Contacts of the helix formed by residues 333 - 343 (chain A) in PDB entry 1ZG3
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 LYS 333 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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301A SER* 3.4 15.7 + - - +
302A ILE 2.9 14.5 + - - +
303A ASP* 2.9 35.5 + - + +
305A THR* 5.8 1.0 + - - -
332A THR* 1.3 71.6 - - - +
334A GLN* 1.3 64.4 + - - +
336A TRP* 3.0 8.4 + - - +
337A GLU* 2.9 29.4 + - - +
348A TYR* 3.4 30.9 + - + +
350A ILE* 4.0 19.1 - - + -
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Residues in contact with GLN 334 (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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302A ILE 5.6 0.2 - - - +
303A ASP* 5.2 2.6 - - - +
304A GLU* 5.5 10.7 + - - +
305A THR* 4.9 16.4 - - - +
332A THR* 3.2 10.5 + - - +
333A LYS* 1.3 88.6 + - - +
335A GLU* 1.3 64.9 + - + +
337A GLU* 2.9 12.3 + - + +
338A LYS* 2.9 24.8 + - - +
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Residues in contact with GLU 335 (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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272A ASP* 5.6 4.0 - - - +
329A LYS* 3.0 29.1 + - - -
330A GLU 4.3 0.9 - - - +
331A ARG* 3.4 26.1 + - + +
332A THR* 3.2 36.8 + - - +
334A GLN* 1.3 79.4 - - + +
336A TRP* 1.3 60.8 + - - +
338A LYS* 3.5 7.8 + - - +
339A LEU* 3.1 29.0 + - + +
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Residues in contact with TRP 336 (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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267A LEU* 3.5 43.3 - - + -
268A HIS* 6.0 0.2 - - - -
279A LEU* 5.3 0.7 - - + -
297A ILE* 4.1 20.6 - - + -
299A ASP* 3.9 24.0 - - + -
300A ILE 3.0 21.5 + - - -
301A SER* 3.4 22.9 - - - +
331A ARG* 3.5 29.1 - - + +
332A THR 3.1 24.5 + - - -
333A LYS* 3.0 10.8 + - + +
335A GLU* 1.3 75.0 - - - +
337A GLU* 1.3 60.1 + - - +
339A LEU* 3.1 21.4 + - + +
340A ILE* 2.8 44.8 + - + +
348A TYR* 5.9 1.8 - - + -
350A ILE* 5.6 3.4 - - + -
360A ILE* 4.0 17.9 - - + -
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Residues in contact with GLU 337 (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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333A LYS* 2.9 15.0 + - - +
334A GLN* 3.4 13.6 - - - +
336A TRP* 1.3 76.3 - - - +
338A LYS* 1.3 62.7 + - - +
340A ILE* 3.8 5.6 - - - +
341A TYR* 2.9 60.7 + - + -
348A TYR* 3.0 34.6 + - + +
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Residues in contact with LYS 338 (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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334A GLN 2.9 14.7 + - - +
335A GLU* 3.8 8.3 - - - +
337A GLU* 1.3 76.7 - - - +
339A LEU* 1.3 60.7 + - + +
341A TYR* 4.2 2.8 - - - +
342A ASP* 2.9 68.0 + - - +
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Residues in contact with LEU 339 (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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272A ASP* 4.1 36.3 - - + +
275A SER* 4.2 10.1 - - - -
276A LEU* 3.8 13.6 - - + +
279A LEU* 4.0 19.4 - - + +
331A ARG* 3.4 40.4 - - - +
335A GLU 3.1 12.9 + - - +
336A TRP* 3.3 24.0 - - + +
338A LYS* 1.3 79.6 - - + +
340A ILE* 1.3 62.0 + - - +
342A ASP* 3.4 8.1 + - - +
343A ALA* 3.1 23.2 + - - +
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Residues in contact with ILE 340 (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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279A LEU* 4.7 6.3 - - + -
297A ILE* 5.0 9.6 - - + -
336A TRP* 2.8 34.8 + - + +
337A GLU* 3.8 4.5 - - - +
339A LEU* 1.3 75.5 - - + +
341A TYR* 1.3 72.3 + - + +
343A ALA* 3.4 8.0 + - - -
345A PHE* 3.3 31.3 + - + -
347A SER 4.5 0.7 - - - +
348A TYR* 3.8 39.7 - - + -
360A ILE* 4.1 11.2 - - + -
362A VAL* 3.7 39.5 - - + -
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Residues in contact with TYR 341 (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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337A GLU* 2.9 51.6 + - + +
338A LYS* 4.4 2.2 - - - +
340A ILE* 1.3 81.9 - - + +
342A ASP* 1.3 64.4 + - - +
343A ALA 3.0 2.5 - - - -
344A GLY* 2.9 21.0 + - - -
345A PHE 3.5 16.7 - - - +
346A SER 3.4 28.3 + - - -
347A SER* 4.3 7.8 - - - -
348A TYR* 3.7 16.9 - + - -
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Residues in contact with ASP 342 (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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276A LEU* 3.7 25.1 - - + +
280A LYS* 3.7 14.9 + - - -
338A LYS* 2.9 57.9 + - - +
339A LEU* 3.7 3.8 - - + +
341A TYR* 1.3 78.5 - - - +
343A ALA* 1.3 60.0 + - - +
344A GLY* 3.5 0.7 + - - -
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Residues in contact with ALA 343 (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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276A LEU* 3.8 9.0 - - + -
279A LEU* 3.9 17.7 - - + -
280A LYS* 4.1 19.8 - - + +
283A LYS* 3.8 13.7 - - - +
339A LEU 3.1 12.6 + - - +
340A ILE* 3.4 12.1 - - - +
341A TYR 3.0 0.2 - - - -
342A ASP* 1.3 78.6 - - - +
344A GLY* 1.3 57.0 + - - +
345A PHE* 3.5 22.8 - - + -
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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