Contacts of the helix formed by residues 338 - 351 (chain A) in PDB entry 1IR1
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 GLU 338 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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331A VAL* 4.4 1.0 - - - +
336A GLU* 5.7 0.4 - - + -
337A GLY* 1.3 76.9 - - - +
339A ARG* 1.3 58.8 + - - +
340A ASP* 3.6 1.3 - - + +
341A ILE* 4.0 19.8 - - + +
342A THR* 2.7 37.6 + - - -
471A ALA* 3.4 28.7 - - + +
473A ASP* 3.4 26.5 + - - +
474A THR* 4.0 14.0 + - - +
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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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331A VAL* 4.0 22.3 - - + +
337A GLY 3.9 2.4 + - - -
338A GLU* 1.3 71.9 + - - +
340A ASP* 1.3 66.3 + - - +
342A THR* 3.3 2.4 + - - -
343A LEU* 2.9 64.0 + - + +
392A GLU* 2.5 42.4 + - - -
393A ILE* 3.7 28.6 - - + +
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Residues in contact with ASP 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 GLU* 3.6 1.4 - - + +
339A ARG* 1.3 89.9 - - - +
341A ILE* 1.3 64.9 + - + +
343A LEU* 3.5 8.9 + - - +
344A GLY 3.1 16.5 + - - -
359A SER 4.1 19.6 - - - +
360A ARG* 3.7 24.2 - - + +
475A VAL* 6.1 1.1 - - + -
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Residues in contact with ILE 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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310A HIS* 3.5 34.1 - - + +
312A ARG* 4.1 6.9 + - - +
338A GLU* 3.5 17.7 + - + +
339A ARG 3.3 0.6 - - - -
340A ASP* 1.3 76.4 - - + +
342A THR* 1.3 65.4 + - - +
344A GLY* 3.0 11.1 + - - -
345A PHE* 3.2 20.1 + - + -
360A ARG 3.9 10.8 - - - +
473A ASP* 3.8 23.3 - - - +
474A THR* 3.9 10.8 - - - +
475A VAL* 3.4 48.7 - - + +
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Residues in contact with THR 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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328A SER 3.8 21.7 + - - +
329A GLY* 5.1 1.3 - - - +
331A VAL* 4.0 15.9 - - + +
337A GLY* 4.0 8.1 - - - -
338A GLU 2.7 30.7 + - - -
339A ARG 3.6 3.8 - - - -
341A ILE* 1.3 73.4 - - - +
343A LEU* 1.3 66.0 + - - +
344A GLY 3.0 1.5 + - - -
345A PHE* 3.3 21.7 + - + -
346A VAL* 3.0 37.5 + - + +
393A ILE* 5.6 2.9 - - + -
394A PHE* 4.3 14.8 - - + -
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Residues in contact with LEU 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A ARG* 2.9 55.3 + - + +
340A ASP* 3.9 11.7 - - - +
342A THR* 1.3 76.9 - - + +
344A GLY* 1.3 64.1 + - - +
346A VAL* 3.9 11.2 - - + +
347A ASP* 3.3 18.9 + - - +
360A ARG* 3.4 21.6 + - - +
393A ILE* 3.4 41.5 - - + +
394A PHE* 6.0 0.2 - - + -
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Residues in contact with GLY 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 ASP 3.1 10.4 + - - -
341A ILE 3.0 9.0 + - - -
342A THR 3.0 1.4 - - - -
343A LEU* 1.3 81.2 - - - +
345A PHE* 1.3 61.0 + - - +
347A ASP* 3.3 11.3 + - - +
348A LEU* 3.3 16.2 + - - +
360A ARG* 4.0 13.9 - - - +
362A ILE* 3.9 23.6 - - - +
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Residues in contact with PHE 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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295A ARG* 4.9 2.0 - - - -
310A HIS* 4.2 13.2 - + - -
