Contacts of the helix formed by residues 342 - 349 (chain B) 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 LEU 342 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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341B ASN* 1.3 70.8 - - - +
343B LEU* 1.3 61.1 + - - +
345B TYR* 4.1 2.7 - - + -
346B LEU* 2.9 43.1 + - + +
362B MET* 3.9 31.6 - - + -
366B ILE* 3.8 28.3 - - + -
385B ALA* 3.4 10.7 + - + +
388B CYS* 2.8 23.6 + - + +
390B VAL* 3.8 23.9 - - + +
396B VAL* 4.6 6.1 - - + -
447B LEU* 4.4 8.5 - - + -
451B ILE* 4.1 20.4 - - + -
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Residues in contact with LEU 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B ASN* 3.1 9.5 + - - +
342B LEU* 1.3 78.8 - - - +
344B ASP* 1.3 66.8 + - - +
346B LEU* 3.3 3.8 + - - +
347B ARG* 3.1 71.4 + - - +
385B ALA* 3.4 10.0 + - + -
386B ARG* 3.9 32.5 - - + +
424B TRP* 6.0 2.2 - - + -
450B GLU* 3.8 20.6 - - - +
455B GLY* 3.7 19.5 - - - +
456B MET 5.3 0.4 - - - +
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Residues in contact with ASP 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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271B GLN* 4.4 7.8 + - - -
339B TYR 6.1 0.7 - - - +
341B ASN* 2.9 37.8 + - - +
343B LEU* 1.3 78.5 - - - +
345B TYR* 1.3 64.2 + - - +
347B ARG* 3.2 14.2 + - - +
348B GLU* 3.0 47.4 + - - +
538B P16 5.9 2.6 - - - -
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Residues in contact with TYR 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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339B TYR* 4.4 31.2 + + + +
340B GLY 5.7 0.2 - - - +
341B ASN 3.0 18.1 + - - +
342B LEU* 3.6 13.2 - - + +
343B LEU 3.2 0.2 - - - -
344B ASP* 1.3 78.8 - - - +
346B LEU* 1.3 64.0 + - + +
348B GLU* 3.7 4.1 - - - +
349B CYS* 2.9 41.3 + - + +
353B GLU* 3.4 12.1 + - - -
354B VAL* 3.6 21.4 - - + +
362B MET* 4.7 3.6 - - - -
390B VAL* 4.1 31.2 - - + -
394B HIS* 2.9 39.4 + + - -
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Residues in contact with LEU 346 (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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342B LEU* 2.9 43.0 + - + +
343B LEU* 3.8 4.5 - - - +
345B TYR* 1.3 76.9 - - + +
347B ARG* 1.3 63.2 + - - +
348B GLU 3.4 0.2 + - - -
349B CYS* 3.5 17.2 + - - +
351B ARG* 4.8 2.8 + - - -
354B VAL* 4.5 7.2 - - + -
359B LEU* 3.6 28.3 - - + -
362B MET* 3.9 13.9 - - + -
385B ALA* 5.4 2.9 - - + -
450B GLU 4.0 7.4 - - - +
451B ILE* 3.8 33.0 - - + +
454B TYR* 3.6 35.1 - - + +
455B GLY* 4.0 3.1 - - - +
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Residues in contact with ARG 347 (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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343B LEU* 3.1 48.2 + - - +
344B ASP* 3.2 15.0 + - - +
346B LEU* 1.3 76.4 - - - +
348B GLU* 1.3 64.6 + - + +
349B CYS 5.0 1.0 - - - +
351B ARG* 5.0 9.0 + - - +
454B TYR 3.8 15.3 - - - +
455B GLY* 2.7 23.8 + - - +
456B MET* 4.4 1.0 + - - +
457B SER* 4.2 19.2 - - - +
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Residues in contact with GLU 348 (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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344B ASP* 3.0 37.2 + - - +
345B TYR* 3.7 3.4 - - - +
347B ARG* 1.3 83.5 - - + +
349B CYS* 1.3 64.5 + - - +
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Residues in contact with CYS 349 (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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345B TYR* 2.9 26.6 + - + +
346B LEU* 3.5 19.3 - - - +
347B ARG 3.6 2.2 - - - +
348B GLU* 1.3 82.5 - - - +
350B ASN* 1.3 64.1 + - - +
351B ARG* 3.4 11.4 + - - +
354B VAL* 3.7 39.0 - - + -
454B TYR* 3.9 18.8 - - - -
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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