Contacts of the helix formed by residues 330 - 343 (chain A) in PDB entry 4IE6
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 330 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103A GLY* 3.2 10.5 - - - +
104A CYS* 4.3 9.0 - - + -
326A CYS* 3.5 30.8 + - + +
328A THR 3.7 0.6 - - - -
329A GLY* 1.3 83.6 - - - +
331A LEU* 1.3 65.4 + - - +
332A ASP* 3.8 7.7 + - - +
333A TYR* 3.1 26.5 + - - +
334A ILE 3.0 18.9 + - - -
378A TRP* 3.5 11.6 - - - -
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Residues in contact with LEU 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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103A GLY* 2.8 25.1 + - - +
330A THR* 1.3 70.4 - - - +
332A ASP* 1.3 67.6 + - - +
334A ILE* 3.1 9.4 + - + +
335A LEU* 2.9 47.2 + - + +
378A TRP* 3.8 3.4 - - - -
395A TRP* 3.6 23.6 - - + -
396A TRP* 4.2 9.6 - - + -
399A PRO* 3.6 32.1 - - + +
403A LEU* 3.9 29.4 - - + -
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Residues in contact with ASP 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A THR* 3.3 7.8 + - - +
331A LEU* 1.3 80.2 - - - +
333A TYR* 1.3 63.2 + - - +
335A LEU* 3.4 12.9 + - - +
336A GLN* 3.0 25.3 + - - +
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Residues in contact with TYR 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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327A SER 3.2 25.4 - - - +
328A THR* 3.4 42.5 - - + +
330A THR* 3.1 24.8 + - - +
332A ASP* 1.3 79.3 - - - +
334A ILE* 1.3 67.5 + - + +
336A GLN* 3.3 13.9 + - - +
337A ARG* 3.1 61.9 + - + +
373A GLU* 2.5 31.5 + - - -
378A TRP* 5.1 0.4 - - - -
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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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330A THR 3.0 13.9 + - - +
331A LEU* 3.4 19.1 - - + +
333A TYR* 1.3 77.7 - - + +
335A LEU* 1.3 64.9 + - - +
337A ARG* 3.3 10.1 + - + +
338A CYS* 3.0 25.2 + - - -
370A ILE* 5.4 1.6 - - + +
373A GLU* 4.1 27.1 - - + +
374A VAL* 4.2 18.2 - - + +
378A TRP* 3.6 55.2 - - + +
403A LEU* 4.1 20.9 - - + -
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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 LEU* 2.9 43.3 + - + +
332A ASP* 3.8 11.2 - - - +
334A ILE* 1.3 77.6 - - - +
336A GLN* 1.3 61.0 + - - +
338A CYS* 3.1 5.0 + - - +
339A GLN* 3.0 23.3 + - - +
399A PRO* 5.4 0.7 - - + +
402A GLN* 3.8 39.0 - - - +
403A LEU* 3.6 24.9 - - + -
406A LEU* 4.0 9.9 - - + +
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Residues in contact with GLN 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 ASP 3.0 18.6 + - - +
333A TYR* 3.3 13.3 + - - +
335A LEU* 1.3 76.9 - - - +
337A ARG* 1.3 64.3 + - + +
339A GLN* 3.4 16.5 + - - +
340A LEU* 3.0 22.3 + - + +
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Residues in contact with ARG 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 TYR* 3.1 49.0 + - + +
334A ILE* 3.6 15.3 - - + +
335A LEU 3.3 0.2 - - - -
336A GLN* 1.3 77.3 - - + +
338A CYS* 1.3 61.6 + - - +
340A LEU* 3.3 18.9 + - - +
341A ALA 3.1 18.5 + - - -
366A GLN* 5.1 5.7 + - - +
369A GLU* 4.9 8.5 + - - +
370A ILE* 3.4 52.3 - - + +
373A GLU* 3.0 26.0 + - - +
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Residues in contact with CYS 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 ILE* 3.0 19.0 + - - -
335A LEU 3.1 7.6 + - - +
337A ARG* 1.3 76.8 - - - +
339A GLN* 1.3 62.0 + - - +
341A ALA* 3.3 3.5 + - - +
342A LEU* 3.0 29.6 + - - +
370A ILE* 4.2 2.7 - - - -
374A VAL* 4.0 28.5 - - - -
403A LEU* 4.2 6.3 - - - -
406A LEU* 3.8 31.4 - - + -
410A MET* 3.7 26.4 - - + +
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Residues in contact with GLN 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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335A LEU 3.0 12.5 + - - +
336A GLN* 3.6 18.5 + - - +
338A CYS* 1.3 75.5 - - - +
340A LEU* 1.3 62.5 + - - +
342A LEU* 3.3 7.2 + - - +
343A GLN* 3.0 53.3 + - + +
406A LEU* 5.5 1.7 - - - +
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Residues in contact with LEU 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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336A GLN* 3.0 13.8 + - + +
337A ARG* 3.4 23.1 - - - +
338A CYS 3.2 0.2 - - - -
339A GLN* 1.3 75.0 - - - +
341A ALA* 1.3 64.9 + - - +
343A GLN* 3.2 43.7 - - - +
344A ASN* 4.2 0.9 + - - +
366A GLN* 3.3 39.7 + - - +
370A ILE* 4.3 8.3 - - + -
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Residues in contact with ALA 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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337A ARG 3.1 3.4 + - - -
338A CYS 3.3 7.4 + - - +
340A LEU* 1.3 80.7 - - - +
342A LEU* 1.3 63.6 + - + +
344A ASN* 3.4 20.3 + - - +
345A VAL* 4.6 2.1 + - - +
366A GLN* 5.4 2.9 - - - +
367A GLY* 4.3 19.6 - - - +
370A ILE* 3.7 37.4 - - + +
410A MET* 4.1 11.9 - - + -
413A VAL* 5.5 2.9 - - - +
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Residues in contact with LEU 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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338A CYS 3.0 18.7 + - - +
339A GLN* 3.7 5.6 - - - +
340A LEU 3.2 0.2 - - - -
341A ALA* 1.3 74.7 - - + +
343A GLN* 1.3 60.3 + - - +
344A ASN 3.0 2.0 - - - -
345A VAL* 2.8 43.9 + - + +
347A ASP* 5.4 3.3 - - - +
406A LEU* 3.5 35.2 - - + +
409A LYS* 3.7 35.2 - - + -
410A MET* 4.1 22.9 - - + -
413A VAL* 4.5 4.3 - - + -
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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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339A GLN* 3.0 41.5 + - + +
340A LEU* 3.2 36.3 - - - +
342A LEU* 1.3 77.4 - - - +
344A ASN* 1.3 55.5 + - - +
345A VAL 3.2 3.9 + - - -
357A LYS* 3.3 24.1 - - - +
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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