Contacts of the helix formed by residues 341 - 349 (chain A) in PDB entry 1OPL
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 ASN 341 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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271A GLN* 3.8 15.8 + - - +
272A TYR* 2.9 30.3 + - - +
339A TYR 4.4 0.5 - - - +
340A GLY* 1.3 74.1 - - - -
342A LEU* 1.3 63.3 + - - +
343A LEU* 3.1 7.4 + - - +
344A ASP* 2.9 46.0 + - - +
345A TYR* 3.0 20.3 + - - +
386A ARG* 3.4 22.1 + - - +
388A CYS 3.2 10.1 - - - +
389A LEU* 4.0 5.3 - - + +
390A VAL* 4.2 0.9 - - - -
539A P16 4.5 5.1 - - - -
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Residues in contact with LEU 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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341A ASN* 1.3 70.0 - - - +
343A LEU* 1.3 60.8 + - - +
345A TYR* 4.1 2.7 - - + -
346A LEU* 2.9 42.0 + - + +
362A MET* 3.9 31.6 - - + -
366A ILE* 3.8 28.0 - - + -
385A ALA* 3.4 12.3 + - + +
388A CYS* 2.8 24.0 + - + +
390A VAL* 3.8 23.0 - - + +
396A VAL* 4.6 5.6 - - + -
447A LEU* 4.4 7.9 - - + -
451A ILE* 4.1 20.9 - - + -
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Residues in contact with LEU 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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341A ASN* 3.1 8.4 + - - +
342A LEU* 1.3 79.5 - - - +
344A ASP* 1.3 68.0 + - - +
346A LEU* 3.3 3.5 + - - +
347A ARG* 3.1 71.2 + - - +
385A ALA* 3.4 9.9 + - + -
386A ARG* 3.9 33.2 - - + +
424A TRP* 6.0 2.0 - - + -
450A GLU* 3.8 21.3 - - - +
455A GLY* 3.7 19.1 - - - +
456A MET 5.3 0.4 - - - +
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Residues in contact with ASP 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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271A GLN* 4.8 4.5 + - - -
339A TYR 6.0 0.9 - - - +
341A ASN* 2.9 39.1 + - - +
343A LEU* 1.3 79.7 - - - +
345A TYR* 1.3 63.3 + - - +
347A ARG* 3.2 13.2 + - - -
348A GLU* 3.0 47.8 + - - +
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Residues in contact with TYR 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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339A TYR* 4.2 40.1 + + + +
341A ASN 3.0 18.3 + - - +
342A LEU* 3.6 13.0 - - + +
343A LEU 3.2 0.2 - - - -
344A ASP* 1.3 77.0 - - - +
346A LEU* 1.3 63.2 + - + +
348A GLU* 3.7 4.0 - - - -
349A CYS* 2.9 41.1 + - + +
353A GLU* 3.4 12.5 + - - -
354A VAL* 3.6 22.1 - - + +
362A MET* 4.7 4.0 - - - -
390A VAL* 4.1 24.0 - - + -
394A HIS* 2.9 39.6 + + - -
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Residues in contact with LEU 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A LEU* 2.9 42.8 + - + +
343A LEU* 3.8 4.3 - - - +
345A TYR* 1.3 76.8 - - + +
347A ARG* 1.3 62.2 + - - +
348A GLU 3.4 0.2 + - - -
349A CYS* 3.5 18.2 + - - +
351A ARG* 4.8 3.1 + - - -
354A VAL* 4.5 7.2 - - + -
359A LEU* 3.6 28.7 - - + -
362A MET* 3.9 13.7 - - + -
385A ALA* 5.4 2.5 - - + -
450A GLU 4.0 8.1 - - - +
451A ILE* 3.8 33.4 - - + +
454A TYR* 3.6 34.3 - - + +
455A GLY* 4.0 3.1 - - - +
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Residues in contact with ARG 347 (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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343A LEU* 3.1 49.8 + - - +
344A ASP* 3.8 13.8 + - - +
346A LEU* 1.3 77.7 - - - +
348A GLU* 1.3 64.2 + - + +
349A CYS 3.6 1.4 + - - +
351A ARG* 5.0 8.4 + - - +
454A TYR 3.8 15.7 - - - +
455A GLY* 2.7 25.3 + - - +
456A MET 4.4 0.6 - - - -
457A SER* 4.2 19.0 - - - +
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Residues in contact with GLU 348 (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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344A ASP* 3.0 36.3 + - - +
345A TYR* 3.7 3.6 + - - +
347A ARG* 1.3 84.3 - - + +
349A CYS* 1.3 65.5 + - - +
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Residues in contact with CYS 349 (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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345A TYR* 2.9 26.4 + - + +
346A LEU* 3.5 18.9 - - - +
347A ARG 3.6 3.0 - - - +
348A GLU* 1.3 83.7 - - - +
350A ASN* 1.3 64.4 + - - +
351A ARG* 3.4 11.4 + - - +
354A VAL* 3.7 37.9 - - + -
454A TYR* 3.9 19.1 - - - -
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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