Contacts of the helix formed by residues 326 - 334 (chain A) in PDB entry 2R8J
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 326 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296A ASP* 4.7 15.3 + - - +
298A GLY* 5.8 5.8 - - - -
300A PHE 5.7 0.9 - - - -
301A GLU* 3.6 11.1 + - - -
323A PRO* 4.3 1.0 - - - +
325A GLU* 1.3 82.4 - - - +
327A SER* 1.3 63.8 + - - +
328A ILE 3.4 2.9 - - - +
329A LYS* 3.8 26.8 + - + +
330A HIS* 3.4 19.8 + - - +
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Residues in contact with SER 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A GLU* 2.6 26.0 + - - +
302A ILE* 3.3 30.9 + - - +
317A ILE* 6.5 0.2 - - - -
322A LEU* 4.5 11.4 - - - +
323A PRO* 4.1 19.7 - - - -
325A GLU 3.2 1.7 - - - -
326A ASN* 1.3 76.8 - - - +
328A ILE* 1.3 62.8 + - - +
330A HIS* 3.2 7.7 + - - +
331A ILE* 3.0 35.1 + - - +
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Residues in contact with ILE 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A LEU* 3.8 23.3 - - + +
300A PHE* 3.7 20.4 - - + +
301A GLU* 3.6 43.7 - - - +
302A ILE* 3.7 4.9 - - - +
305A PHE* 3.7 25.1 - - + -
326A ASN* 3.4 0.8 - - - +
327A SER* 1.3 75.0 - - - +
329A LYS* 1.3 65.3 + - - +
330A HIS 3.3 0.3 + - - -
331A ILE* 3.7 7.1 + - + -
332A ARG* 3.4 27.0 + - - +
378A SER* 3.7 33.6 - - - +
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Residues in contact with LYS 329 (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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296A ASP* 3.3 35.9 + - + +
326A ASN* 3.8 29.5 + - + +
327A SER 3.3 0.2 - - - -
328A ILE* 1.3 79.3 - - - +
330A HIS* 1.3 62.4 + - - +
332A ARG* 3.5 15.1 - - - +
333A GLU* 2.5 59.2 + - - +
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Residues in contact with HIS 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A LEU 5.7 0.9 - - - -
321A ASP 4.8 10.1 + - - -
322A LEU* 4.4 9.3 - - + +
323A PRO* 3.4 30.6 - - + +
326A ASN 3.4 12.7 + - - +
327A SER* 3.2 14.1 + - - +
328A ILE 3.1 0.4 - - - -
329A LYS* 1.3 75.5 - - - +
331A ILE* 1.3 66.1 + - - +
332A ARG 2.8 5.9 + - - -
333A GLU* 2.8 16.5 + - - +
334A THR* 2.9 46.9 + - + -
335A TRP* 5.1 1.3 - + - -
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Residues in contact with ILE 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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302A ILE* 3.9 25.4 - - + -
320A LEU* 4.7 4.9 - - + -
322A LEU* 3.5 39.5 - - + -
327A SER 3.0 15.1 + - - +
328A ILE* 4.1 6.5 - - - +
330A HIS* 1.3 75.6 + - - +
332A ARG* 1.3 60.1 + - - +
335A TRP* 2.9 35.1 + - + +
342A LEU* 3.8 25.5 - - + +
374A LEU* 4.4 25.6 - - + +
375A PHE* 5.2 3.3 - - - +
378A SER* 4.5 6.6 + - - +
379A ARG* 4.5 1.6 + - - -
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Residues in contact with ARG 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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292A LEU* 3.2 41.8 - - - +
295A LEU* 4.3 4.8 - - - +
296A ASP* 3.0 41.0 + - - -
328A ILE* 3.4 13.3 + - - +
329A LYS* 3.5 26.7 - - - +
330A HIS 2.8 1.4 + - - -
331A ILE* 1.3 80.9 - - - +
333A GLU* 1.3 65.9 + - + +
335A TRP 3.4 0.5 - - - -
336A PRO* 3.4 12.3 - - - +
378A SER* 2.9 28.7 + - - +
379A ARG* 2.8 61.1 + - + +
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Residues in contact with GLU 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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329A LYS* 2.5 53.7 + - + +
330A HIS* 2.8 12.1 + - - +
332A ARG* 1.3 76.9 + - + +
334A THR* 1.3 54.9 + - - +
335A TRP 3.1 5.6 - - - -
336A PRO* 2.9 24.3 - - - +
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Residues in contact with THR 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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330A HIS* 2.9 38.9 + - + -
333A GLU* 1.3 77.2 - - - +
335A TRP* 1.3 106.3 + - + +
336A PRO* 3.5 3.2 - - - +
345A PHE* 6.2 1.1 - - + -
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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