Contacts of the helix formed by residues 327 - 338 (chain A) in PDB entry 4IQJ
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 327 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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319A LEU* 3.6 13.1 - - - +
323A PRO 3.4 25.6 - - - +
324A ASP 4.6 2.2 - - - +
325A ARG* 3.2 15.6 + - - +
326A ILE* 1.3 73.4 - - - +
328A GLU* 1.3 69.8 + - - +
329A ALA* 3.7 9.7 + - - +
330A PHE* 3.2 23.3 + - - +
331A TYR* 3.3 12.3 + - - +
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Residues in contact with GLU 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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319A LEU* 4.0 17.2 - - + +
327A THR* 1.3 78.7 - - - +
329A ALA* 1.3 62.3 + - - +
331A TYR* 3.3 1.9 + - - -
332A ARG* 3.1 46.7 + - - +
346A ASP 5.6 0.2 - - - -
347A GLU* 3.2 39.7 - - + +
350A LEU* 3.5 11.6 - - + +
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Residues in contact with ALA 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 THR* 3.2 9.5 + - - +
328A GLU* 1.3 81.3 - - - +
330A PHE* 1.3 60.4 + - - +
332A ARG* 3.7 10.6 + - - +
333A GLU* 3.4 26.0 + - - +
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Residues in contact with PHE 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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325A ARG 4.1 7.6 - - - +
326A ILE* 4.2 18.8 - - + -
327A THR* 3.2 21.7 + - - +
328A GLU 3.2 1.0 - - - -
329A ALA* 1.3 79.6 - - - +
331A TYR* 1.3 72.3 + + - +
333A GLU* 3.3 19.8 + - + +
334A VAL* 3.3 20.2 + - + +
380A ALA* 3.5 35.7 - - + -
381A GLU* 3.4 27.8 - - + -
384A LEU* 3.5 33.9 - - + -
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Residues in contact with TYR 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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315A PHE* 2.8 46.0 + + + +
318A LEU* 3.5 19.4 - - - +
319A LEU* 3.4 34.5 - - + -
326A ILE* 3.8 12.1 - - + -
327A THR 3.3 6.1 + - - +
328A GLU* 3.3 1.3 + - - +
330A PHE* 1.3 88.8 - + - +
332A ARG* 1.3 65.1 + - - +
334A VAL* 3.3 8.0 + - + +
335A LEU* 3.0 28.2 + - - +
350A LEU* 3.6 26.5 - - + -
351A ALA* 5.1 2.5 - - + -
354A LEU* 3.4 29.7 - - + +
384A LEU* 4.5 19.7 - - + -
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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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328A GLU* 3.1 36.6 + - - +
329A ALA* 3.9 9.8 - - - +
331A TYR* 1.3 76.4 - - - +
333A GLU* 1.3 53.2 + - - +
335A LEU* 3.8 7.2 - - + +
336A ARG* 2.7 39.9 + - + +
346A ASP 4.5 13.7 + - - +
350A LEU* 3.5 32.9 - - + +
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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 ALA 3.4 14.3 + - - +
330A PHE* 3.3 16.0 + - + +
331A TYR 3.2 0.4 - - - -
332A ARG* 1.3 79.4 - - - +
334A VAL* 1.3 53.6 + - + +
336A ARG* 3.4 32.4 + - - +
337A LEU* 2.8 48.9 + - + +
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Residues in contact with VAL 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 PHE* 3.3 25.7 + - + +
331A TYR* 3.3 9.6 + - + +
332A ARG 3.3 0.4 - - - -
333A GLU* 1.3 76.7 - - + +
335A LEU* 1.3 66.6 + - - +
337A LEU* 3.4 14.8 + - + +
338A LEU* 3.3 23.5 + - + +
354A LEU* 4.1 9.4 - - + -
362A TRP* 3.7 34.8 - - + -
365A LEU* 4.0 9.8 - - + +
384A LEU* 3.5 27.8 - - + -
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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 TYR 3.0 21.7 + - - +
332A ARG* 3.8 5.6 - - + +
334A VAL* 1.3 76.0 - - - +
336A ARG* 1.3 58.2 + - - +
338A LEU* 3.0 32.7 + - + +
350A LEU* 4.0 34.8 - - + +
353A ALA* 4.0 25.4 - - + +
354A LEU* 3.5 31.9 - - + +
357A VAL* 4.6 8.5 - - + -
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Residues in contact with ARG 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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332A ARG 2.7 25.1 + - - +
333A GLU* 3.4 30.3 + - - +
335A LEU* 1.3 73.7 - - - +
337A LEU* 1.3 72.4 + - - +
338A LEU 3.4 5.2 + - - -
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Residues in contact with LEU 337 (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 GLU* 2.8 41.0 + - + +
334A VAL* 3.5 13.9 - - + +
335A LEU 3.2 0.4 - - - -
336A ARG* 1.3 85.0 - - - +
338A LEU* 1.3 63.4 + - - +
365A LEU* 4.3 17.3 - - + -
368A ARG* 4.0 30.5 + - - +
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Residues in contact with LEU 338 (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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334A VAL* 3.3 18.8 + - + +
335A LEU* 3.0 22.8 + - + +
336A ARG* 4.0 5.4 - - - -
337A LEU* 1.3 83.2 - - - +
357A VAL* 4.0 33.9 - - + -
361A ALA* 4.2 21.5 - - + +
362A TRP* 4.9 1.1 - - + -
364A GLU* 5.0 8.3 - - + +
365A LEU* 3.7 35.2 - - + -
368A ARG* 5.5 1.3 - - - +
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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