Contacts of the helix formed by residues 338 - 348 (chain A) in PDB entry 2WZJ
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 THR 338 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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333A VAL* 5.3 1.1 - - - -
336A GLY 4.7 4.7 - - - +
337A TYR* 1.3 74.4 - - - +
339A ARG* 1.3 64.1 + - - +
340A GLU* 3.4 21.5 + - - +
341A GLU* 2.9 46.2 + - - +
342A ILE* 3.1 11.6 + - - +
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Residues in contact with ARG 339 (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 THR* 3.3 30.8 - - + +
330A GLU* 2.9 41.2 + - - +
333A VAL* 3.6 26.9 - - + +
337A TYR 3.9 0.6 + - - -
338A THR* 1.3 72.1 - - - +
340A GLU* 1.3 60.5 + - - +
342A ILE* 3.6 15.2 + - - +
343A GLN* 3.3 21.5 + - - +
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Residues in contact with GLU 340 (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 THR* 3.0 17.6 + - - +
339A ARG* 1.3 77.9 - - - +
341A GLU* 1.3 67.0 + - + +
343A GLN* 3.4 5.9 + - - +
344A ASP* 2.9 44.0 + - - +
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Residues in contact with GLU 341 (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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336A GLY 4.2 2.6 - - - +
337A TYR* 3.6 24.6 - - + -
338A THR* 2.9 52.8 + - - +
340A GLU* 1.3 78.6 - - + +
342A ILE* 1.3 63.5 + - - +
344A ASP* 4.4 7.0 - - - +
345A SER* 2.7 34.0 + - - +
354A VAL* 4.0 12.5 - - + +
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Residues in contact with ILE 342 (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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323A TYR 4.5 5.6 - - - +
329A THR* 4.1 26.0 - - + +
332A MET* 3.8 35.2 - - + -
333A VAL* 4.4 1.8 - - + +
337A TYR* 4.1 20.0 - - + +
338A THR 3.1 14.5 + - - +
339A ARG* 3.6 16.8 - - - +
341A GLU* 1.3 78.5 - - - +
343A GLN* 1.3 64.3 + - + +
345A SER* 3.8 1.6 - - - -
346A LEU* 3.3 40.5 + - + +
354A VAL* 3.6 9.9 - - + +
358A TYR* 4.1 18.2 - - + -
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Residues in contact with GLN 343 (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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323A TYR* 3.5 23.5 - - - +
324A LYS* 3.6 36.1 - - - +
339A ARG 3.3 10.8 + - - +
340A GLU* 3.7 9.2 - - - +
341A GLU 3.3 0.2 - - - -
342A ILE* 1.3 79.8 - - - +
344A ASP* 1.3 67.0 + - - +
346A LEU* 3.3 3.8 + - - +
347A VAL* 2.9 33.9 + - + +
323B TYR* 3.0 34.1 - - + +
324B LYS* 4.2 13.4 - - - +
343B GLN* 5.2 0.6 - - - +
347B VAL* 5.1 8.5 - - - +
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Residues in contact with ASP 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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340A GLU* 2.9 33.9 + - - +
341A GLU* 4.1 6.8 - - + +
343A GLN* 1.3 76.3 - - - +
345A SER* 1.3 60.0 + - - +
347A VAL* 3.8 1.3 - - - +
348A GLY* 2.9 29.8 + - - -
350A ARG* 4.8 4.1 + - - +
320B LEU* 3.9 36.0 - - + +
321B PRO* 3.9 15.0 - - + +
323B TYR* 3.5 19.7 + - - -
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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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341A GLU* 2.7 22.7 + - - +
342A ILE 3.8 0.9 - - - -
344A ASP* 1.3 78.2 - - - +
346A LEU* 1.3 58.9 + - - +
349A GLN* 3.2 4.0 + - - -
350A ARG* 3.0 38.0 + - - +
352A ASN* 2.9 38.6 + - - -
354A VAL* 3.5 15.7 - - - +
355A MET* 3.9 8.1 - - - +
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Residues in contact with LEU 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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323A TYR* 3.4 44.9 - - + +
342A ILE* 3.3 25.4 + - + +
343A GLN 4.1 2.0 - - - +
344A ASP 3.2 1.0 - - - -
345A SER* 1.3 77.6 - - - +
347A VAL* 1.3 63.1 - - - +
349A GLN* 3.0 26.6 + - - +
354A VAL* 5.8 0.7 - - + -
355A MET* 3.5 40.4 - - + +
358A TYR* 3.5 52.3 - - + -
359A LEU* 5.0 3.6 - - + -
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Residues in contact with VAL 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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323A TYR* 4.4 11.4 - - + -
343A GLN* 2.9 23.3 - - + +
344A ASP 3.8 2.0 - - - +
346A LEU* 1.3 77.5 - - + +
348A GLY* 1.3 58.9 + - - +
349A GLN* 3.1 9.4 + - - +
321B PRO* 4.2 7.6 - - + -
323B TYR* 3.6 50.7 - - + -
346B LEU 4.2 5.8 - - - +
347B VAL* 3.9 31.1 - - + +
349B GLN* 3.9 24.6 - - - +
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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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344A ASP 2.9 15.1 + - - -
345A SER 4.3 0.2 - - - -
347A VAL* 1.3 75.4 - - - +
349A GLN* 1.3 72.6 + - - +
350A ARG* 3.2 18.9 + - - -
321B PRO* 4.0 15.8 - - - +
349B GLN* 5.9 0.7 - - - -
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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