Contacts of the helix formed by residues 356 - 369 (chain N) in PDB entry 6AH0
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 356 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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354N PRO 2.0 30.3 + - - +
355N GLY* 1.3 69.2 - - - -
357N THR* 1.3 54.4 + - - +
358N ALA 3.4 2.2 - - - -
359N LYS* 3.1 6.2 + - - -
360N ALA* 2.9 25.0 + - - -
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Residues in contact with THR 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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355N GLY 4.2 0.8 + - - -
356N ASP* 1.3 68.4 - - - +
358N ALA* 1.3 65.6 + - - +
360N ALA* 3.2 3.0 + - - +
361N VAL* 2.9 21.3 + - - -
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Residues in contact with ALA 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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356N ASP 3.4 0.6 - - - -
357N THR* 1.3 75.0 - - - +
359N LYS* 1.3 57.9 + - - +
361N VAL* 3.2 3.2 + - - +
362N VAL* 2.9 25.8 + - - -
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Residues in contact with LYS 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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354N PRO* 4.8 7.0 - - - -
356N ASP 3.1 7.7 + - - -
358N ALA* 1.3 74.7 - - - +
360N ALA* 1.3 57.2 + - - +
362N VAL* 3.2 2.5 + - - +
363N ALA* 2.9 27.5 + - - -
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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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350N ALA* 5.6 5.4 - - - +
354N PRO* 4.3 14.0 + - - -
356N ASP 2.9 14.1 + - - -
357N THR* 3.2 4.5 + - - +
359N LYS* 1.3 75.4 - - - +
361N VAL* 1.3 52.7 + - - +
363N ALA* 5.3 0.2 - - - +
364N GLN* 2.4 40.3 + - - +
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Residues in contact with VAL 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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357N THR 2.9 13.5 + - - -
358N ALA* 3.6 4.3 - - - +
360N ALA* 1.3 75.7 - - - +
362N VAL* 1.3 56.1 + - - +
365N ALA* 2.3 40.2 + - - +
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Residues in contact with VAL 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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358N ALA 2.9 14.1 + - - -
359N LYS* 3.2 3.6 + - - +
361N VAL* 1.3 77.9 - - - +
363N ALA* 1.3 57.6 + - - +
366N VAL* 3.0 22.4 + - - +
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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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346N TRP* 5.7 2.7 - - - +
350N ALA* 5.7 4.9 - - - +
359N LYS 2.9 16.2 + - - -
360N ALA* 5.3 0.2 - - - +
362N VAL* 1.3 71.9 - - - +
364N GLN* 1.3 58.2 + - - +
366N VAL 3.9 0.2 - - - -
367N ARG* 2.9 25.3 + - - -
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Residues in contact with GLN 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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346N TRP 6.0 1.6 - - - -
350N ALA* 5.4 8.4 - - - +
360N ALA* 2.4 26.8 + - - +
363N ALA* 1.3 65.4 - - - +
365N ALA* 1.3 58.4 + - - +
367N ARG* 3.2 2.4 + - - +
368N HIS* 2.9 26.5 + - - -
381N GLU* 5.6 7.9 - - - +
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Residues in contact with ALA 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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360N ALA 3.5 0.4 + - - -
361N VAL* 2.3 32.3 + - - +
364N GLN* 1.3 68.5 - - - +
366N VAL* 1.3 55.8 + - - +
368N HIS* 3.2 2.4 + - - +
369N LEU* 2.9 27.2 + - - -
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Residues in contact with VAL 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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361N VAL 3.5 0.2 + - - -
362N VAL* 3.0 21.4 + - - +
363N ALA 4.0 0.2 - - - -
365N ALA* 1.3 76.4 - - - +
367N ARG* 1.3 53.3 + - - +
369N LEU* 5.1 0.9 - - - +
370N PRO* 2.6 34.9 - - - +
371N GLN 4.1 1.9 + - - -
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Residues in contact with ARG 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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346N TRP* 5.9 7.9 - - - +
363N ALA 2.9 17.0 + - - -
364N GLN* 3.7 3.1 - - - +
366N VAL* 1.3 78.1 - - - +
368N HIS* 1.3 60.3 + - - +
369N LEU 3.5 0.2 + - - -
370N PRO 3.6 2.8 - - - -
371N GLN* 4.3 2.6 + - - +
372N SER 3.5 15.6 + - - +
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Residues in contact with HIS 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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364N GLN 2.9 14.3 + - - -
365N ALA* 3.7 2.7 - - - +
367N ARG* 1.3 77.9 - - - +
369N LEU* 1.3 57.3 + - - +
372N SER 3.0 17.8 - - - +
373N VAL* 3.8 13.0 - - - +
374N ARG* 6.4 0.4 - - - +
377N ILE 5.5 10.3 - - - -
378N ARG* 5.8 3.6 - - - +
381N GLU* 6.4 1.8 - - - +
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Residues in contact with LEU 369 (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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365N ALA 2.9 14.9 + - - -
366N VAL* 3.4 2.7 - - - +
368N HIS* 1.3 76.0 - - - +
370N PRO* 1.3 64.5 - - - +
372N SER 4.8 1.1 - - - -
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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