Contacts of the helix formed by residues 347 - 359 (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 GLU 347 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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344N LYS* 3.3 41.3 - - + +
345N ASN* 4.1 0.7 + - - +
346N LYS* 1.3 95.3 + - + +
348N GLY* 1.3 65.1 + - - +
349N LEU 3.4 2.5 - - - -
350N HIS* 3.0 18.6 + - + +
351N ASN* 2.8 37.7 + - - +
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Residues in contact with GLY 348 (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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341N ALA 3.6 11.4 - - - -
342N ILE* 3.1 26.8 - - - +
344N LYS 3.0 18.2 + - - -
345N ASN 4.7 0.2 + - - -
346N LYS 3.5 1.2 - - - -
347N GLU* 1.3 76.9 - - - +
349N LEU* 1.3 56.5 + - - +
351N ASN* 3.1 3.5 + - - +
352N ALA* 2.8 29.0 + - - +
372N GLN* 4.2 2.7 - - - -
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Residues in contact with LEU 349 (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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346N LYS 5.0 2.3 + - - +
347N GLU 3.4 0.6 - - - -
348N GLY* 1.3 73.6 - - - +
350N HIS* 1.3 56.9 + - - +
352N ALA* 3.3 5.4 + - + +
353N LYS* 3.0 26.9 + - - +
368N CYS* 3.5 39.7 - - + +
369N VAL* 3.8 22.4 - - + +
372N GLN* 3.6 35.1 - - + +
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Residues in contact with HIS 350 (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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346N LYS 5.5 1.1 + - - +
347N GLU* 3.0 20.3 + - + +
349N LEU* 1.3 79.2 - - - +
351N ASN* 1.3 78.6 + - - +
353N LYS* 3.1 17.6 + - - +
354N GLU* 3.0 49.0 + - + +
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Residues in contact with ASN 351 (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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341N ALA* 2.9 42.9 + - + +
344N LYS* 4.3 2.4 - - - +
347N GLU* 2.8 40.1 + - - +
348N GLY 3.5 6.1 - - - +
350N HIS* 1.3 85.4 - - - +
352N ALA* 1.3 65.4 + - - +
354N GLU* 3.3 12.1 + - - +
355N ILE* 2.9 37.3 + - + +
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Residues in contact with ALA 352 (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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342N ILE* 3.7 30.6 - - + +
348N GLY 2.8 16.5 + - - +
349N LEU* 3.3 12.1 - - + +
351N ASN* 1.3 72.5 - - - +
353N LYS* 1.3 56.1 + - - +
355N ILE* 4.5 0.2 - - - -
356N LEU* 2.7 44.5 + - + +
368N CYS* 4.0 28.9 - - + +
371N VAL* 5.3 0.7 - - + -
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Residues in contact with LYS 353 (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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349N LEU 3.0 12.2 + - - +
350N HIS* 3.1 13.7 + - - +
352N ALA* 1.3 78.0 - - - +
354N GLU* 1.3 55.9 + - + +
356N LEU 3.8 0.2 - - - -
357N THR* 2.6 46.1 + - - +
363N PRO* 3.0 32.0 + - + +
364N SER* 4.3 4.2 - - - +
365N ASP* 3.7 25.3 + - - +
368N CYS* 3.5 13.2 - - - -
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Residues in contact with GLU 354 (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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350N HIS* 3.0 49.2 + - + +
351N ASN* 3.7 12.3 - - - +
353N LYS* 1.3 72.5 - - + +
355N ILE* 1.3 69.3 + - + +
357N THR* 3.3 7.5 + - - +
358N ARG* 3.0 37.4 + - - +
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Residues in contact with ILE 355 (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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334N PHE* 3.8 31.4 - - + -
338N ASP* 3.8 32.5 - - + +
341N ALA* 4.2 7.2 - - + -
342N ILE* 3.7 24.5 - - + -
351N ASN* 2.9 31.5 + - + +
352N ALA* 3.8 3.8 - - - +
354N GLU* 1.3 80.2 - - + +
356N LEU* 1.3 65.3 + - + +
358N ARG* 3.2 36.0 + - - +
359N LEU* 3.4 14.9 + - + +
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Residues in contact with LEU 356 (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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310N LEU* 4.3 5.4 - - + -
320N PHE* 4.1 20.0 - - + -
334N PHE* 4.5 7.0 - - + -
342N ILE* 5.5 0.2 - - + -
352N ALA* 2.7 30.1 + - + +
355N ILE* 1.3 69.9 - - + +
357N THR* 1.3 56.1 + - - +
359N LEU* 2.6 54.3 + - + +
361N VAL* 3.7 9.7 + - + +
363N PRO* 3.5 30.5 - - + -
367N ASP 4.4 6.1 - - - +
368N CYS* 4.4 6.5 - - - -
371N VAL* 3.8 43.1 - - + -
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Residues in contact with THR 357 (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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353N LYS* 2.6 38.7 + - - +
354N GLU* 3.5 7.4 - - - +
356N LEU* 1.3 71.9 - - - +
358N ARG* 1.3 62.6 + - + +
360N GLY* 3.1 14.0 + - - -
361N VAL 3.2 18.9 - - - +
362N GLU* 5.9 0.4 - - - -
363N PRO* 3.5 14.5 - - - +
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Residues in contact with ARG 358 (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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327N GLU* 4.8 8.5 - - - +
338N ASP* 4.8 5.1 + - - -
354N GLU* 3.0 25.3 + - - +
355N ILE* 3.2 34.9 + - - +
357N THR* 1.3 77.0 - - + +
359N LEU* 1.3 62.5 + - + +
360N GLY* 3.1 2.7 + - - -
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Residues in contact with LEU 359 (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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307N ARG* 6.2 0.7 - - + -
310N LEU* 5.1 1.1 - - + -
320N PHE* 5.5 1.1 - - + -
325N THR* 2.4 32.0 + - - +
327N GLU* 3.3 14.4 - - + +
328N LEU* 3.7 34.5 - - + +
333N LYS* 4.1 32.3 - - + +
334N PHE* 4.3 20.9 - - + -
355N ILE* 3.4 15.7 + - + +
356N LEU* 2.6 45.7 + - + +
358N ARG* 1.3 73.1 - - + +
360N GLY* 1.3 48.6 + - - -
361N VAL* 3.2 10.3 - - + +
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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