Contacts of the helix formed by residues 356 - 368 (chain A) in PDB entry 1T0K
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 THR 356 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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350A ALA* 4.8 2.0 - - - +
353A GLY 5.4 2.7 - - - +
355A GLN* 1.3 75.6 - - - +
357A VAL* 1.3 66.8 + - - +
358A ASP* 3.9 7.8 + - - +
359A GLU* 2.8 36.0 + - - +
360A ALA* 2.8 20.3 + - - +
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Residues in contact with VAL 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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189A LYS* 3.9 5.6 - - + +
192A LEU* 3.4 45.3 - - + +
193A THR* 3.3 36.1 - - + +
196A VAL* 4.7 15.5 - - + -
200A LYS* 5.8 2.7 - - - +
350A ALA* 4.3 12.4 + - + +
355A GLN 4.0 0.2 + - - -
356A THR* 1.3 72.7 - - - +
358A ASP* 1.3 68.2 + - - +
360A ALA* 3.1 1.2 + - - +
361A LEU* 2.9 33.1 + - + +
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Residues in contact with ASP 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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184A ASP* 4.5 1.6 - - - +
189A LYS* 3.2 47.2 + - - +
356A THR* 3.3 7.7 + - - +
357A VAL* 1.3 79.9 - - - +
359A GLU* 1.3 58.3 + - + +
361A LEU* 4.3 1.0 - - - +
362A LYS* 2.9 32.7 + - - +
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Residues in contact with GLU 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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354A ARG 4.9 1.9 - - - +
355A GLN* 3.8 22.5 + - + +
356A THR* 2.8 45.0 + - - +
358A ASP* 1.3 71.4 - - + +
360A ALA* 1.3 64.2 + - - +
362A LYS* 3.3 6.1 + - - +
363A ASP* 3.0 28.4 + - - +
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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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192A LEU* 4.9 1.1 - - + -
346A ALA* 3.5 44.2 - - + +
349A ASN* 4.8 0.7 - - + -
350A ALA* 3.9 10.8 - - + +
355A GLN* 3.8 23.3 - - + +
356A THR 2.8 14.3 + - - +
357A VAL* 3.7 6.1 - - - +
359A GLU* 1.3 73.8 - - - +
361A LEU* 1.3 58.6 + - - +
363A ASP* 3.3 3.8 + - - +
364A ALA 3.1 20.8 + - - -
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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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158A TRP* 6.3 0.4 - - + -
161A ILE* 5.0 10.8 - - + -
183A VAL* 3.4 33.9 - - + +
184A ASP* 3.9 11.1 - - - +
188A ALA 3.9 4.3 - - - +
189A LYS* 3.5 42.0 - - + +
192A LEU* 3.4 35.2 - - + -
343A VAL* 5.5 4.5 - - + -
346A ALA* 4.0 12.6 - - + -
357A VAL* 2.9 15.3 + - + +
358A ASP 4.3 0.9 - - - +
360A ALA* 1.3 72.2 - - - +
362A LYS* 1.4 57.4 + - - +
363A ASP 3.1 0.7 - - - -
364A ALA* 3.2 4.1 + - + +
365A GLN* 2.8 34.1 + - - +
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Residues in contact with LYS 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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184A ASP* 3.7 23.0 + - - +
358A ASP 2.9 20.9 + - - +
359A GLU* 3.3 7.2 + - - +
361A LEU* 1.4 75.0 - - - +
363A ASP* 1.3 69.8 + - - +
365A GLN* 3.3 13.9 - - + +
366A THR* 3.6 12.0 + - - +
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Residues in contact with ASP 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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355A GLN* 2.8 33.4 + - - +
359A GLU 3.0 12.0 + - - +
360A ALA 3.6 4.9 - - - +
361A LEU 3.1 0.2 - - - -
362A LYS* 1.3 87.1 + - - +
364A ALA* 1.3 60.5 + - - +
366A THR* 3.2 5.9 + - - -
367A ASN* 2.8 44.9 + - - +
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Residues in contact with ALA 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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183A VAL* 3.8 14.6 - - + -
342A ALA* 3.6 37.2 - - + +
343A VAL* 4.3 4.5 - - + +
346A ALA* 4.3 8.5 - - + -
360A ALA 3.1 15.6 + - - +
361A LEU* 3.2 6.3 + - + +
363A ASP* 1.3 73.4 - - - +
365A GLN* 1.4 67.6 + - - +
367A ASN* 4.0 2.0 + - - -
368A SER* 2.9 30.1 + - - -
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Residues in contact with GLN 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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179A LYS 5.1 4.8 + - - -
181A VAL* 2.9 40.3 + - - +
183A VAL* 3.5 10.1 - - - +
184A ASP* 3.3 38.9 + - + +
361A LEU 2.8 13.8 + - - +
362A LYS* 3.3 13.7 - - + +
364A ALA* 1.4 77.1 - - - +
366A THR* 1.4 59.7 + - - +
368A SER* 4.1 3.8 - - - -
369A SER* 4.0 12.5 + - - -
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Residues in contact with THR 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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362A LYS* 3.6 14.2 + - - +
363A ASP* 3.2 8.5 + - - -
364A ALA 3.1 0.4 - - - -
365A GLN* 1.4 77.3 - - - +
367A ASN* 1.4 69.3 + - - +
368A SER 2.9 6.7 + - - -
369A SER* 3.0 21.6 + - - +
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Residues in contact with ASN 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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338A ALA* 3.9 14.2 - - - +
342A ALA* 4.0 19.6 - - + +
363A ASP* 2.8 41.6 + - - +
364A ALA* 4.0 1.2 + - - -
366A THR* 1.4 77.0 - - - +
368A SER* 1.3 59.0 + - - +
369A SER 3.4 6.9 + - - +
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Residues in contact with SER 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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169A PHE* 4.1 4.3 - - - -
181A VAL* 3.6 29.7 - - - +
183A VAL* 5.0 2.2 - - - -
335A GLN* 2.6 30.9 - - - +
338A ALA* 4.0 1.8 - - - +
339A PHE* 3.4 32.2 - - - +
342A ALA* 4.0 8.2 - - - +
364A ALA* 2.9 20.6 + - - -
365A GLN 4.1 2.7 - - - -
366A THR 2.9 0.4 + - - -
367A ASN* 1.3 74.7 - - - +
369A SER* 1.3 54.1 + - - +
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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