Contacts of the helix formed by residues 330 - 347 (chain A) in PDB entry 2ILU
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 ASN 330 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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180A PHE* 3.8 28.9 - - + -
328A LEU* 3.1 3.3 + - - +
329A ILE* 1.3 96.5 + - - +
331A ALA* 1.3 66.6 + - - +
332A ALA* 3.3 9.5 + - - +
333A ALA* 3.0 21.7 + - - +
334A LEU* 3.1 19.4 + - - +
363A TYR* 3.8 20.5 - - + +
482A NDP 2.6 27.0 + - - -
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Residues in contact with ALA 331 (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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330A ASN* 1.3 75.0 - - - +
332A ALA* 1.3 64.5 + - - +
334A LEU* 3.1 5.7 + - - +
335A GLU* 3.0 37.3 + - - +
363A TYR* 3.4 30.7 - - + +
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Residues in contact with ALA 332 (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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330A ASN* 3.3 11.0 + - - +
331A ALA* 1.3 77.7 - - - +
333A ALA* 1.3 63.8 + - - +
335A GLU* 3.3 10.1 + - - +
336A ARG* 3.0 53.7 + - - +
482A NDP 4.6 17.9 - - + +
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Residues in contact with ALA 333 (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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152A TRP* 5.8 1.1 - - + -
283A GLN* 5.5 1.6 - - - +
328A LEU* 4.1 11.0 - - + -
329A ILE* 3.9 14.4 - - + -
330A ASN* 3.0 22.3 + - - +
332A ALA* 1.3 75.6 - - - +
334A LEU* 1.3 61.3 + - - +
336A ARG* 3.5 3.7 + - - +
337A VAL* 3.0 31.5 + - - +
385A PHE* 4.3 18.4 - - + -
482A NDP 3.9 16.8 - - - +
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Residues in contact with LEU 334 (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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328A LEU* 3.5 21.6 - - + +
330A ASN 3.1 8.7 + - - +
331A ALA* 3.1 10.0 + - - +
333A ALA* 1.3 78.1 - - - +
335A GLU* 1.3 62.9 + - + +
337A VAL* 3.3 3.6 + - - +
338A GLU* 3.1 36.8 + - - +
357A ALA* 4.5 4.3 - - + -
358A VAL 4.7 8.5 - - - +
362A GLY 4.6 2.2 - - - +
363A TYR* 3.5 41.1 - - + -
364A TYR 3.5 23.1 - - - +
365A TYR* 4.1 16.2 - - + -
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Residues in contact with GLU 335 (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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331A ALA* 3.0 29.1 + - + +
332A ALA* 3.7 10.3 + - - +
334A LEU* 1.3 73.5 - - + +
336A ARG* 1.3 66.6 + - + +
338A GLU* 3.0 27.5 + - - +
339A GLN* 3.0 27.7 + - + +
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Residues in contact with ARG 336 (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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332A ALA* 3.0 38.1 + - - +
333A ALA 3.9 4.0 - - - +
335A GLU* 1.3 75.9 - - + +
337A VAL* 1.3 63.2 + - - +
339A GLN* 3.8 15.1 + - - +
340A LYS* 3.0 60.8 + - - +
385A PHE* 3.2 20.3 - - + -
482A NDP 3.3 55.1 + - - -
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Residues in contact with VAL 337 (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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328A LEU* 3.9 10.3 - - + -
333A ALA 3.0 17.6 + - - +
334A LEU* 3.5 7.6 - - - +
335A GLU 3.2 0.6 - - - -
336A ARG* 1.3 75.1 - - - +
338A GLU* 1.3 57.6 - - - +
340A LYS* 4.0 2.9 - - - +
341A VAL* 3.0 35.3 + - + +
365A TYR* 3.6 35.9 - - + -
384A THR* 3.7 10.5 - - + +
385A PHE* 3.8 4.9 - - + -
386A GLY* 3.2 39.3 - - - +
388A VAL* 4.0 9.6 - - + -
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Residues in contact with GLU 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A LEU* 3.1 28.5 - - + +
335A GLU* 3.0 21.8 + - - +
337A VAL* 1.3 73.9 - - - +
339A GLN* 1.3 58.5 + - + +
341A VAL* 3.0 6.7 + - - +
342A ALA* 2.7 37.4 + - - +
357A ALA* 3.4 34.5 - - + +
365A TYR* 4.2 9.0 - - + -
