Contacts of the strand formed by residues 339 - 343 (chain B) in PDB entry 2O1S
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 339 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328B TRP* 4.8 0.4 - - + -
329B LEU* 4.0 13.7 - - + +
332B THR* 3.5 36.1 - - + -
333B ALA* 4.1 5.4 - - + +
336B ASP* 3.0 7.9 + - - +
337B ASN 3.6 1.0 - - - -
338B LYS* 1.3 75.9 - - - +
340B MSE 1.3 84.3 + - - +
341B ALA* 4.0 3.1 - - + +
355B PHE* 3.7 32.1 - - + -
362B ARG* 3.1 29.3 + - - +
386B LYS 3.6 4.3 - - - -
388B ILE* 3.6 30.3 - - + -
465B TYR* 3.4 14.9 + - + +
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Residues in contact with MSE 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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139A LYS* 4.0 18.6 - - + +
337B ASN 3.5 22.2 - - - +
338B LYS 3.6 6.5 - - - +
339B LEU* 1.3 92.4 - - - +
341B ALA* 1.3 60.6 + - - +
342B ILE* 4.8 1.0 - - - +
361B ASP 4.0 5.4 - - - +
362B ARG* 3.5 32.8 - - - +
364B PHE* 4.0 14.8 - - + -
380B LEU* 3.9 27.4 - - + -
385B TYR* 3.5 33.0 - - + -
386B LYS 3.2 5.5 + - - +
387B PRO* 3.3 5.4 - - + +
388B ILE* 2.8 28.8 + - - +
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Residues in contact with ALA 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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325B PHE* 5.7 1.1 - - + -
329B LEU* 4.2 24.9 - - + -
339B LEU* 4.0 1.0 - - + +
340B MSE 1.3 73.2 - - - +
342B ILE* 1.3 61.6 + - - +
352B MSE 5.1 7.2 - - - -
355B PHE* 3.5 30.5 - - + -
362B ARG 2.8 10.5 + - - +
363B TYR* 3.5 5.4 - - + -
364B PHE* 2.9 26.2 + - - +
388B ILE* 3.5 7.2 - - + +
390B ALA* 6.2 0.4 - - + -
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Residues in contact with ILE 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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340B MSE 4.8 0.9 - - - +
341B ALA* 1.3 77.8 - - - +
343B THR* 1.3 67.9 + - - +
344B PRO* 4.7 0.4 - - - -
352B MSE 5.1 1.8 - - - -
364B PHE* 3.3 15.3 - - + +
366B VAL* 4.1 20.9 - - + -
373B ALA* 4.1 20.9 - - + +
376B PHE* 3.8 19.7 - - + -
377B ALA* 3.7 30.5 - - + +
380B LEU* 3.7 24.7 - - + -
387B PRO* 4.3 6.7 - - + -
388B ILE 2.9 9.8 + - - +
389B VAL* 3.7 8.4 - - + +
390B ALA* 2.9 29.9 + - - +
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Residues in contact with THR 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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342B ILE* 1.3 77.8 - - - +
344B PRO* 1.3 70.5 - - - +
345B ALA 3.2 1.0 + - - -
346B MSE 3.4 21.2 + - - +
347B ARG 4.4 0.2 - - - +
350B SER* 4.6 0.2 + - - -
352B MSE 3.1 33.7 - - + +
363B TYR* 3.4 29.2 - - + +
364B PHE 3.0 6.8 + - - +
365B ASP* 3.9 15.9 - - - +
366B VAL* 3.1 22.5 + - - +
390B ALA 3.7 5.0 + - - -
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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