Contacts of the helix formed by residues 335 - 343 (chain A) in PDB entry 1Z1B
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 SER 335 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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328A GLN* 3.0 13.6 + - - -
333A HIS* 3.2 14.3 - - - +
334A LYS* 1.3 80.3 - - - +
336A ASP* 1.3 62.7 + - - +
337A THR* 3.1 24.9 + - - -
338A MET* 4.1 11.5 + - - +
339A ALA 4.0 3.6 + - - -
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Residues in contact with ASP 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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328A GLN* 3.6 14.8 - - - +
334A LYS 4.1 1.0 + - - -
335A SER* 1.3 71.5 + - - +
337A THR* 1.3 58.0 + - - +
338A MET 3.2 2.2 - - - -
339A ALA* 3.2 3.0 + - + +
340A SER* 2.8 38.5 + - - -
343A ARG* 6.1 1.8 - - - +
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Residues in contact with THR 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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335A SER* 3.1 12.6 + - - -
336A ASP* 1.3 76.8 - - - +
338A MET* 1.3 67.0 + - + +
340A SER* 3.8 7.3 + - - -
341A GLN* 3.4 38.2 + - - +
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Residues in contact with MET 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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333A HIS* 3.6 30.5 - - + +
335A SER* 4.1 11.2 + - - +
336A ASP 3.2 0.4 - - - -
337A THR* 1.3 82.3 - - + +
339A ALA* 1.3 56.7 + - - +
341A GLN* 2.8 52.5 + - - +
342A PTR 2.9 41.3 + - - -
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Residues in contact with ALA 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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328A GLN* 3.7 46.9 - - + +
333A HIS* 4.0 11.1 + - - +
335A SER 4.0 1.2 + - - +
336A ASP* 3.2 6.3 + - + +
338A MET* 1.3 78.3 - - - +
340A SER* 1.3 58.8 + - - +
342A PTR 3.3 6.2 + - - +
343A ARG* 3.1 35.1 + - - +
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Residues in contact with SER 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A ASP* 2.8 22.4 + - - -
337A THR* 3.8 7.6 + - - -
339A ALA* 1.3 72.6 - - - +
341A GLN* 1.3 60.3 + - - +
343A ARG* 3.4 44.0 + - - +
344A ASP* 4.0 7.4 + - - +
334B LYS 6.0 1.1 - - - -
335B SER* 5.1 11.6 + - - -
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Residues in contact with GLN 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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179A ARG* 3.1 16.6 + - - -
337A THR* 3.4 25.3 + - - +
338A MET* 2.8 40.0 + - + +
340A SER* 1.3 80.2 - - - +
342A PTR 1.3 60.4 + - + +
343A ARG 3.2 1.3 - - - -
344A ASP* 3.1 20.5 - - + +
346A ARG* 4.5 9.7 + - - +
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Residues in contact with PTR 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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179A ARG* 3.6 10.5 - - - -
212A ARG* 5.5 2.1 + - - -
235A LYS* 5.9 0.5 + - - -
308A HIS* 4.9 14.9 + + - -
311A ARG* 4.3 21.9 + - + -
312A SER* 3.5 38.0 + - - -
315A ALA* 4.4 18.4 - - + -
316A ARG* 3.5 12.9 - - - +
331A LEU* 4.3 11.0 - - + -
333A HIS* 3.3 35.8 + + - -
338A MET* 2.9 50.1 + - - -
339A ALA* 3.3 5.6 + - - +
341A GLN* 1.3 74.6 + - + +
343A ARG* 1.3 58.6 + - - +
344A ASP 3.0 9.0 + - - +
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Residues in contact with ARG 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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316A ARG* 4.6 12.9 - - + +
319A GLU* 3.4 34.1 + - + +
324A ASP* 5.4 8.5 - - - +
336A ASP* 5.2 2.6 + - - +
339A ALA* 3.1 20.8 + - - +
340A SER* 3.4 47.9 + - - +
341A GLN 3.2 0.2 - - - -
342A PTR 1.3 74.4 + - - -
344A ASP* 1.3 61.6 + - - +
345A ASP* 3.6 4.2 + - - +
334B LYS 5.0 8.9 + - - -
335B SER* 6.2 0.6 - - - +
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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