Contacts of the helix formed by residues 343 - 357 (chain A) in PDB entry 2ES0
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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329A ARG* 3.0 38.0 + - - +
333A TRP* 3.0 28.2 + - + +
339A GLU 3.3 14.8 + - - +
340A ILE 3.0 6.2 - - - +
342A LYS* 1.3 79.7 - - + +
344A GLN* 1.3 58.2 + - - +
345A VAL 2.9 15.8 + - - -
346A GLY 3.1 1.9 + - - -
347A ARG* 2.8 26.9 + - - +
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Residues in contact with GLN 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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329A ARG* 5.6 0.4 - - - +
342A LYS 3.7 4.4 + - - +
343A ASP* 1.3 74.7 + - - +
345A VAL* 1.3 71.8 + - + +
347A ARG* 3.6 30.9 + - - +
348A ASP* 2.9 38.8 + - - +
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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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325A PRO* 4.1 17.9 - - + -
329A ARG* 3.4 27.4 - - - +
333A TRP* 4.1 14.6 - - + -
343A ASP* 2.9 3.2 + - - +
344A GLN* 1.3 89.5 - - + +
346A GLY* 1.3 63.5 + - - +
348A ASP* 3.5 6.9 + - - +
349A GLN* 3.2 26.8 + - + +
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Residues in contact with GLY 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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333A TRP* 3.3 43.6 - - - -
340A ILE* 3.8 10.1 - - - +
343A ASP* 3.1 8.0 + - - -
345A VAL* 1.3 75.0 - - - +
347A ARG* 1.3 59.2 + - - +
349A GLN* 3.2 4.5 + - - +
350A PHE* 2.9 28.4 + - - +
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Residues in contact with ARG 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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340A ILE* 3.4 16.0 + - + +
341A LEU* 3.0 39.7 + - + +
342A LYS 4.2 5.3 + - - -
343A ASP 2.8 15.8 + - - +
344A GLN* 3.6 37.5 + - - +
346A GLY* 1.3 77.6 - - - +
348A ASP* 1.3 63.8 + - - +
350A PHE* 3.3 2.8 + - - +
351A LEU* 2.8 28.9 + - - +
363A LEU* 3.9 18.0 - - + +
366A TRP* 5.1 0.9 - - - -
367A LEU* 3.7 37.5 - - + +
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Residues in contact with ASP 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 GLN* 2.9 28.6 + - - +
345A VAL* 3.8 8.9 - - + +
346A GLY 3.3 0.2 - - - -
347A ARG* 1.3 85.7 + - - +
349A GLN* 1.3 62.8 + - + +
351A LEU* 3.4 15.3 + - - +
352A ARG* 3.1 36.7 + - - +
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Residues in contact with GLN 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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333A TRP* 4.1 23.1 - - + -
345A VAL* 3.2 19.8 + - + +
346A GLY 3.2 10.2 + - - +
348A ASP* 1.3 75.5 - - - +
350A PHE* 1.3 65.4 + - - +
352A ARG* 3.2 27.0 + - - +
353A PHE* 3.1 20.3 + - - +
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Residues in contact with PHE 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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337A PHE* 3.5 35.9 - + - -
340A ILE* 3.7 20.9 - - + -
341A LEU* 5.3 1.1 - - + -
346A GLY 2.9 13.8 + - - +
347A ARG* 3.5 7.9 - - + +
349A GLN* 1.3 76.1 - - - +
351A LEU* 1.3 54.4 + - - +
353A PHE* 3.2 23.9 + + + +
354A LEU* 2.9 63.8 + - + +
363A LEU* 3.9 21.8 - - + -
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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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347A ARG 2.8 18.9 + - - +
348A ASP* 3.5 15.0 - - - +
349A GLN 3.2 0.2 - - - -
350A PHE* 1.3 75.9 - - - +
352A ARG* 1.3 59.0 + - + +
354A LEU* 3.2 2.8 + - - +
355A GLU* 2.9 42.7 + - - +
360A SER* 3.9 29.2 - - - +
363A LEU* 4.0 22.9 - - + -
364A ARG* 4.3 17.5 - - + -
367A LEU* 5.8 5.8 - - + -
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Residues in contact with ARG 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 ASP* 3.1 23.0 + - - +
349A GLN* 3.2 28.8 + - - +
351A LEU* 1.3 77.7 - - + +
353A PHE* 1.3 61.7 + - - +
355A GLU* 3.4 19.7 + - - +
356A SER* 3.2 20.4 + - - -
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Residues in contact with PHE 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 GLN 3.1 12.3 + - - +
350A PHE* 3.3 24.2 - + + +
352A ARG* 1.3 73.9 - - - +
354A LEU* 1.3 80.4 + - + +
356A SER* 2.7 28.4 + - - -
357A GLU* 3.0 47.8 + - + +
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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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350A PHE* 2.9 58.6 + - + +
351A LEU* 3.2 6.9 + - - +
353A PHE* 1.3 84.5 - - + +
355A GLU* 1.3 56.7 + - - +
357A GLU* 3.0 4.3 + - + +
358A PHE 2.9 23.9 + - - -
359A SER* 2.9 38.1 + - - +
360A SER* 3.7 15.3 - - - -
362A ASN* 5.2 2.9 - - + -
363A LEU* 3.6 34.3 - - + +
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Residues in contact with GLU 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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351A LEU* 2.9 32.9 + - - +
352A ARG* 3.5 24.7 - - - +
353A PHE 3.2 0.2 - - - -
354A LEU* 1.3 76.5 - - - +
356A SER* 1.3 59.8 + - - +
358A PHE* 3.2 25.6 + - - +
360A SER* 3.7 22.9 + - - +
364A ARG* 5.7 2.4 + - - -
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Residues in contact with SER 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 ARG 3.2 9.5 + - - -
353A PHE* 2.7 33.7 + - - -
355A GLU* 1.3 75.5 - - - +
357A GLU* 1.3 61.1 + - - +
358A PHE* 3.3 12.6 + - - -
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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
----------------------------------------------------------
353A PHE* 3.1 55.2 - - + +
354A LEU* 3.0 10.1 + - + +
356A SER* 1.3 78.9 + - - +
358A PHE* 1.3 69.6 + - - +
359A SER* 3.4 15.8 + - - +
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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