Contacts of the helix formed by residues 338 - 345 (chain A) in PDB entry 1Z3S
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 338 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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337A ARG* 1.3 75.8 - - - +
339A TRP* 1.3 65.5 + - - +
340A LYS* 3.6 8.0 + - - +
341A GLU* 2.6 44.0 + - - +
342A TYR* 3.0 22.9 + - - -
425A THR* 4.1 2.0 - - - -
426A LYS* 3.7 20.6 - - - +
427A ASP* 3.4 19.5 - - - +
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Residues in contact with TRP 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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338A THR* 1.3 74.0 - - - +
340A LYS* 1.3 67.4 + - + +
342A TYR* 3.4 2.7 + - + +
343A LYS* 3.0 24.7 + - + +
357A ASN* 5.6 0.6 + - - -
395A GLU* 3.0 33.7 + - + -
398A ASN* 3.9 30.3 - - + -
399A TYR* 3.6 32.5 - + - -
423A PHE* 3.3 37.5 - + + -
424A SER* 4.6 0.4 - - - -
425A THR* 3.3 32.3 + - + +
427A ASP* 2.8 23.3 + - - +
428A GLY* 4.8 4.7 - - - -
430A ASN* 3.7 10.1 - - - -
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Residues in contact with LYS 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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338A THR* 3.2 8.2 + - - +
339A TRP* 1.3 84.4 - - + +
341A GLU* 1.3 59.4 + - + +
343A LYS* 3.0 26.0 + - + +
344A VAL* 3.0 30.0 + - + +
427A ASP* 4.9 0.6 + - - -
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Residues in contact with GLU 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 ARG* 2.9 39.9 + - + +
338A THR* 2.6 48.5 + - - +
340A LYS* 1.3 78.9 - - + +
342A TYR* 1.3 57.0 + - - +
344A VAL* 4.4 7.0 - - - -
345A GLY* 2.8 32.7 + - - +
346A PHE* 3.4 13.7 - - + -
426A LYS* 5.3 0.3 + - - -
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Residues in contact with TYR 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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335A PHE* 2.6 42.0 + - - -
337A ARG* 3.6 21.3 - - + -
338A THR 3.0 23.7 + - - +
339A TRP* 4.0 3.6 - - + +
341A GLU* 1.3 77.0 - - - +
343A LYS* 1.3 57.7 + - - +
346A PHE* 3.4 20.0 - + - -
354A TRP* 2.9 40.7 + + - -
357A ASN* 2.8 34.3 + - - +
423A PHE* 3.8 13.9 - + + -
425A THR* 3.7 9.9 - - + -
444A GLY* 3.1 24.3 + - - -
456A ASN* 3.2 26.0 + - - +
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Residues in contact with LYS 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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339A TRP* 3.0 16.2 + - + +
340A LYS* 3.0 19.7 + - + +
342A TYR* 1.3 80.3 - - - +
344A VAL* 1.3 64.9 + - + +
345A GLY 3.6 0.2 - - - -
356A GLY* 3.5 1.7 - - - -
357A ASN* 3.0 12.9 + - - +
358A GLU* 3.0 45.9 + - + +
359A PHE 4.6 0.5 + - - -
395A GLU* 2.9 36.9 + - - +
399A TYR* 3.3 27.8 - - + +
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Residues in contact with VAL 344 (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 PHE* 6.3 3.8 - - - -
309A ILE* 5.2 5.4 - - - +
340A LYS* 3.0 34.2 + - + +
341A GLU* 4.0 5.4 - - - +
343A LYS* 1.3 90.2 - - + +
345A GLY* 1.3 70.5 + - - +
355A LEU 3.4 11.9 - - - +
356A GLY* 3.9 0.2 - - - -
358A GLU* 5.5 1.6 - - + -
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Residues in contact with GLY 345 (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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341A GLU* 2.8 21.0 + - - +
343A LYS 3.6 2.2 - - - -
344A VAL* 1.3 85.9 - - - +
346A PHE* 1.3 63.7 + - - +
354A TRP* 4.5 1.6 - - - -
355A LEU* 3.4 24.2 - - - -
356A GLY* 3.6 4.6 - - - -
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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