311A PHE* 3.8 37.7 - + + -
312A ARG* 3.9 27.0 - - + +
315A ALA* 4.8 4.7 - - + -
328A SER* 3.4 35.7 - - - -
341A ILE* 3.2 32.7 + - + -
342A THR* 3.3 30.9 + - + -
344A GLY* 1.3 73.6 - - - +
346A VAL* 1.3 70.9 + - + +
347A ASP 3.2 0.2 - - - -
348A LEU* 3.2 12.6 + - + +
349A LEU* 3.0 30.9 + - + +
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Residues in contact with VAL 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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328A SER* 4.3 13.9 - - - -
342A THR* 3.0 28.1 + - + +
343A LEU* 3.9 12.1 - - + +
344A GLY 3.2 0.4 - - - -
345A PHE* 1.3 78.3 - - + +
347A ASP* 1.3 64.3 + - - +
349A LEU* 3.1 8.6 + - - +
350A ARG* 3.0 59.2 + - - +
376A PRO* 4.2 11.7 - - + -
393A ILE 6.1 0.2 - - - +
394A PHE* 4.1 28.5 - - + -
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Residues in contact with ASP 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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343A LEU 3.3 9.7 + - - +
344A GLY 3.6 8.7 - - - +
345A PHE 3.2 0.4 - - - -
346A VAL* 1.3 82.1 - - - +
348A LEU* 1.3 57.3 + - - +
350A ARG* 4.5 13.5 + - - +
351A ASP* 3.0 54.7 + - - +
354A THR* 3.5 18.5 + - + +
360A ARG* 2.9 28.7 + - - +
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Residues in contact with LEU 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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137A ASP* 5.2 0.4 - - - +
312A ARG* 4.1 25.8 - - + +
315A ALA* 6.1 2.0 - - + -
316A LYS* 3.8 39.6 - - + +
319A ARG* 2.8 19.8 + - - -
344A GLY 3.3 10.5 + - - +
345A PHE* 3.2 23.2 + - + +
347A ASP* 1.3 77.0 - - - +
349A LEU* 1.3 58.6 + - + +
354A THR* 3.9 28.0 - - + -
362A ILE* 4.7 16.6 - - + -
366A GLN* 4.2 15.3 - - + -
368A TRP* 3.4 16.2 + - - +
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Residues in contact with LEU 349 (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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311A PHE* 5.3 1.8 - - + -
315A ALA* 3.7 41.3 - - + +
316A LYS* 5.5 0.4 - - - -
318A LEU* 5.6 0.4 - - + -
319A ARG* 3.3 21.3 + - + +
326A ILE* 3.6 33.7 - - + -
328A SER* 4.9 4.5 - - - -
345A PHE* 3.0 24.7 + - + +
346A VAL* 3.5 13.5 - - - +
347A ASP 3.1 0.4 - - - -
348A LEU* 1.3 81.8 - - - +
350A ARG* 1.3 59.7 + - + +
374A VAL* 2.9 43.8 + - + +
376A PRO* 4.7 13.9 - - + -
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Residues in contact with ARG 350 (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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155A ILE* 3.9 12.3 - - + +
319A ARG* 4.0 1.1 + - - -
346A VAL* 3.0 35.5 + - + +
347A ASP* 4.5 10.1 + - - -
349A LEU* 1.3 78.8 - - + +
351A ASP* 1.3 73.9 + - - +
373A GLY* 3.8 17.3 + - - -
374A VAL 3.4 17.5 - - - +
376A PRO* 3.6 21.0 - - + +
393A ILE 5.5 1.4 + - - -
394A PHE* 2.8 28.5 + - - +
397A ASP* 2.8 46.8 + - - +
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Residues in contact with ASP 351 (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 ARG* 2.8 32.4 + - - -
347A ASP* 3.0 41.0 + - - +
350A ARG* 1.3 88.6 + - - +
352A ASP* 1.3 61.8 + - - +
353A TYR 3.4 20.4 - - - +
354A THR* 4.3 1.7 + - - +
368A TRP* 3.3 5.3 + - - -
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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