Contacts of the helix formed by residues 356 - 370 (chain N) in PDB entry 3O3U
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 N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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350N ALA* 4.7 0.2 - - - -
355N GLN* 1.3 78.3 - - - +
357N VAL* 1.3 65.0 + - - +
358N ASP* 3.6 8.1 + - - +
359N ALA* 2.9 26.9 + - + +
360N ALA* 2.9 23.4 + - - +
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Residues in contact with VAL 357 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189N LYS* 3.9 11.7 - - - +
192N LEU* 4.1 11.0 - - + -
193N THR* 3.6 32.1 - - + +
196N VAL* 3.8 33.4 - - + -
350N ALA* 4.1 9.8 - - + +
355N GLN 3.8 1.0 + - - -
356N THR* 1.3 72.0 - - - +
358N ASP* 1.3 73.3 + - - +
360N ALA* 3.8 0.3 - - - +
361N LEU* 2.9 43.0 + - + +
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Residues in contact with ASP 358 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189N LYS* 3.4 47.7 + - - +
193N THR* 5.4 0.9 + - - -
356N THR* 3.2 8.1 + - - +
357N VAL* 1.3 81.2 - - - +
359N ALA* 1.3 58.1 + - - +
361N LEU* 3.9 0.9 - - - +
362N ALA* 2.9 29.8 + - - +
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Residues in contact with ALA 359 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355N GLN* 3.7 22.8 - - + +
356N THR* 2.9 21.0 + - + +
358N ASP* 1.3 75.4 - - - +
360N ALA* 1.3 64.8 - - - +
362N ALA* 3.4 6.2 + - - +
363N ALA* 3.1 23.6 + - - +
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Residues in contact with ALA 360 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192N LEU* 5.2 0.2 - - + -
346N ALA* 3.6 34.5 - - + +
350N ALA* 4.3 9.4 - - + +
355N GLN* 3.4 25.9 - - + +
356N THR 2.9 17.1 + - - +
357N VAL* 3.8 3.1 - - - +
359N ALA* 1.3 78.3 - - - +
361N LEU* 1.3 58.4 + - + +
363N ALA* 3.4 4.0 + - - +
364N ALA* 3.0 26.7 + - - +
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Residues in contact with LEU 361 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158N TRP* 6.5 0.4 - - + -
161N ILE* 5.6 7.6 - - + -
183N VAL* 3.4 36.7 - - + +
184N ASP* 3.4 9.3 - - + +
188N ALA* 3.9 8.3 - - + +
189N LYS* 3.7 40.8 - - + +
192N LEU* 3.8 22.9 - - + -
343N VAL* 5.8 4.0 - - + -
346N ALA* 4.1 11.7 - - + -
347N VAL* 6.1 0.2 - - + -
357N VAL* 2.9 25.3 + - + +
358N ASP 4.2 2.0 - - - +
360N ALA* 1.3 74.2 - - - +
362N ALA* 1.3 61.8 + - - +
364N ALA* 3.7 2.0 - - - +
365N GLN* 2.9 31.2 + - - +
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Residues in contact with ALA 362 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184N ASP* 3.9 18.2 - - + +
189N LYS* 6.2 1.1 - - - +
358N ASP 2.9 19.2 + - - +
359N ALA* 3.7 7.4 - - - +
360N ALA 3.3 0.2 - - - -
361N LEU* 1.3 76.8 - - - +
363N ALA* 1.3 63.5 + - - +
365N GLN* 3.4 2.9 + - - +
366N THR* 3.2 26.2 + - - -
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Residues in contact with ALA 363 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355N GLN* 4.8 7.9 - - - +
359N ALA 3.1 17.1 + - - +
360N ALA* 3.7 6.3 - - - +
362N ALA* 1.3 76.3 - - - +
364N ALA* 1.3 64.0 + - - +
366N THR* 3.3 7.2 + - - -
367N ASN* 3.0 36.1 + - - +
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Residues in contact with ALA 364 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183N VAL* 3.7 21.3 - - + -
342N ALA* 3.5 36.9 - - + +
343N VAL* 4.4 0.9 - - - +
346N ALA* 3.8 10.1 - - + -
360N ALA 3.0 17.2 + - - +
361N LEU* 3.3 0.9 + - - +
363N ALA* 1.3 75.6 - - - +
365N GLN* 1.3 59.3 + - - +
367N ASN* 3.3 2.5 + - - +
368N ALA* 2.8 33.3 + - - +
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Residues in contact with GLN 365 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179N LYS 5.1 2.4 + - - -
181N VAL* 2.9 35.2 + - - +
183N VAL* 2.9 36.7 + - - +
184N ASP* 3.1 33.2 + - + +
361N LEU 2.9 17.7 + - - +
362N ALA 3.5 4.5 - - - +
364N ALA* 1.3 76.2 - - - +
366N THR* 1.3 63.4 + - - +
368N ALA* 3.4 2.7 + - - +
369N ALA* 3.0 33.3 + - + +
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Residues in contact with THR 366 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362N ALA 3.2 12.5 + - - -
363N ALA* 3.6 10.6 - - - -
365N GLN* 1.3 80.6 - - - +
367N ASN* 1.3 67.8 + - - +
369N ALA* 3.4 2.7 + - - -
370N ALA* 3.0 26.5 + - + +
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Residues in contact with ASN 367 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338N ALA* 4.5 10.6 - - - +
342N ALA* 3.9 17.1 - - + +
345N THR* 6.2 2.8 - - - +
363N ALA* 3.0 29.6 + - - +
364N ALA* 3.8 6.1 - - - +
366N THR* 1.3 83.6 - - - +
368N ALA* 1.3 63.0 + - - +
370N ALA* 3.4 18.9 + - - +
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Residues in contact with ALA 368 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169N PHE* 4.2 16.1 - - + -
178N ILE 4.7 0.7 - - - +
181N VAL* 4.0 21.5 - - + -
183N VAL* 4.8 2.2 - - + -
335N GLN* 5.1 5.4 - - - +
338N ALA* 4.4 17.2 - - - +
339N PHE* 4.0 27.6 - - + -
342N ALA* 4.1 3.8 - - + +
364N ALA 2.8 21.4 + - - +
365N GLN 4.0 2.9 - - - +
367N ASN* 1.3 73.3 - - - +
369N ALA* 1.3 60.2 + - - +
370N ALA 3.3 3.2 + - - +
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Residues in contact with ALA 369 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178N ILE 4.2 8.6 - - - +
179N LYS* 2.7 50.5 + - - +
181N VAL* 3.9 21.1 - - + -
365N GLN* 3.0 23.1 + - + +
366N THR* 3.8 3.8 - - - +
368N ALA* 1.3 74.6 - - - +
370N ALA* 1.3 61.7 + - - +
371N ALA 3.6 0.2 + - - -
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Residues in contact with ALA 370 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179N LYS* 4.6 1.8 - - - +
335N GLN* 5.9 2.8 - - - +
366N THR* 3.0 19.1 + - + +
367N ASN* 3.5 14.5 - - - +
368N ALA 3.3 5.3 - - - +
369N ALA* 1.3 80.0 - - - +
371N ALA* 1.3 69.7 + - - +
372N SER* 3.4 4.3 + - - -
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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