Contacts of the helix formed by residues 347 - 358 (chain A) in PDB entry 3A9E
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 VAL 347 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A 754 4.3 22.0 - - + -
269A PRO* 5.8 1.1 - - + -
270A VAL* 4.4 16.8 - - + -
273A ILE* 5.6 2.9 - - + -
342A ALA* 3.1 25.0 + - + +
345A ALA* 4.3 14.4 - - + +
346A GLY* 1.3 85.0 - - - +
348A GLY* 1.3 64.8 + - - +
349A ALA* 3.3 4.0 - - - +
350A ILE* 3.5 13.0 - - + +
351A PHE* 3.1 25.9 + - + +
440A HIS* 4.0 25.4 - - + +
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Residues in contact with GLY 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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342A ALA 3.7 2.6 + - - -
343A HIS* 3.4 45.0 - - - +
346A GLY 3.7 1.8 - - - -
347A VAL* 1.3 75.0 - - - +
349A ALA* 1.3 59.1 + - - +
351A PHE* 4.2 4.0 - - - -
352A ASP* 2.8 36.6 + - - -
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Residues in contact with ALA 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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343A HIS* 4.4 1.6 - - - -
347A VAL 3.3 0.8 - - - -
348A GLY* 1.3 78.3 - - - +
350A ILE* 1.3 61.9 + - - +
352A ASP* 3.6 7.6 - - - +
353A ARG* 3.3 22.8 + - - +
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Residues in contact with ILE 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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1A 754 3.7 26.7 - - + -
347A VAL* 3.5 17.0 - - + +
349A ALA* 1.3 76.8 - - - +
351A PHE* 1.3 69.5 + - - +
353A ARG* 3.3 25.1 + - - +
354A VAL* 3.2 22.3 + - - +
433A ILE* 3.9 27.1 - - + +
436A LYS* 3.7 34.5 - - + -
437A CYS* 4.7 3.8 - - - +
440A HIS* 3.9 26.7 - - + +
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Residues in contact with PHE 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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1A 754 4.6 17.5 - - + -
273A ILE* 5.0 4.5 - - + -
328A GLY* 4.2 0.9 - - - -
329A ILE* 3.6 40.8 - - + -
337A VAL* 3.2 39.7 - - + -
339A ARG* 4.0 17.3 - - - -
342A ALA* 3.4 21.3 - - + -
347A VAL* 3.1 21.2 + - + +
348A GLY* 3.8 3.8 - - - +
350A ILE* 1.3 79.7 - - + +
352A ASP* 1.3 64.1 + - - +
354A VAL* 3.4 10.1 + - + +
355A LEU* 3.2 54.9 + - + +
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Residues in contact with ASP 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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339A ARG* 3.1 38.2 + - - +
343A HIS* 3.0 27.3 + - - -
348A GLY 2.8 20.4 + - - +
349A ALA* 3.6 7.2 + - - +
351A PHE* 1.3 77.9 - - - +
353A ARG* 1.3 64.6 + - - +
355A LEU* 3.2 6.6 + - - +
356A THR* 2.9 35.5 + - + +
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Residues in contact with ARG 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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349A ALA 3.3 14.3 + - - +
350A ILE* 3.3 24.9 + - + +
352A ASP* 1.3 78.5 - - - +
354A VAL* 1.3 55.7 + - - +
356A THR* 4.0 2.0 - - - -
357A GLU* 2.8 75.5 + - - +
429A ALA* 4.4 3.0 + - - +
432A SER* 2.9 48.3 + - - -
433A ILE* 3.6 22.6 - - + +
436A LYS* 4.8 5.4 - - - +
340B GLN* 5.8 3.1 - - - +
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Residues in contact with VAL 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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1A 754 4.0 20.0 - - + -
315A ILE* 4.7 1.6 - - + -
318A PHE* 3.9 16.6 - - + -
319A SER* 3.6 22.2 - - - +
329A ILE* 4.6 7.2 - - + -
350A ILE 3.2 14.1 + - - +
351A PHE* 3.6 12.8 - - + +
353A ARG* 1.3 77.6 - - - +
355A LEU* 1.3 57.8 + - - +
358A LEU* 3.1 8.7 + - + +
359A VAL* 2.8 33.9 + - + -
433A ILE* 3.7 30.3 - - + -
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Residues in contact with LEU 355 (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 ASP* 4.1 18.2 - - - +
328A GLY 3.5 33.4 - - - +
329A ILE* 4.0 9.2 - - + -
339A ARG* 4.0 25.6 - - + +
351A PHE* 3.2 37.2 + - + +
352A ASP* 3.2 11.5 + - - +
354A VAL* 1.3 77.5 - - - +
356A THR* 1.3 58.9 + - + +
359A VAL* 3.6 11.3 - - + +
360A SER* 2.7 40.7 + - - +
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Residues in contact with THR 356 (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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352A ASP* 2.9 22.0 + - + +
353A ARG* 4.0 2.3 - - - -
355A LEU* 1.3 82.2 - - + +
357A GLU* 1.3 76.2 + - - +
358A LEU 3.6 0.2 - - - -
360A SER* 3.7 13.5 - - - +
361A LYS* 3.4 26.6 - - - +
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Residues in contact with GLU 357 (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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353A ARG* 2.8 73.4 + - - +
356A THR* 1.3 84.5 + - - +
358A LEU* 1.3 66.9 + - - +
361A LYS* 3.3 23.8 - - - +
426A ARG* 4.1 9.2 + - - -
429A ALA* 3.9 23.6 - - + +
433A ILE* 4.4 3.3 - - + +
338B ASP* 5.4 13.0 - - + +
340B GLN* 5.0 8.5 - - - +
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Residues in contact with LEU 358 (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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315A ILE* 3.6 22.9 - - + -
316A ALA* 5.6 0.2 - - - -
319A SER* 3.5 25.6 - - - +
354A VAL* 3.1 14.2 + - + +
357A GLU* 1.3 84.2 - - - +
359A VAL* 1.3 68.1 + - - +
360A SER 3.4 0.7 - - - -
361A LYS* 3.4 2.1 + - - +
362A MET* 3.0 41.1 + - + +
426A ARG* 4.3 9.4 - - + +
429A ALA* 4.2 4.5 - - + -
430A LEU* 3.9 37.9 - - + +
433A ILE* 3.7 26.7 - - + -
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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