Contacts of the helix formed by residues 335 - 343 (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 ASN 335 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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303N GLY* 3.7 5.1 - - - -
304N GLU 5.3 0.2 - - - +
332N GLY 3.0 23.7 + - - +
333N LYS* 3.8 8.5 + - - +
334N PHE* 1.3 76.7 - - - +
336N THR* 1.4 63.5 + - - +
337N SER* 3.2 12.1 - - - +
338N ASP* 3.0 31.6 + - - +
339N VAL* 3.2 12.8 + - - +
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Residues in contact with THR 336 (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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299N GLY* 2.6 43.1 + - - -
302N LEU* 3.5 10.7 + - + -
303N GLY* 2.9 22.2 + - - +
335N ASN* 1.4 71.8 - - - +
337N SER* 1.3 60.0 + - - +
339N VAL* 3.0 9.9 + - + +
340N SER* 2.9 30.2 + - - +
416N LEU* 4.0 26.5 - - + -
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Residues in contact with SER 337 (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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335N ASN* 3.2 7.8 - - - +
336N THR* 1.3 79.3 - - - +
338N ASP* 1.3 59.5 + - - +
340N SER* 3.3 8.1 + - - -
341N ALA* 2.9 29.6 + - - +
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Residues in contact with ASP 338 (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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333N LYS 4.2 4.0 - - - +
334N PHE* 3.6 27.1 - - + -
335N ASN* 3.0 34.1 + - - +
337N SER* 1.3 78.0 - - - +
339N VAL* 1.3 66.3 + - - +
341N ALA* 3.8 1.2 - - - +
342N ILE* 2.9 31.4 + - - +
355N ILE* 3.8 33.5 - - + +
358N ARG* 4.8 5.2 + - - -
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Residues in contact with VAL 339 (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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302N LEU* 4.5 6.7 - - + -
303N GLY* 3.8 21.8 - - - +
306N VAL* 3.9 13.9 - - + -
334N PHE* 3.8 12.1 - - + -
335N ASN 3.2 11.9 + - - +
336N THR* 3.0 14.0 + - + +
338N ASP* 1.3 77.0 - - - +
340N SER* 1.3 63.7 + - - +
342N ILE* 3.4 1.7 + - - +
343N GLU* 3.1 44.5 + - - +
375N CYS* 4.0 19.7 - - + +
379N SER* 4.2 11.0 - - - +
420N HIS* 4.0 8.7 - - + +
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Residues in contact with SER 340 (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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336N THR* 2.9 19.7 + - - +
337N SER* 3.5 10.9 - - - -
339N VAL* 1.3 73.7 - - - +
341N ALA* 1.3 66.2 + - - +
343N GLU 3.2 9.7 + - - -
344N LYS* 3.5 3.3 + - - +
416N LEU* 4.7 1.0 - - - +
419N THR* 4.4 11.8 + - - -
420N HIS* 3.3 36.9 + - - +
421N PRO* 3.4 28.5 - - - +
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Residues in contact with ALA 341 (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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337N SER 2.9 19.7 + - - +
338N ASP* 3.8 4.3 - - - +
340N SER* 1.3 71.4 - - - +
342N ILE* 1.3 63.0 + - - +
344N LYS* 3.2 22.0 + - - +
348N GLY* 3.6 1.6 - - - -
351N ASN* 2.9 37.3 + - + +
355N ILE* 4.2 9.9 - - + -
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Residues in contact with ILE 342 (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* 3.5 35.2 - - + -
338N ASP 2.9 17.5 + - - +
339N VAL 3.7 3.4 - - - +
341N ALA* 1.3 75.5 - - - +
343N GLU* 1.3 56.2 + - - +
348N GLY* 3.1 22.7 - - - +
351N ASN* 4.4 0.2 - - - -
352N ALA* 3.7 33.0 - - + +
355N ILE* 3.7 17.3 - - + -
356N LEU* 5.5 0.4 - - + -
371N VAL* 4.3 7.4 - - + -
372N GLN* 3.2 45.2 + - + +
375N CYS* 3.9 13.2 - - + -
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Residues in contact with GLU 343 (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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339N VAL* 3.1 21.6 + - - +
340N SER 3.2 3.5 + - - +
342N ILE* 1.3 75.2 - - - +
344N LYS* 1.3 64.4 + - - +
345N ASN* 3.5 0.5 + - - -
372N GLN* 4.7 7.7 + - + +
375N CYS* 3.1 20.0 - - + +
376N THR* 3.6 21.6 + - - +
379N SER* 2.6 22.3 + - - -
420N HIS* 2.8 27.5 + - + -
421N PRO* 3.7 4.7 - - + -
422N GLN* 3.1 20.4 + - + +
426N ARG* 2.8 33.1 + - - -
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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