Contacts of the helix formed by residues 309 - 323 (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 PRO 309 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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307N HIS 3.7 2.6 - - - +
308N HIS* 1.3 72.5 - - - +
310N PRO* 1.3 56.1 - - - +
311N ALA 3.1 0.9 - - - -
312N TRP* 2.8 24.2 + - - +
313N ILE* 3.0 13.7 + - - -
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Residues in contact with PRO 310 (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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1792A LYS* 5.7 9.9 - - - +
308N HIS 2.8 3.8 - - - +
309N PRO* 1.3 78.6 - - - +
311N ALA* 1.3 58.9 + - - +
313N ILE* 4.0 0.9 + - - -
314N ALA* 3.5 16.5 + - - -
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Residues in contact with ALA 311 (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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298N LEU 5.2 3.1 - - - +
301N VAL 5.8 4.0 - - - -
302N ARG* 5.1 15.9 + - - +
308N HIS 3.2 8.3 + - - -
309N PRO 3.1 0.6 - - - -
310N PRO* 1.3 76.6 - - - +
312N TRP* 1.3 57.8 - - - +
314N ALA* 4.1 2.6 - - - +
315N SER* 3.5 14.7 + - - -
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Residues in contact with TRP 312 (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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302N ARG* 6.3 0.9 - - - +
308N HIS 4.2 1.2 + - - -
309N PRO* 2.8 15.1 + - - +
311N ALA* 1.3 75.8 - - - +
313N ILE* 1.3 60.5 - - - +
314N ALA 3.2 1.3 - - - -
315N SER* 3.4 3.1 + - - -
316N ALA* 3.2 16.6 + - - -
331N LEU 5.7 2.4 - - - +
332N ILE* 5.8 3.5 - - - -
335N GLY* 6.3 3.1 - - - -
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Residues in contact with ILE 313 (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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309N PRO 3.0 11.9 + - - -
310N PRO 4.5 0.7 - - - -
312N TRP* 1.3 71.5 - - - +
314N ALA* 1.3 54.8 + - - +
316N ALA* 3.5 2.1 - - - +
317N ARG* 2.6 34.0 + - - -
345N VAL* 6.6 0.2 - - - +
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Residues in contact with ALA 314 (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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1797A ASN* 6.5 0.9 - - - +
310N PRO 3.5 15.6 + - - -
311N ALA* 4.4 2.0 - - - +
312N TRP 3.2 0.8 - - - -
313N ILE* 1.3 77.6 - - - +
315N SER* 1.3 58.2 + - - +
317N ARG* 4.3 0.7 - - - +
318N LEU* 2.6 35.1 + - - +
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Residues in contact with SER 315 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298N LEU* 5.8 9.0 - - - +
311N ALA 3.5 11.7 + - - -
312N TRP 3.4 7.6 + - - -
313N ILE 3.3 0.4 - - - -
314N ALA* 1.3 75.9 - - - +
316N ALA* 1.3 58.3 + - - +
319N GLU* 3.6 16.1 + - - +
328N ALA* 5.4 2.6 - - - -
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Residues in contact with ALA 316 (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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312N TRP 3.2 9.8 + - - -
313N ILE* 3.2 6.6 + - - +
314N ALA 3.1 0.6 - - - -
315N SER* 1.3 79.4 - - - +
317N ARG* 1.3 56.6 + - - +
319N GLU* 3.9 0.2 - - - -
320N GLU* 2.8 26.0 + - - -
328N ALA* 4.7 21.9 - - - +
331N LEU* 6.1 0.9 - - - +
332N ILE* 5.6 5.4 - - - +
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Residues in contact with ARG 317 (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 2.6 20.5 + - - -
314N ALA* 4.5 0.7 - - - +
316N ALA* 1.3 70.6 - - - +
318N LEU* 1.3 63.2 + - - +
320N GLU* 3.2 9.0 + - - +
321N VAL* 3.2 11.1 + - - -
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Residues in contact with LEU 318 (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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314N ALA* 2.6 20.8 + - - +
317N ARG* 1.3 71.4 - - - +
319N GLU* 1.3 60.7 + - - +
321N VAL* 3.5 1.6 + - - -
322N THR* 3.4 16.5 + - - -
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Residues in contact with GLU 319 (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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314N ALA 4.0 0.4 + - - -
315N SER* 3.6 20.2 + - - +
316N ALA 3.9 0.2 - - - -
317N ARG 3.2 0.6 - - - -
318N LEU* 1.3 75.1 - - - +
320N GLU* 1.3 52.2 + - - +
322N THR* 3.2 2.1 + - - +
323N GLY* 2.8 31.2 + - - -
324N LYS* 3.2 6.1 + - - -
328N ALA* 5.9 3.8 - - - +
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Residues in contact with GLU 320 (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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316N ALA 2.8 18.7 + - - -
317N ARG* 3.2 3.7 + - - +
319N GLU* 1.3 77.6 - - - +
321N VAL* 1.3 61.2 + - - +
323N GLY 3.6 4.0 - - - +
324N LYS* 3.5 26.6 + - - +
328N ALA* 5.8 2.0 - - - +
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Residues in contact with VAL 321 (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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317N ARG 3.2 11.7 + - - -
318N LEU 3.5 2.4 + - - -
319N GLU 3.3 0.4 - - - -
320N GLU* 1.3 79.3 - - - +
322N THR* 1.3 62.7 + - - +
323N GLY 5.0 0.3 - - - +
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Residues in contact with THR 322 (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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318N LEU 3.4 9.4 + - - -
319N GLU* 3.2 5.4 + - - +
321N VAL* 1.3 80.0 - - - +
323N GLY* 1.3 55.6 + - - +
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Residues in contact with GLY 323 (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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319N GLU 2.8 12.8 + - - -
320N GLU 3.6 5.0 - - - +
321N VAL 3.4 0.4 - - - +
322N THR* 1.3 74.2 - - - +
324N LYS* 1.3 63.8 + - - -
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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