Contacts of the helix formed by residues 361 - 368 (chain A) in PDB entry 1TH1
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 GLY 361 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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325A VAL* 4.0 2.9 - - - +
329A ARG* 4.1 10.6 + - - -
358A VAL 3.1 8.4 + - - -
359A GLU 3.2 3.0 + - - -
360A ALA* 1.3 80.2 - - - +
362A GLY* 1.3 58.2 + - - +
364A GLN* 3.3 24.4 + - - +
365A ALA* 3.1 27.5 + - - +
395A GLN* 4.7 3.4 - - - -
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Residues in contact with GLY 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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325A VAL* 3.8 18.8 - - - -
357A ILE* 2.9 28.1 + - - -
358A VAL 3.8 1.2 + - - -
360A ALA 3.4 1.2 - - - -
361A GLY* 1.3 75.8 - - - +
363A MET* 1.3 59.4 + - - +
365A ALA* 3.9 1.0 - - - +
366A LEU* 3.0 41.4 + - - +
388A LEU* 5.0 0.9 - - - -
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Residues in contact with MET 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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357A ILE 4.7 0.4 + - - -
358A VAL* 4.5 14.6 - - + -
361A GLY 3.4 0.8 - - - -
362A GLY* 1.3 75.2 - - - +
364A GLN* 1.3 66.2 + - - +
367A GLY* 3.0 23.0 + - - -
385A LEU* 3.5 46.5 - - + +
388A LEU* 3.7 29.8 - - - -
389A SER* 4.2 4.3 - - - -
392A ALA* 3.8 31.9 - - + -
395A GLN* 4.9 2.0 - - + -
398A MET* 3.9 20.2 - - + -
401A LEU* 3.9 12.4 - - + +
423A ILE* 4.9 0.9 - - + -
427A LEU* 3.9 19.3 - - + -
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Residues in contact with GLN 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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329A ARG* 5.9 1.8 - - - +
358A VAL 4.8 0.2 + - - -
361A GLY* 3.3 30.9 + - - +
363A MET* 1.3 78.3 - - - +
365A ALA* 1.3 62.4 + - - +
367A GLY* 3.3 10.1 + - - -
368A LEU* 3.3 21.3 + - + +
395A GLN* 3.2 25.9 + - - +
396A GLU 3.2 16.6 - - - +
397A GLY* 3.5 19.3 - - - +
398A MET* 4.0 11.2 - - - +
401A LEU* 5.4 6.3 - - + -
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Residues in contact with ALA 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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325A VAL* 3.8 30.5 - - + +
328A MET* 4.2 12.3 - - + +
329A ARG* 4.3 14.3 - - + +
361A GLY 3.1 17.8 + - - +
362A GLY* 3.9 3.6 - - - +
363A MET 3.4 0.2 - - - -
364A GLN* 1.3 74.3 - - - +
366A LEU* 1.3 63.5 + - + +
368A LEU* 3.5 17.8 - - - +
369A HIS* 3.4 21.3 + - - -
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Residues in contact with LEU 366 (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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328A MET* 4.2 15.5 - - + -
341A SER* 4.7 4.5 - - - -
344A LEU* 4.2 21.3 - - + -
357A ILE* 5.3 0.9 - - + -
362A GLY* 3.0 24.8 + - - +
363A MET 4.0 0.2 - - - +
365A ALA* 1.3 73.5 - - + +
367A GLY* 1.3 63.5 + - - +
368A LEU 3.2 1.5 + - - -
369A HIS* 3.3 10.8 + - - -
370A LEU* 3.8 9.9 - - - +
381A CYS* 3.8 41.1 - - + +
384A THR* 3.6 31.6 - - + -
385A LEU* 3.9 23.3 - - + -
388A LEU* 4.1 13.9 - - + -
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Residues in contact with GLY 367 (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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363A MET 3.0 15.4 + - - -
364A GLN* 3.3 8.0 + - - -
365A ALA 3.2 0.8 - - - -
366A LEU* 1.3 79.0 - - - +
368A LEU* 1.3 59.6 - - - +
369A HIS 3.3 1.0 + - - -
370A LEU* 3.6 29.7 + - - +
371A THR* 5.7 0.3 + - - -
385A LEU* 4.6 0.2 - - - +
401A LEU* 4.1 14.1 - - - -
404A THR* 4.9 7.8 + - - +
233B LYS* 5.9 1.9 + - - +
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Residues in contact with LEU 368 (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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328A MET 4.7 0.7 - - - +
329A ARG* 3.9 28.7 - - + -
364A GLN* 3.3 16.6 + - + +
365A ALA* 3.5 13.9 - - - +
366A LEU 3.2 0.4 - - - -
367A GLY* 1.3 77.6 - - - +
369A HIS* 1.3 66.5 + - + +
370A LEU 3.6 0.4 - - - -
371A THR* 4.9 3.9 + - - -
372A ASP 5.6 0.2 + - - -
192B PRO* 3.6 49.2 - - + +
193B GLN* 4.1 17.0 - - + +
196B SER* 3.4 29.2 - - - +
200B ARG* 4.9 1.3 - - - +
233B LYS* 5.5 3.6 - - + +
234B SER* 5.2 7.0 - - - -
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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