Contacts of the helix formed by residues 342 - 353 (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 SER 342 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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340N PRO 3.4 9.9 + - - +
341N LYS* 1.3 77.0 - - - +
343N GLU* 1.3 62.7 + - - +
344N ASP 3.4 2.0 - - - +
345N VAL* 4.3 4.5 + - - +
346N TRP* 4.2 8.8 + - - -
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Residues in contact with GLU 343 (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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341N LYS 3.3 4.6 + - - -
342N SER* 1.3 72.2 - - - +
344N ASP* 1.3 60.4 + - - +
345N VAL 3.3 0.4 - - - -
346N TRP* 3.1 4.4 + - - +
347N LEU* 2.9 25.3 + - - -
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Residues in contact with ASP 344 (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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342N SER* 3.4 1.4 - - - +
343N GLU* 1.3 76.7 - - - +
345N VAL* 1.3 56.7 + - - +
347N LEU* 3.2 3.2 + - - +
348N GLU* 2.9 26.3 + - - -
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Residues in contact with VAL 345 (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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313N ILE* 6.6 0.2 - - - +
332N ILE 5.2 4.8 - - - +
342N SER* 4.3 6.2 + - - +
343N GLU 3.3 0.4 - - - -
344N ASP* 1.3 75.7 - - - +
346N TRP* 1.3 56.2 + - - +
348N GLU* 3.2 2.8 + - - +
349N ALA* 2.9 26.9 + - - -
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Residues in contact with TRP 346 (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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342N SER 4.2 6.4 + - - -
343N GLU 3.1 9.1 + - - -
345N VAL* 1.3 76.2 - - - +
347N LEU* 1.3 63.3 + - - +
349N ALA* 3.2 10.6 + - - +
350N ALA* 3.3 11.4 + - - -
363N ALA 5.7 2.8 - - - +
364N GLN* 6.0 1.6 - - - -
367N ARG* 5.9 8.1 - - - +
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Residues in contact with LEU 347 (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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343N GLU 2.9 13.9 + - - -
344N ASP* 3.2 4.0 + - - +
346N TRP* 1.3 77.1 - - - +
348N GLU* 1.3 63.2 + - - +
350N ALA* 3.7 0.9 + - - -
351N ARG* 3.7 12.8 + - - -
377N ILE* 6.3 2.7 - - - +
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Residues in contact with GLU 348 (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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344N ASP 2.9 14.3 + - - -
345N VAL* 3.2 4.2 + - - +
347N LEU* 1.3 75.6 - - - +
349N ALA* 1.3 61.3 - - - +
351N ARG* 3.4 9.4 + - - -
352N LEU* 3.4 11.1 + - - -
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Residues in contact with ALA 349 (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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332N ILE* 5.2 13.2 - - - +
345N VAL 2.9 15.3 + - - -
346N TRP* 3.2 3.0 + - - +
348N GLU* 1.3 77.9 - - - +
350N ALA* 1.3 57.3 + - - +
352N LEU* 4.2 0.2 - - - -
353N GLN* 2.9 30.0 + - - -
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Residues in contact with ALA 350 (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 3.3 12.0 + - - -
347N LEU 3.7 1.7 + - - -
348N GLU 3.3 0.2 - - - -
349N ALA* 1.3 77.7 - - - +
351N ARG* 1.3 56.9 + - - +
354N PRO* 2.9 32.0 - - - +
360N ALA* 5.6 5.2 - - - +
363N ALA* 5.7 3.6 - - - +
364N GLN* 5.4 13.2 - - - +
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Residues in contact with ARG 351 (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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347N LEU 3.7 8.7 + - - -
348N GLU 3.4 5.4 + - - -
349N ALA 3.2 0.4 - - - -
350N ALA* 1.3 75.7 - - - +
352N LEU* 1.3 66.1 + - - +
354N PRO* 4.3 1.6 - - - +
355N GLY 5.1 2.1 + - - -
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Residues in contact with LEU 352 (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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329N ARG* 6.4 0.4 - - - -
348N GLU 3.4 11.3 + - - -
349N ALA* 4.2 0.7 - - - +
351N ARG* 1.3 77.7 - - - +
353N GLN* 1.3 63.0 + - - +
354N PRO 3.6 0.2 - - - -
355N GLY 4.7 2.3 + - - -
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Residues in contact with GLN 353 (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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329N ARG* 5.8 7.4 - - - +
349N ALA 2.9 16.8 + - - -
352N LEU* 1.3 77.5 - - - +
354N PRO* 1.3 64.8 - - - +
355N GLY 3.4 1.0 + - - -
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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