Contacts of the helix formed by residues 275 - 284 (chain N) in PDB entry 1CZA
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 275 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28N ALA* 4.1 24.5 - - + +
29N MET* 3.4 15.2 - - + +
273N ILE 3.8 9.0 - - - +
274N ARG* 1.3 75.6 - - - +
276N GLU* 1.4 64.7 + - - +
277N PHE* 3.1 29.2 + - + -
278N ASP* 2.7 28.0 + - - +
279N ARG* 3.0 32.0 + - - +
381N ARG* 4.0 8.3 - - - +
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Residues in contact with GLU 276 (chain N).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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275N THR* 1.4 74.2 - - - +
277N PHE* 1.4 88.2 + - + +
279N ARG* 3.2 16.0 + - - +
280N ALA* 3.0 23.3 + - - +
312N LYS* 3.2 41.8 + - - +
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Residues in contact with PHE 277 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25N TYR* 4.6 10.8 - + - -
26N LEU* 3.9 21.3 - - + -
29N MET* 3.5 20.2 - - + -
275N THR* 3.1 17.8 + - + +
276N GLU* 1.4 97.9 - - + +
278N ASP* 1.3 56.6 + - - +
280N ALA* 3.3 6.7 + - + +
281N ILE* 2.9 29.6 + - - +
305N LEU* 3.6 13.5 - - + +
308N LEU* 3.8 17.8 - - + +
309N ILE* 3.6 39.7 - - + -
312N LYS* 3.8 29.2 - - + -
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Residues in contact with ASP 278 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29N MET* 4.9 0.2 - - - -
274N ARG* 3.2 29.9 + - + +
275N THR* 2.7 37.6 + - - +
277N PHE* 1.3 75.0 - - - +
279N ARG* 1.4 64.6 + - - +
281N ILE* 3.3 10.3 - - - +
282N ASP* 3.0 19.2 + - - +
295N LYS* 4.7 1.5 - - - +
296N MET* 3.5 14.6 - - + +
305N LEU* 3.6 11.0 - - - +
381N ARG* 2.8 41.5 + - - -
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Residues in contact with ARG 279 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271N GLU* 2.8 51.5 + - - +
274N ARG* 3.4 33.7 + - - +
275N THR* 3.0 29.6 + - - +
276N GLU* 3.6 13.3 - - - +
278N ASP* 1.4 77.7 - - - +
280N ALA* 1.3 55.2 + - - +
282N ASP* 3.8 2.2 - - - +
283N ALA* 2.9 30.1 + - - +
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Residues in contact with ALA 280 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276N GLU 3.0 16.2 + - - +
277N PHE* 3.6 7.0 - - + +
278N ASP 3.3 0.2 - - - -
279N ARG* 1.3 74.2 - - - +
281N ILE* 1.3 65.0 + - - +
282N ASP 3.3 0.2 + - - -
283N ALA* 3.3 5.0 + - - -
284N TYR* 3.2 32.5 + - + +
308N LEU* 4.2 20.4 - - + -
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Residues in contact with ILE 281 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277N PHE 2.9 15.9 + - - +
278N ASP* 3.3 13.2 - - - +
280N ALA* 1.3 77.5 - - - +
282N ASP* 1.3 64.7 + - - +
284N TYR* 3.6 3.4 + - - +
285N SER* 3.3 20.7 + - - -
295N LYS* 4.7 17.0 - - + +
301N TYR* 3.5 48.0 - - + +
304N GLU* 3.3 32.8 - - + -
305N LEU* 3.7 18.8 - - + +
308N LEU* 3.9 11.3 - - + +
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Residues in contact with ASP 282 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274N ARG* 3.6 13.6 + - - +
278N ASP 3.0 19.7 + - - +
279N ARG* 3.8 2.9 - - - +
281N ILE* 1.3 75.4 - - - +
283N ALA* 1.3 66.0 + - - +
285N SER* 2.7 23.0 + - - -
288N PRO* 3.5 6.2 - - - +
289N GLY* 2.8 38.1 + - - -
292N LEU* 3.4 16.6 - - + +
295N LYS* 2.8 31.2 + - + -
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Residues in contact with ALA 283 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279N ARG 2.9 18.3 + - - +
280N ALA* 3.3 6.0 + - - +
282N ASP* 1.3 79.0 - - - +
284N TYR* 1.3 73.8 + - + +
285N SER 3.5 0.9 + - - +
288N PRO* 3.6 21.5 - - - +
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Residues in contact with TYR 284 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280N ALA* 3.2 22.0 + - + +
281N ILE* 3.8 4.0 - - - +
283N ALA* 1.3 87.8 - - + +
285N SER* 1.4 63.4 + - - +
331N ARG* 3.5 56.0 - - - +
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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