Contacts of the helix formed by residues 327 - 336 (chain A) in PDB entry 2JDQ
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 327 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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286A ASN* 3.2 17.7 + - - +
326A GLY* 1.3 82.3 - - - +
328A ASP* 1.3 58.4 + - - +
329A ILE* 2.9 19.1 + - - +
330A GLN* 2.9 43.7 + - - +
331A THR* 2.6 22.7 + - - +
474B GLU* 4.6 3.8 - - - +
738E LYS* 5.1 2.0 - - - +
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Residues in contact with ASP 328 (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* 1.3 78.0 - - - +
329A ILE* 1.3 61.3 + - + +
330A GLN 3.5 0.2 - - - -
331A THR* 3.9 6.3 - - - -
332A GLN* 3.1 13.3 + - - +
367A ALA 4.7 1.7 - - - +
368A GLY* 4.5 9.6 - - - -
369A ASN* 3.4 36.3 + - - +
372A GLN* 2.8 35.0 + - - +
738E LYS* 4.7 8.3 - - - -
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Residues in contact with ILE 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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327A ASP* 2.9 13.6 + - - +
328A ASP* 1.3 74.5 - - + +
330A GLN* 1.3 64.5 + - - +
332A GLN* 3.1 8.7 + - - +
333A VAL* 3.0 23.6 + - - +
470B ALA* 4.0 23.3 - - + +
473B GLU* 4.1 20.9 - - + +
474B GLU* 3.2 23.3 - - + +
478B LEU* 3.3 46.7 - - + -
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Residues in contact with GLN 330 (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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286A ASN* 2.7 39.6 + - - +
289A ILE* 3.8 9.3 - - + +
290A GLN* 3.5 11.5 - - - +
293A ILE* 3.6 21.8 - - + +
323A ILE* 4.2 9.3 - - - +
326A GLY* 3.1 14.1 - - - -
327A ASP* 2.9 41.6 + - - +
329A ILE* 1.3 76.6 - - - +
331A THR* 1.3 60.3 + - - +
333A VAL* 3.3 20.7 - - - +
334A ILE* 3.8 2.1 + - - +
474B GLU* 3.2 32.9 + - - +
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Residues in contact with THR 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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324A VAL* 3.8 30.1 - - - +
326A GLY 2.9 17.7 - - - +
327A ASP 2.6 33.8 + - - +
328A ASP* 4.1 3.8 - - - -
329A ILE 3.3 0.4 - - - -
330A GLN* 1.3 72.3 - - - +
332A GLN* 1.3 64.9 + - - +
334A ILE* 3.2 13.7 + - - +
335A LEU* 3.2 17.8 + - - +
365A ILE* 4.6 12.0 - - - +
372A GLN* 3.8 17.8 + - - +
738E LYS* 3.2 17.9 + - - +
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Residues in contact with GLN 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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328A ASP 3.1 14.6 + - - +
329A ILE* 3.1 11.0 + - - +
331A THR* 1.3 74.7 + - - +
333A VAL* 1.3 66.2 + - - +
334A ILE 3.0 0.2 + - - -
335A LEU* 3.0 18.7 + - - +
336A ASN* 2.8 58.4 + - - +
369A ASN* 5.5 0.3 + - - -
371A ALA* 5.8 1.7 - - - +
372A GLN* 3.0 30.7 + - - +
375A THR* 5.6 4.8 - - - +
465B ILE* 4.2 20.6 - - + +
470B ALA* 4.9 6.3 - - + -
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Residues in contact with VAL 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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293A ILE* 4.0 20.0 - - + -
298A CYS* 3.8 27.4 - - + -
329A ILE 3.0 22.6 + - - +
330A GLN* 3.3 17.7 - - - +
331A THR 3.2 0.2 - - - -
332A GLN* 1.3 78.1 - - - +
334A ILE* 1.3 56.0 + - - +
336A ASN* 3.9 13.1 - - - +
337A CYS* 3.4 17.7 - - - -
470B ALA* 3.9 16.8 - - + +
471B LEU* 3.9 23.8 - - + -
474B GLU* 4.2 7.4 - - + -
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Residues in contact with ILE 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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298A CYS* 3.7 26.9 - - + -
302A VAL* 3.8 18.6 - - + -
320A VAL* 4.1 19.1 - - + +
323A ILE* 3.9 26.7 - - + -
324A VAL* 3.7 28.9 - - + -
330A GLN 3.8 2.2 + - - +
331A THR 3.2 7.9 + - - +
332A GLN 3.1 0.4 - - - -
333A VAL* 1.3 72.5 - - - +
335A LEU* 1.3 70.4 + - + +
336A ASN 3.1 1.6 - - - -
337A CYS* 3.2 15.9 + - - +
339A ALA* 3.5 32.4 + - + +
365A ILE* 5.3 2.0 - - + -
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Residues in contact with LEU 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 THR* 3.5 13.0 - - - +
332A GLN* 3.0 22.0 + - - +
334A ILE* 1.3 80.7 - - + +
336A ASN* 1.3 58.7 + - - +
337A CYS 2.9 6.5 + - - -
338A SER* 3.1 14.0 + - - -
339A ALA* 4.0 4.8 + - + +
340A LEU* 4.2 19.7 - - + -
365A ILE* 3.8 39.5 - - + -
372A GLN* 3.5 36.6 - - + -
375A THR* 3.7 22.2 - - + +
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Residues in contact with ASN 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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299A ARG* 3.0 17.3 + - - +
332A GLN* 2.8 47.2 + - - +
333A VAL* 3.9 8.5 - - - +
334A ILE 3.1 0.4 - - - -
335A LEU* 1.3 76.7 - - - +
337A CYS* 1.3 55.5 + - - +
338A SER* 3.2 4.6 + - - -
465B ILE* 3.5 31.2 - - - +
466B ASN 4.6 0.4 + - - -
467B PRO* 4.0 31.3 + - + +
470B ALA* 4.3 10.9 - - - +
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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