Contacts of the helix formed by residues 338 - 345 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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337B ARG* 1.3 76.7 - - - +
339B TRP* 1.3 65.0 + - - +
340B LYS* 3.8 7.4 + - - +
341B GLU* 2.7 40.8 + - - +
342B TYR* 3.0 22.0 + - - -
425B THR* 4.1 1.6 - - - -
426B LYS* 3.6 20.4 - - - +
427B ASP* 3.4 22.9 - - + +
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Residues in contact with TRP 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338B THR* 1.3 72.3 - - - +
340B LYS* 1.3 69.9 + - + +
342B TYR* 3.1 5.0 + - + +
343B LYS* 2.9 24.8 + - + +
357B ASN* 6.1 0.4 - - - -
395B GLU* 2.9 45.0 + - + -
398B ASN* 3.8 35.0 - - - -
399B TYR* 3.9 21.0 - + - -
423B PHE* 3.5 31.6 - + + -
425B THR* 3.5 33.1 + - + +
427B ASP* 2.9 22.3 + - - +
428B GLY* 4.9 4.5 - - - -
430B ASN* 3.7 10.1 - - - -
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Residues in contact with LYS 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338B THR* 3.3 7.4 + - - +
339B TRP* 1.3 84.0 - - + +
341B GLU* 1.3 58.4 + - + +
343B LYS* 2.9 13.7 + - + +
344B VAL* 2.9 45.6 + - + +
427B ASP* 5.2 0.4 + - - -
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Residues in contact with GLU 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337B ARG* 2.6 50.1 + - + +
338B THR* 2.7 46.7 + - - +
340B LYS* 1.3 80.0 - - + +
342B TYR* 1.3 56.6 + - - +
344B VAL* 4.4 6.3 - - - -
345B GLY* 2.9 35.3 + - - -
346B PHE* 3.5 10.2 - - + -
426B LYS* 4.9 1.9 + - - -
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Residues in contact with TYR 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335B PHE* 2.5 44.4 + - - +
337B ARG* 3.6 20.2 - - + -
338B THR 3.0 20.8 + - - +
339B TRP* 3.7 7.0 - - + +
341B GLU* 1.3 76.0 - - - +
343B LYS* 1.3 58.0 + - - +
346B PHE* 3.6 17.7 - + - -
354B TRP* 3.1 32.6 + + - -
357B ASN* 2.9 27.9 + - - +
423B PHE* 3.7 26.7 - + + -
425B THR* 3.6 13.5 - - + -
444B GLY* 3.0 24.6 + - - -
456B ASN* 3.3 23.7 - - - +
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Residues in contact with LYS 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302B PHE* 6.1 0.3 - - - -
339B TRP* 2.9 16.0 + - + +
340B LYS* 2.9 17.2 + - + +
342B TYR* 1.3 78.4 - - - +
344B VAL* 1.3 72.0 + - + +
356B GLY* 3.5 1.9 - - - -
357B ASN* 3.3 13.0 + - - +
358B GLU* 3.3 39.6 + - + +
359B PHE 4.7 0.9 + - - -
395B GLU* 3.5 27.2 + - - +
399B TYR* 3.4 29.2 - - + +
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Residues in contact with VAL 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302B PHE* 6.0 4.5 - - - -
307B GLU* 6.0 1.8 - - - +
309B ILE* 4.4 7.8 - - - +
340B LYS* 2.9 36.3 + - + +
341B GLU* 4.0 5.4 - - - +
343B LYS* 1.3 90.0 - - + +
345B GLY* 1.3 70.8 + - - +
355B LEU 3.5 10.4 - - - +
356B GLY* 4.2 0.2 - - - -
358B GLU* 5.7 0.9 - - - -
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Residues in contact with GLY 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341B GLU* 2.9 13.7 + - - +
343B LYS 3.4 3.0 + - - -
344B VAL* 1.3 93.3 - - - +
346B PHE* 1.3 62.1 + - - +
354B TRP* 4.5 3.4 - - - -
355B LEU* 3.5 24.5 - - - -
356B GLY* 3.8 4.7 - - - -
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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