Contacts of the helix formed by residues 343 - 354 (chain A) in PDB entry 3EIJ
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 343 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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338A TYR* 3.4 12.8 - - - +
341A SER* 3.1 19.5 + - - +
342A GLY* 1.3 74.4 - - - +
344A ILE* 1.3 62.8 + - - +
345A SER* 3.3 20.3 + - - -
346A GLU* 3.3 28.6 + - + +
347A ALA* 3.2 15.1 + - - +
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Residues in contact with ILE 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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338A TYR* 3.6 31.4 - - + +
342A GLY 3.3 12.3 + - - +
343A ASP* 1.3 72.4 + - - +
345A SER* 1.3 61.0 + - - +
347A ALA* 3.0 4.5 + - - +
348A GLU* 2.8 34.3 + - + +
385A ASP* 4.6 12.3 - - + +
386A LEU* 4.1 20.7 - - + +
389A SER* 3.1 31.4 - - - +
390A LEU* 5.8 0.9 - - + -
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Residues in contact with SER 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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343A ASP* 3.3 10.0 + - - -
344A ILE* 1.3 82.5 - - - +
346A GLU* 1.3 56.7 + - - +
348A GLU* 3.3 8.2 + - - +
349A HIS* 2.9 32.8 + - - +
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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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256A ARG* 2.9 44.3 + - - -
259A GLN* 3.9 10.8 - - - +
297A LYS* 3.5 20.1 + - + -
337A GLU* 4.3 17.5 - - + +
341A SER* 5.6 0.2 - - - +
343A ASP* 3.3 32.6 + - + +
344A ILE 3.3 0.6 - - - -
345A SER* 1.3 78.1 - - - +
347A ALA* 1.3 58.5 - - - +
349A HIS* 4.0 2.6 - - - +
350A CYS* 3.0 38.6 + - + +
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Residues in contact with ALA 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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334A LEU* 3.9 29.6 - - + +
338A TYR* 4.1 22.2 - - + -
343A ASP 3.2 11.2 + - - +
344A ILE 3.0 8.1 + - - +
346A GLU* 1.3 78.0 - - - +
348A GLU* 1.3 61.0 + - - +
350A CYS* 3.8 1.1 - - - -
351A LEU* 2.9 30.7 + - - +
386A LEU* 4.1 12.6 - - + -
390A LEU* 5.4 1.1 - - + -
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Residues in contact with GLU 348 (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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344A ILE* 2.8 19.7 + - + +
345A SER* 3.7 8.2 + - - +
347A ALA* 1.3 74.3 - - - +
349A HIS* 1.3 66.3 + - - +
351A LEU* 3.1 12.5 + - - +
352A LYS* 3.1 43.0 + - - +
389A SER* 4.5 8.5 + - - -
390A LEU* 3.8 25.3 - - + +
393A SER* 2.7 32.5 + - - -
395A THR* 3.4 8.6 + - + +
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Residues in contact with HIS 349 (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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256A ARG* 2.5 62.5 + - - +
345A SER* 2.9 18.8 + - - +
346A GLU* 4.0 3.8 - - - +
348A GLU* 1.3 77.8 - - - +
350A CYS* 1.3 68.8 + - + +
352A LYS* 3.1 12.3 + - - +
353A GLU* 3.1 51.0 + - + +
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Residues in contact with CYS 350 (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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256A ARG* 5.3 1.6 - - - +
334A LEU* 3.3 38.8 - - - -
337A GLU* 6.0 2.0 - - - -
346A GLU* 3.0 27.8 + - + +
347A ALA* 4.2 0.9 - - - -
349A HIS* 1.3 86.2 - - + +
351A LEU* 1.3 60.9 + - - +
353A GLU* 3.4 19.1 - - - +
354A LEU* 3.6 13.1 + - - +
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Residues in contact with LEU 351 (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 ILE* 4.1 18.6 - - + -
334A LEU* 3.6 20.2 - - + -
347A ALA 2.9 20.8 + - - +
348A GLU 3.1 6.5 - - - +
349A HIS 3.1 0.2 - - - -
350A CYS* 1.3 77.3 - - - +
352A LYS* 1.3 62.8 + - - +
354A LEU* 3.1 24.2 + - + +
355A GLU 3.9 1.4 + - - -
356A VAL* 5.0 1.1 - - + +
360A HIS* 4.2 30.4 + - + +
363A LEU* 4.4 16.4 - - + -
390A LEU* 4.2 22.9 - - + -
395A THR* 3.9 25.6 - - + -
396A ILE* 4.7 4.3 - - + -
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Residues in contact with LYS 352 (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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348A GLU* 3.1 42.4 + - + +
349A HIS* 3.1 7.8 + - - +
351A LEU* 1.3 70.3 - - - +
353A GLU* 1.3 53.9 + - - +
354A LEU 2.9 5.4 - - - -
355A GLU* 2.5 38.7 + - - +
360A HIS* 5.5 6.5 - - + -
393A SER* 5.1 4.9 + - - -
395A THR* 3.9 26.3 + - + +
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Residues in contact with GLU 353 (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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213A ALA* 4.4 11.3 - - - +
216A ARG* 3.7 28.4 + - - -
256A ARG* 4.7 1.7 + - - -
260A LEU* 5.2 3.5 - - - +
349A HIS* 3.1 48.1 + - + +
350A CYS* 3.4 14.1 - - - +
352A LYS* 1.3 75.6 - - - +
354A LEU* 1.3 60.8 + - + +
355A GLU* 3.4 6.4 + - - +
358B HIS* 3.6 19.2 + - - -
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Residues in contact with LEU 354 (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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327A LEU* 5.0 2.2 - - + -
330A GLU* 3.8 38.8 - - + +
331A ILE* 3.9 28.0 - - + -
334A LEU* 4.1 17.7 - - + -
350A CYS* 3.6 11.4 - - - +
351A LEU* 3.1 16.7 + - + +
352A LYS 2.7 1.2 + - - -
353A GLU* 1.3 80.0 - - + +
355A GLU* 1.3 70.9 + - - +
356A VAL* 3.6 20.5 - - + +
358B HIS* 3.6 13.1 + - + +
359B PHE* 4.3 16.6 - - + -
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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