Contacts of the helix formed by residues 353 - 362 (chain A) in PDB entry 1TAU
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 ALA 353 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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307A VAL* 5.9 1.6 - - - -
309A PHE* 5.1 1.6 - - - -
348A ALA* 3.2 35.5 - - - +
350A GLY 3.1 16.7 + - - +
351A LEU 3.5 1.2 + - - -
352A LEU* 1.3 73.9 - - - +
354A LYS* 1.3 66.2 + - - +
356A LEU* 2.8 18.6 + - - +
357A SER* 3.0 13.1 + - - -
369A PRO* 3.9 11.9 - - + -
370A GLY 4.3 3.1 - - - +
371A ASP 4.1 8.5 - - - +
372A ASP* 3.9 6.2 + - + -
438A SER* 6.2 0.4 - - - -
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Residues in contact with LYS 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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352A LEU 5.0 0.9 - - - -
353A ALA* 1.3 77.5 - - - +
355A ASP* 1.3 69.9 + - - +
357A SER* 2.6 21.6 + - - -
358A VAL* 3.0 25.8 + - + +
369A PRO* 3.7 5.2 - - - +
372A ASP* 5.1 3.9 + - - +
438A SER* 3.0 39.6 - - - +
441A LEU* 3.9 14.5 - - - +
442A ALA* 3.6 21.3 - - + +
445A GLU* 2.8 20.0 + - - +
563A ARG* 5.9 0.2 - - - +
564A PHE 2.8 28.1 + - - +
565A ASN* 5.0 3.5 - - - +
566A GLN* 5.1 4.3 - - - +
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Residues in contact with ASP 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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309A PHE* 4.5 8.5 - - + -
311A LEU* 5.3 3.3 - - + +
314A LYS* 4.3 13.4 - - - +
316A PRO* 3.2 45.4 - - + +
352A LEU* 2.8 37.6 + - + +
354A LYS* 1.3 93.0 + - - +
356A LEU* 1.3 64.5 + - - +
358A VAL* 3.7 1.4 + - - -
359A LEU* 3.4 9.2 + - - +
445A GLU* 4.3 2.6 - - - +
563A ARG* 4.9 6.1 + - - -
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Residues in contact with LEU 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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307A VAL* 3.4 31.4 - - + -
309A PHE* 3.5 44.6 - - + -
311A LEU* 5.1 2.2 - - + -
321A LEU* 4.3 12.8 - - + -
324A LEU* 4.2 5.4 - - + -
342A LEU* 3.9 30.9 - - + +
345A LEU* 5.0 0.4 - - + -
348A ALA* 3.8 15.9 - - + -
352A LEU 3.3 2.0 + - - -
353A ALA 2.8 12.6 + - - +
355A ASP* 1.3 74.9 - - - +
357A SER* 1.3 59.2 + - - +
359A LEU* 3.2 10.2 + - + +
360A ALA* 2.8 25.3 + - - +
367A LEU* 4.2 3.8 - - + -
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Residues in contact with SER 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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348A ALA* 4.7 2.1 - - - +
353A ALA 3.0 5.9 + - - -
354A LYS* 2.6 32.1 + - - -
356A LEU* 1.3 74.9 - - - +
358A VAL* 1.3 52.8 + - - +
360A ALA* 3.0 6.3 + - - +
361A LEU* 2.7 42.5 + - - +
367A LEU* 2.9 31.1 - - - +
369A PRO* 3.5 17.0 - - - +
442A ALA* 3.6 10.5 - - - +
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Residues in contact with VAL 358 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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316A PRO* 4.3 7.4 - - + -
317A MET* 2.9 41.7 - - + +
354A LYS* 3.0 27.2 + - + +
355A ASP* 3.9 7.6 - - - +
356A LEU 3.4 0.2 - - - -
357A SER* 1.3 75.0 - - - +
359A LEU* 1.3 56.4 + - - +
361A LEU* 3.2 11.2 - - - +
362A ARG 3.0 15.4 + - - -
442A ALA* 3.4 24.6 - - - +
445A GLU* 3.9 22.4 - - + +
446A ALA 3.8 17.7 - - - +
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Residues in contact with LEU 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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311A LEU* 3.6 31.4 - - + -
316A PRO* 3.7 23.9 - - + +
317A MET* 4.2 3.1 - - - -
319A ALA* 3.7 14.8 - - + +
321A LEU* 3.8 31.9 - - + -
339A TYR* 3.9 18.4 - - + -
342A LEU* 4.2 3.6 - - + -
355A ASP 3.4 9.0 + - - +
356A LEU* 3.2 11.3 + - + +
357A SER 3.1 0.4 - - - -
358A VAL* 1.3 76.8 - - - +
360A ALA* 1.3 68.1 + - - +
362A ARG* 3.1 29.2 + - - +
363A GLU* 3.1 18.1 + - + +
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Residues in contact with ALA 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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342A LEU* 4.2 10.8 - - + -
356A LEU 2.8 16.0 + - - +
357A SER 3.6 4.9 - - - +
359A LEU* 1.3 74.1 - - - +
361A LEU* 1.3 56.8 + - - +
363A GLU* 3.1 11.4 + - - +
365A LEU* 2.6 47.4 + - + +
367A LEU* 3.6 36.6 - - + -
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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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357A SER* 2.7 28.1 + - - +
358A VAL* 3.2 10.1 - - - +
360A ALA* 1.3 72.9 - - - +
362A ARG* 1.3 56.7 + - - +
364A GLY* 2.9 20.8 + - - -
365A LEU 3.1 13.3 + - - +
366A GLY* 3.9 14.8 - - - -
367A LEU 4.6 2.7 - - - +
442A ALA* 3.9 25.4 - - + -
443A HIS* 4.0 28.3 - - + +
446A ALA* 3.5 28.0 - - + -
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Residues in contact with ARG 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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316A PRO 4.4 0.6 + - - -
317A MET* 3.1 53.8 + - + -
318A TRP 4.9 0.4 - - - -
319A ALA 2.5 33.5 + - - +
320A ASP* 4.8 0.4 - - - +
339A TYR* 3.3 11.9 + - - -
358A VAL 3.0 5.9 + - - -
359A LEU* 3.1 17.5 + - - +
361A LEU* 1.3 74.5 - - - +
363A GLU* 1.3 95.1 + - - +
364A GLY 3.3 2.6 + - - -
446A ALA* 5.1 1.3 - - + +
554A HIS* 4.3 12.0 + - - -
556A ARG* 3.8 34.0 + - - +
557A THR* 5.8 7.4 - - + -
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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