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Residues in contact with GLN 339 (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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335A GLU* 3.0 18.9 + - + +
336A ARG* 3.8 24.2 + - - +
338A GLU* 1.3 79.0 - - + +
340A LYS* 1.3 54.5 + - - +
342A ALA* 3.2 5.4 + - - +
343A ARG* 2.6 67.0 + - - +
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Residues in contact with LYS 340 (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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336A ARG* 3.0 55.2 + - - +
337A VAL* 4.0 3.4 - - - +
339A GLN* 1.3 74.8 - - - +
341A VAL* 1.3 58.0 + - + +
343A ARG* 3.8 20.0 - - - +
344A ALA* 2.9 30.1 + - - +
379A ILE* 4.0 19.7 - - + +
382A GLU* 4.1 29.4 - - + +
383A GLU 3.6 20.2 + - - +
384A THR* 4.4 18.6 + - + +
385A PHE* 3.8 9.9 - - - -
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Residues in contact with VAL 341 (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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337A VAL 3.0 26.0 + - - +
338A GLU 3.0 4.5 + - - +
340A LYS* 1.3 72.7 - - + +
342A ALA* 1.3 69.0 + - - +
344A ALA* 3.1 7.7 + - - +
345A VAL* 2.9 38.5 + - + +
351A VAL* 5.3 1.1 - - + -
355A GLY* 4.1 16.4 - - - +
365A TYR* 3.5 26.0 - - + +
368A THR* 4.7 1.8 - - + -
370A LEU* 4.7 13.5 - - + -
379A ILE* 5.2 2.2 - - + -
384A THR* 6.2 0.2 - - + -
388A VAL* 3.8 33.9 - - + -
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Residues in contact with ALA 342 (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 GLU 2.7 20.5 + - - +
339A GLN* 3.5 6.1 - - - +
341A VAL* 1.3 74.2 - - - +
343A ARG* 1.3 63.4 + - + +
345A VAL* 3.1 16.3 + - - +
346A GLU* 3.0 23.9 + - + +
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Residues in contact with ARG 343 (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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339A GLN* 2.6 57.1 + - - +
340A LYS* 3.9 21.0 - - - +
342A ALA* 1.3 72.9 - - + +
344A ALA* 1.3 61.4 + - - +
346A GLU* 3.4 27.5 + - - +
347A GLU* 3.3 25.0 - - - +
378A SER* 5.3 5.5 + - - +
382A GLU* 4.7 15.2 + - - -
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Residues in contact with ALA 344 (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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340A LYS 2.9 20.1 + - - +
341A VAL 3.2 6.3 - - - +
343A ARG* 1.3 74.5 - - - +
345A VAL* 1.3 65.3 + - - +
347A GLU* 3.1 23.0 + - - +
348A GLY 3.5 0.5 + - - -
349A ALA* 3.0 25.0 + - + +
370A LEU* 4.1 11.2 - - + -
377A MET* 4.2 3.6 - - - +
378A SER* 5.6 1.1 + - - -
379A ILE* 4.0 27.6 - - + +
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Residues in contact with VAL 345 (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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341A VAL* 2.9 24.5 + - + +
342A ALA* 3.1 8.5 + - - +
344A ALA* 1.3 74.8 - - - +
346A GLU* 1.3 60.8 + - + +
348A GLY* 3.3 10.2 + - - -
349A ALA* 3.5 26.6 + - + +
351A VAL* 3.5 31.2 - - + -
370A LEU* 4.4 1.3 - - + -
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Residues in contact with GLU 346 (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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342A ALA* 3.0 20.3 - - - +
343A ARG* 3.5 21.9 - - - +
344A ALA 3.1 0.4 - - - -
345A VAL* 1.3 77.6 - - + +
347A GLU* 1.3 61.8 + - + +
348A GLY 3.3 1.4 + - - -
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Residues in contact with GLU 347 (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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343A ARG* 3.3 22.4 - - - +
344A ALA* 3.1 10.6 + - - +
346A GLU* 1.3 78.7 - - + +
348A GLY* 1.3 56.7 + - - +
349A ALA 3.7 0.4 - - - -
377A MET* 3.3 33.8 - - + +
378A SER* 2.7 42.6 + - - -
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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