Contacts of the strand formed by residues 339 - 343 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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329A LEU* 4.3 7.9 - - + +
332A THR* 4.1 11.4 - - + -
333A ALA* 4.2 19.1 - - + +
336A ASP* 3.7 7.2 + - - +
337A ASN 3.5 0.8 - - - -
338A LYS* 1.3 76.9 - - - +
340A MSE 1.3 90.3 + - - +
341A ALA* 3.9 4.5 - - + +
355A PHE* 3.9 29.4 - - + -
362A ARG* 3.0 24.0 + - - +
386A LYS 3.7 3.1 - - - -
388A ILE* 3.1 33.4 - - + -
465A TYR* 3.4 27.4 + - + +
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Residues in contact with MSE 340 (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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337A ASN 3.2 25.4 - - - +
338A LYS 3.9 6.7 - - - +
339A LEU* 1.3 99.9 - - - +
341A ALA* 1.3 55.6 + - - +
342A ILE* 4.9 1.2 - - - +
361A ASP 4.1 0.2 - - - +
362A ARG* 3.5 30.5 - - - +
364A PHE* 4.1 10.1 - - + -
380A LEU* 3.7 31.0 - - + -
385A TYR* 3.6 30.5 - - + -
386A LYS 3.2 5.1 + - - +
387A PRO* 3.2 5.6 - - + +
388A ILE* 2.7 34.1 + - - +
139B LYS* 3.8 29.2 - - + -
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Residues in contact with ALA 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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329A LEU* 3.9 19.1 - - + -
339A LEU* 3.9 1.5 - - + +
340A MSE 1.3 72.8 - - - +
342A ILE* 1.3 65.5 + - - +
352A MSE 3.4 24.7 - - + +
355A PHE* 3.6 20.2 - - + -
362A ARG 2.9 10.4 + - - +
363A TYR* 3.6 1.4 - - - -
364A PHE* 3.1 24.7 + - - +
388A ILE* 3.3 9.0 - - + +
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Residues in contact with ILE 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 ALA* 1.3 80.3 - - - +
343A THR* 1.3 62.5 + - - +
344A PRO* 4.8 0.2 - - - -
352A MSE 4.3 2.7 - - - -
364A PHE* 3.4 15.0 - - + +
366A VAL* 4.1 16.8 - - + -
373A ALA* 3.9 29.8 - - + +
376A PHE* 3.5 30.5 - - + -
377A ALA* 3.8 29.6 - - + -
380A LEU* 3.9 11.9 - - + -
387A PRO* 4.4 4.3 - - + -
388A ILE 2.8 17.0 + - - +
389A VAL* 3.7 5.8 - - + +
390A ALA* 2.8 35.7 + - - +
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Residues in contact with THR 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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342A ILE* 1.3 78.9 - - - +
344A PRO* 1.3 71.5 - - - +
345A ALA 3.2 4.4 + - - +
346A MSE 3.1 30.1 + - - +
347A ARG* 4.0 9.2 - - - +
350A SER* 4.6 0.7 + - - -
352A MSE 3.8 16.1 - - - -
363A TYR* 3.4 33.2 - - + +
364A PHE 3.0 13.7 + - - +
365A ASP* 4.1 5.2 - - + -
366A VAL* 3.3 20.3 + - - +
390A ALA 3.7 3.7 + - - -
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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