLN 285 (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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251A ILE* 3.9 11.1 - - + +
282A GLN* 3.2 50.5 + - - +
283A GLY 3.2 0.2 - - - -
284A PRO* 1.3 87.4 - - - +
286A GLN* 1.3 56.9 + - - +
288A GLU* 3.9 5.9 - - - +
289A LEU* 3.0 31.4 + - - +
313A TYR* 5.5 0.2 - - - -
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Residues in contact with GLN 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A SER* 2.8 28.5 + - - +
251A ILE* 3.9 13.0 - - + -
259A PHE* 3.6 28.1 - - + -
275A THR* 2.6 27.4 + - - -
276A HIS 2.9 21.4 + - - -
277A THR* 3.6 10.8 - - - +
282A GLN 2.8 17.6 + - - +
283A GLY 3.6 3.8 - - - +
285A GLN* 1.3 75.4 - - - +
287A ALA* 1.3 59.5 + - - +
289A LEU* 3.4 1.1 + - - +
290A LEU* 2.9 36.7 + - + +
302A ILE* 3.6 16.6 - - + +
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Residues in contact with ALA 287 (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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283A GLY 3.1 11.0 + - - +
284A PRO 3.7 3.1 - - - +
286A GLN* 1.3 78.3 - - - +
288A GLU* 1.3 55.7 + - - +
290A LEU* 4.1 2.6 - - - +
291A THR* 2.7 38.7 + - - +
300A ILE* 5.7 0.2 - - - -
302A ILE* 4.1 8.2 - - + +
317A THR* 4.2 4.3 - - + +
320A HIS* 3.6 33.2 - - + -
322A VAL* 4.1 23.6 - - + -
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Residues in contact with GLU 288 (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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284A PRO 2.9 17.5 + - - +
285A GLN* 3.9 7.4 - - - +
287A ALA* 1.3 76.5 - - - +
289A LEU* 1.3 58.3 + - - +
291A THR* 3.2 4.8 + - - -
292A SER* 2.8 47.4 + - - +
320A HIS* 3.2 26.9 + - + +
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Residues in contact with LEU 289 (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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251A ILE* 3.8 16.6 - - + -
256A GLN* 3.9 32.1 - - - +
259A PHE* 3.8 32.8 - - + -
260A ARG* 5.8 1.1 - - + -
285A GLN 3.0 19.2 + - - +
286A GLN 3.8 3.1 - - - +
288A GLU* 1.3 79.9 - - - +
290A LEU* 1.3 61.2 + - - +
292A SER* 2.8 23.2 + - - +
293A LEU* 3.1 37.0 + - + +
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Residues in contact with LEU 290 (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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244A LEU* 3.7 25.8 - - + -
259A PHE* 3.7 42.8 - - + +
263A ALA* 4.7 5.8 - - + -
273A ILE* 4.3 18.6 - - + -
275A THR* 4.5 6.7 - - + -
286A GLN 2.9 22.8 + - - +
287A ALA 4.2 1.1 - - - +
289A LEU* 1.3 76.3 - - - +
291A THR* 1.3 60.9 + - - +
293A LEU* 3.3 10.3 + - + +
294A GLY 3.4 0.2 + - - -
295A ALA* 2.9 26.9 + - + +
300A ILE* 3.7 37.5 - - + -
302A ILE* 4.6 1.1 - - + -
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Residues in contact with THR 291 (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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287A ALA 2.7 25.8 + - - +
288A GLU* 3.2 13.0 + - - -
290A LEU* 1.3 76.7 - - - +
292A SER* 1.3 56.7 + - - +
294A GLY* 2.9 19.9 + - - -
295A ALA 3.7 12.7 - - - +
297A PRO* 4.0 31.6 - - + -
300A ILE* 4.4 6.3 - - + -
320A HIS* 4.1 18.1 + - + +
322A VAL* 4.4 3.4 - - + -
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Residues in contact with SER 292 (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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288A GLU* 2.8 31.5 + - - +
289A LEU* 2.8 27.0 + - - +
291A THR* 1.3 77.3 + - - +
293A LEU* 1.3 61.7 + - - +
294A GLY 3.1 3.0 + - - -
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Residues in contact with LEU 293 (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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259A PHE* 4.2 4.5 - - + +
260A ARG* 3.9 45.8 - - + +
263A ALA* 3.6 20.5 - - + +
267A ARG* 3.4 22.0 + - - -
289A LEU* 3.1 42.3 + - + +
290A LEU* 3.7 4.3 - - - +
291A THR 3.1 0.8 - - - -
292A SER* 1.3 79.8 - - - +
294A GLY* 1.3 58.2 + - - +
295A ALA 3.5 0.7 - - - -
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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