Contacts of the helix formed by residues 352 - 359 (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 MSE 352 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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325A PHE* 4.1 3.8 - - + -
329A LEU* 4.0 17.7 - - + -
341A ALA* 3.4 39.5 - - + -
342A ILE 4.1 6.5 - - - +
343A THR* 3.8 16.8 - - - -
347A ARG* 2.8 26.5 + - + +
350A SER* 3.8 15.3 - - - +
351A GLY* 1.3 74.3 - - - +
353A VAL* 1.3 59.0 + - - +
354A GLU 3.6 0.9 - - - -
355A PHE* 3.9 13.2 - - + -
356A SER* 2.9 28.9 + - - -
363A TYR* 3.9 22.2 - - + -
390A ALA* 3.6 26.9 - - + -
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Residues in contact with VAL 353 (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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347A ARG* 4.0 23.6 - - - +
348A GLU* 3.9 37.7 - - + +
351A GLY* 3.6 3.0 - - - -
352A MSE 1.3 73.8 - - - +
354A GLU* 1.3 69.6 + - - +
356A SER* 2.7 23.7 + - - -
357A ARG* 3.1 44.2 + - - +
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Residues in contact with GLU 354 (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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323A LYS* 5.2 4.0 + - - -
327A ASP* 4.4 13.3 - - - +
330A CYS* 4.0 14.9 - - - +
351A GLY 5.2 1.7 + - - +
353A VAL* 1.3 80.3 - - - +
355A PHE* 1.3 63.3 + - - +
357A ARG* 3.2 11.3 + - - +
358A LYS* 3.0 57.9 + - + +
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Residues in contact with PHE 355 (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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326A GLY* 4.7 1.8 - - - +
329A LEU* 3.7 42.0 - - + -
330A CYS* 3.5 16.8 - - - -
333A ALA* 3.9 23.6 - - + -
339A LEU* 3.9 8.5 - - + -
341A ALA* 3.6 28.7 - - + -
351A GLY 5.3 1.0 + - - +
352A MSE 3.7 17.6 - - + +
353A VAL 3.1 0.4 - - - -
354A GLU* 1.3 80.2 - - - +
356A SER* 1.3 58.0 + - - +
358A LYS 3.3 0.5 + - - -
359A PHE* 2.9 44.8 + + + -
362A ARG* 3.8 18.4 - - + -
363A TYR* 3.8 31.6 - + + -
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Residues in contact with SER 356 (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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347A ARG* 3.2 25.7 + - - -
352A MSE 2.9 14.5 + - - -
353A VAL 2.7 17.3 + - - -
355A PHE* 1.3 77.1 - - - +
357A ARG* 1.3 61.2 + - - +
360A PRO* 3.3 25.8 - - - +
363A TYR* 3.6 44.4 - - - -
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Residues in contact with ARG 357 (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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347A ARG* 4.6 10.7 - - - +
353A VAL* 3.1 38.5 + - - +
354A GLU* 3.6 10.5 - - - +
355A PHE 3.1 0.2 - - - -
356A SER* 1.3 83.2 + - - +
358A LYS* 1.3 64.1 + - + +
360A PRO* 3.6 13.7 - - - +
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Residues in contact with LYS 358 (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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330A CYS* 4.7 6.5 - - + -
354A GLU* 3.0 51.8 + - + +
357A ARG* 1.3 79.8 - - + +
359A PHE* 1.3 94.1 + - + +
360A PRO* 3.4 6.2 - - - +
361A ASP* 4.8 0.3 - - - +
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Residues in contact with PHE 359 (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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330A CYS* 3.6 32.5 - - + -
333A ALA* 3.8 33.4 - - + -
334A ALA* 3.9 13.9 - - + -
355A PHE* 2.9 26.9 + + + +
356A SER 3.8 3.1 - - - -
358A LYS* 1.3 105.6 - - + +
360A PRO* 1.3 53.9 - - - +
361A ASP* 3.0 12.3 - - - -
362A ARG* 2.8 46.9 + - + +
363A TYR* 3.2 12.0 + - - +
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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