Contacts of the helix formed by residues 333 - 343 (chain D) in PDB entry 1ZQ1
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 LEU 333 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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265D LEU* 3.9 21.8 - - + -
268D ILE* 4.1 32.1 - - + -
319D PHE* 5.0 8.3 - - + -
322D LEU* 3.6 20.6 - - + +
323D ILE* 3.5 13.9 + - - +
325D ARG 3.0 10.1 + - - +
327D ILE* 4.2 6.3 - - + +
332D ARG* 1.3 69.4 - - - +
334D GLY* 1.3 59.9 + - - +
336D GLU* 3.3 10.9 + - + +
337D PHE* 3.2 40.5 + - + -
399D ARG* 4.2 17.9 - - - +
403D ALA* 4.6 12.8 - - + -
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Residues in contact with GLY 334 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323D ILE* 2.7 35.5 + - - -
332D ARG* 2.7 7.0 + - - +
333D LEU* 1.3 70.5 - - - +
335D THR* 1.3 58.3 + - - -
337D PHE* 2.8 22.4 + - - +
338D ALA* 2.9 13.7 + - - +
348D ILE* 3.9 4.0 - - - +
350D HIS* 4.5 14.4 - - - -
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Residues in contact with THR 335 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330D GLY 4.6 1.1 + - - +
331D ARG* 3.5 42.6 - - + +
332D ARG* 2.6 45.7 + - - +
334D GLY* 1.3 71.4 - - - -
336D GLU* 1.3 59.9 + - - -
338D ALA* 3.3 9.1 + - + +
339D ASP* 3.0 28.8 + - - +
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Residues in contact with GLU 336 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261D ARG* 2.6 35.9 + - - -
265D LEU* 4.7 0.2 - - - +
327D ILE* 3.6 23.9 - - + +
331D ARG* 3.3 13.4 + - - +
332D ARG 4.2 0.2 - - - +
333D LEU* 3.4 15.0 - - + +
335D THR* 1.3 77.5 - - - +
337D PHE* 1.3 63.8 + - + +
339D ASP* 3.4 9.4 + - - +
340D ARG* 3.3 28.2 + - - +
399D ARG* 4.0 32.1 + - - +
410D GLU* 4.7 1.8 - - - +
412D ARG* 3.0 25.9 + - - -
422D TYR* 5.2 0.5 - - - +
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Residues in contact with PHE 337 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316D LEU* 4.0 10.5 - - + -
319D PHE* 4.5 11.4 - + - -
323D ILE* 3.9 42.0 - - + -
333D LEU* 3.2 32.1 + - + -
334D GLY 2.8 11.1 + - - +
336D GLU* 1.3 80.4 - - - +
338D ALA* 1.3 63.4 + - - +
339D ASP 3.3 0.2 + - - -
340D ARG* 3.4 5.7 + - - +
341D ALA* 2.9 22.7 + - - +
348D ILE* 3.5 14.1 - - + -
380D VAL* 4.4 7.4 - - + -
396D VAL* 3.9 22.9 - - + +
399D ARG* 4.2 16.4 - - + -
400D ALA* 3.9 37.5 - - + -
403D ALA* 5.2 0.4 - - + -
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Residues in contact with ALA 338 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334D GLY 2.9 11.0 + - - +
335D THR* 3.3 13.7 + - + +
337D PHE* 1.3 76.9 - - - +
339D ASP* 1.3 51.3 + - - +
341D ALA* 3.1 8.1 + - - +
342D LYS* 2.6 36.7 + - - +
345D VAL 4.9 0.2 - - - +
347D GLY* 5.0 7.0 - - - -
348D ILE* 3.6 25.2 - - + +
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Residues in contact with ASP 339 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331D ARG* 2.9 28.7 + - - -
335D THR* 3.0 19.6 + - - +
336D GLU* 3.5 16.6 - - - +
337D PHE 3.2 0.2 - - - -
338D ALA* 1.3 74.9 - - - +
340D ARG* 1.3 63.9 + - - +
342D LYS* 2.9 23.5 + - - +
343D LYS* 3.8 2.3 + - - +
421D GLU* 3.7 17.5 - - - +
422D TYR* 3.7 36.4 + - + +
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Residues in contact with ARG 340 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336D GLU* 3.3 15.2 + - - +
337D PHE 3.8 4.7 - - - +
339D ASP* 1.3 75.0 - - - +
341D ALA* 1.3 61.3 + - - +
343D LYS* 3.3 21.7 - - - +
395D GLU* 3.8 39.4 + - - +
396D VAL* 5.4 0.2 - - - -
398D LYS* 4.0 19.4 - - - +
399D ARG* 2.9 44.5 - - + +
402D GLU* 2.7 35.6 + - - -
408D PRO* 4.5 4.6 - - - +
410D GLU* 3.7 18.0 + - - -
422D TYR* 3.9 41.0 + - + -
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Residues in contact with ALA 341 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337D PHE 2.9 18.9 + - - +
338D ALA 3.3 4.9 - - - +
340D ARG* 1.3 73.6 - - - +
342D LYS* 1.3 54.1 + - - +
343D LYS 2.8 16.1 + - - -
344D TYR* 2.9 14.6 + - - +
345D VAL* 3.0 13.8 + - + +
347D GLY 5.3 0.7 - - - +
348D ILE* 3.4 27.8 - - + -
392D ALA* 4.3 17.7 - - + +
395D GLU* 4.6 1.8 - - - -
396D VAL* 4.0 13.7 - - + -
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Residues in contact with LYS 342 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338D ALA 2.6 16.1 + - - +
339D ASP* 2.9 18.3 + - - +
341D ALA* 1.3 71.4 - - - +
343D LYS* 1.3 61.7 + - - +
344D TYR* 3.0 2.9 + - - -
345D VAL 2.8 22.9 + - - +
346D PRO* 5.1 6.9 - - + +
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Residues in contact with LYS 343 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339D ASP 3.8 2.2 + - - +
340D ARG 3.3 16.2 + - - +
341D ALA 2.8 0.8 + - - -
342D LYS* 1.3 77.4 - - - +
344D TYR* 1.3 100.0 + - + +
395D GLU* 3.8 23.4 + - + +
422D TYR* 6.2 3.6 - - + -
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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