Contacts of the helix formed by residues 354 - 365 (chain A) in PDB entry 1O6K
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 ASP 354 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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352A ASN* 3.0 16.4 + - - +
353A GLN* 1.3 86.4 - - - +
355A HIS* 1.3 59.8 + - - +
356A GLU* 3.3 21.8 - - - +
357A ARG* 3.2 38.9 + - + +
358A LEU* 3.0 26.3 + - - +
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Residues in contact with HIS 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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314A PRO* 3.8 38.0 - - + +
315A GLU* 4.4 9.0 + - - -
352A ASN 5.2 0.2 - - - -
353A GLN 3.7 12.5 + - - -
354A ASP* 1.3 71.2 - - - +
356A GLU* 1.3 60.5 + - + +
358A LEU* 3.3 13.9 + - + +
359A PHE* 2.9 51.2 + + + -
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Residues in contact with GLU 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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354A ASP* 3.3 18.4 + - - +
355A HIS* 1.3 78.0 - - + +
357A ARG* 1.3 81.9 + - - +
359A PHE* 3.6 10.0 + - + +
360A GLU* 3.3 26.2 + - - +
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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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352A ASN* 3.7 31.9 - - - +
354A ASP* 3.2 20.6 + - + +
355A HIS 3.3 0.2 - - - -
356A GLU* 1.3 94.6 + - - +
358A LEU* 1.3 64.6 + - - +
360A GLU* 2.9 46.4 + - - +
361A LEU* 3.1 26.4 + - + +
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Residues in contact with LEU 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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314A PRO* 3.8 36.1 - - + +
315A GLU* 3.9 23.3 - - + +
350A PHE 3.6 26.2 - - - +
351A TYR* 4.0 13.2 - - - -
352A ASN* 3.9 16.5 - - - +
354A ASP 3.0 13.5 + - - +
355A HIS* 3.5 20.0 - - + +
357A ARG* 1.3 77.8 - - - +
359A PHE* 1.3 59.4 + - + +
361A LEU* 3.1 7.1 + - - +
362A ILE* 3.0 43.5 + - + +
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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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310A PHE* 4.5 12.3 - + - -
314A PRO* 3.8 40.4 - - + -
317A LEU* 3.8 20.4 - - + -
322A LEU* 3.6 33.4 - - + +
355A HIS* 2.9 37.0 + + + +
356A GLU* 3.8 9.6 - - + +
357A ARG 3.3 0.2 - - - -
358A LEU* 1.3 77.7 - - + +
360A GLU* 1.3 64.1 + - + +
362A ILE* 3.5 3.0 + - + +
363A LEU* 3.2 34.5 + - + +
10C PHE* 5.1 2.5 - + - -
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Residues in contact with GLU 360 (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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356A GLU* 3.3 10.5 + - - +
357A ARG* 2.9 53.5 + - - +
358A LEU 3.2 0.4 - - - -
359A PHE* 1.3 76.4 - - + +
361A LEU* 1.3 60.4 + - + +
363A LEU* 3.5 4.9 + - + -
364A MET* 2.8 47.7 + - + +
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Residues in contact with LEU 361 (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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350A PHE* 3.6 21.2 - - + -
351A TYR 3.5 39.5 - - - +
352A ASN* 4.1 10.8 - - + +
357A ARG* 3.1 19.3 + - + +
358A LEU* 3.1 8.5 + - - +
360A GLU* 1.3 77.7 - - + +
362A ILE* 1.3 59.4 + - - +
364A MET* 5.3 0.2 - - - -
365A GLU* 2.9 55.7 + - + +
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Residues in contact with ILE 362 (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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314A PRO 3.4 25.1 - - - +
315A GLU 4.3 8.5 - - - +
317A LEU 3.3 27.6 - - - +
319A PRO* 3.6 23.6 - - + +
322A LEU* 3.9 20.4 - - + -
334A TRP* 3.9 9.2 - - + -
350A PHE* 4.0 26.2 - - + -
358A LEU* 3.0 30.9 + - + +
359A PHE* 3.9 6.1 - - + +
360A GLU 3.4 0.2 - - - -
361A LEU* 1.3 74.6 - - - +
363A LEU* 1.3 57.8 + - - +
387A LYS* 2.8 22.5 + - - -
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Residues in contact with LEU 363 (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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319A PRO* 3.5 34.0 - - + +
322A LEU* 4.1 27.4 - - + +
323A GLU* 4.2 17.3 - - + +
359A PHE* 3.2 25.0 + - + +
360A GLU* 4.0 2.5 - - + +
362A ILE* 1.3 78.5 - - - +
364A MET* 1.3 84.3 + - + +
387A LYS* 3.3 19.2 - - - +
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Residues in contact with MET 364 (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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360A GLU* 2.8 32.9 + - + +
363A LEU* 1.3 103.5 - - + +
365A GLU* 1.3 62.3 + - - +
366A GLU* 3.8 1.6 + - - +
387A LYS* 4.3 3.9 - - - -
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Residues in contact with GLU 365 (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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350A PHE* 3.2 17.9 - - + -
360A GLU 4.0 0.2 + - - -
361A LEU* 2.9 46.8 + - + +
364A MET* 1.3 73.9 - - - +
366A GLU* 1.3 90.9 + - - +
387A LYS* 2.8 29.8 + - - -
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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