Contacts of the helix formed by residues 338 - 351 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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331D VAL* 4.4 0.2 - - - -
336D GLU* 5.2 0.4 - - + +
337D GLY* 1.3 75.2 - - - +
339D ARG* 1.3 60.4 + - - +
340D ASP 3.6 1.3 - - - +
341D ILE* 3.5 20.3 + - + +
342D THR* 2.6 37.4 + - - -
471D ALA* 3.3 26.6 - - + +
473D ASP* 3.5 26.3 + - - +
474D THR* 4.8 10.3 - - + +
475D VAL* 6.1 0.9 - - + -
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Residues in contact with ARG 339 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331D VAL* 4.2 22.3 - - + +
337D GLY 3.9 2.0 + - - -
338D GLU* 1.3 75.4 + - - +
340D ASP* 1.3 64.4 + - - +
342D THR* 3.6 1.7 - - - -
343D LEU* 2.9 51.8 + - + +
389D ALA* 6.1 0.8 - - - +
392D GLU* 2.9 38.8 + - - -
393D ILE* 3.3 39.8 - - + +
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Residues in contact with ASP 340 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338D GLU* 3.6 2.0 - - + +
339D ARG* 1.3 85.5 + - - +
341D ILE* 1.3 63.6 + - - +
343D LEU* 3.4 15.5 + - - +
344D GLY 3.0 17.3 + - - -
359D SER 4.1 20.1 - - - +
360D ARG* 3.7 21.1 - - + +
475D VAL* 5.1 5.6 - - + -
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Residues in contact with ILE 341 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310D HIS* 3.5 34.1 - - + +
312D ARG* 4.2 10.3 + - - +
338D GLU* 3.5 16.9 + - + +
339D ARG 3.3 0.4 - - - -
340D ASP* 1.3 77.1 - - - +
342D THR* 1.3 63.5 + - - +
344D GLY* 3.1 9.9 + - - -
345D PHE* 3.2 21.5 + - + -
360D ARG 3.9 13.1 - - - +
473D ASP* 3.8 25.8 - - - +
474D THR* 4.1 5.2 - - - -
475D VAL* 3.3 46.0 - - + +
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Residues in contact with THR 342 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328D SER 3.9 19.9 + - - +
329D GLY* 5.1 1.4 - - - +
331D VAL* 4.0 19.4 - - + +
337D GLY* 4.0 5.4 - - - -
338D GLU 2.6 31.9 + - - -
339D ARG 3.6 3.4 - - - -
341D ILE* 1.3 75.2 - - - +
343D LEU* 1.3 70.7 + - + +
344D GLY 3.1 0.2 + - - -
345D PHE* 3.3 18.7 + - + -
346D VAL* 3.0 39.1 + - + +
393D ILE* 5.3 0.7 - - + -
394D PHE* 4.2 15.5 - - + -
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Residues in contact with LEU 343 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339D ARG* 2.9 51.8 + - + +
340D ASP* 3.4 13.9 + - - +
342D THR* 1.3 76.1 - - + +
344D GLY* 1.3 63.4 + - - +
346D VAL* 3.8 9.9 - - + +
347D ASP* 3.3 21.0 + - - +
360D ARG* 3.4 23.3 + - - +
393D ILE* 3.6 42.8 - - + +
394D PHE* 5.9 0.2 - - + -
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Residues in contact with GLY 344 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312D ARG* 6.3 0.2 - - - -
340D ASP 3.0 13.7 + - - -
341D ILE 3.5 4.5 - - - -
342D THR 3.0 0.6 - - - -
343D LEU* 1.3 80.8 - - - +
345D PHE* 1.3 61.8 + - - +
347D ASP* 3.4 4.9 + - - +
348D LEU* 3.3 23.6 + - - +
360D ARG* 3.9 19.2 - - - +
362D ILE* 3.9 20.5 - - - +
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Residues in contact with PHE 345 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295D ARG* 5.0 2.0 - - - -
310D HIS* 4.2 12.8 - + - -
311D PHE* 3.8 37.5 - + + -
312D ARG* 3.9 26.3 - - + +
315D ALA* 4.8 4.5 - - + -
328D SER* 3.4 35.9 - - - -
341D ILE* 3.2 33.0 + - + -
342D THR* 3.6 30.1 - - + -
344D GLY* 1.3 74.6 - - - +
346D VAL* 1.3 69.2 + - + +
348D LEU* 3.3 12.1 + - + +
349D LEU* 3.0 32.6 + - + +
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Residues in contact with VAL 346 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328D SER* 4.4 9.2 - - - +
342D THR* 3.0 39.9 + - + +
343D LEU* 3.8 11.9 - - + +
345D PHE* 1.3 82.0 - - + +
347D ASP* 1.3 65.6 + - - +
349D LEU* 3.1 6.8 + - - +
350D ARG* 3.0 60.4 + - - +
376D PRO* 4.2 11.7 - - + -
393D ILE 6.0 0.2 - - - +
394D PHE* 4.1 20.2 - - + -
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Residues in contact with ASP 347 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343D LEU 3.3 10.1 + - - +
344D GLY 3.6 8.1 - - - +
345D PHE 3.3 0.2 - - - -
346D VAL* 1.3 81.5 - - - +
348D LEU* 1.3 57.6 + - - +
350D ARG* 4.4 15.0 + - - -
351D ASP* 2.9 53.6 + - - +
354D THR* 3.6 16.1 + - + +
360D ARG* 2.8 29.6 + - - +
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Residues in contact with LEU 348 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137D ASP* 5.2 0.4 - - - +
312D ARG* 4.3 22.2 - - + +
315D ALA* 6.2 1.8 - - + -
316D LYS* 3.9 36.9 - - + +
319D ARG* 2.9 19.8 + - - -
344D GLY 3.3 15.0 + - - +
345D PHE* 3.6 17.3 - - + +
346D VAL 3.2 0.8 - - - -
347D ASP* 1.3 77.5 - - - +
349D LEU* 1.3 59.8 + - + +
354D THR* 3.7 31.2 - - + +
362D ILE* 4.5 20.6 - - + -
366D GLN* 4.2 15.0 - - + -
368D TRP* 3.4 16.6 + - - +
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Residues in contact with LEU 349 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311D PHE* 5.2 2.0 - - + -
315D ALA* 3.8 40.6 - - + +
316D LYS* 5.5 0.2 - - - -
318D LEU* 5.6 0.7 - - + -
319D ARG* 3.3 20.7 + - + +
326D ILE* 3.6 33.4 - - + -
328D SER* 4.9 4.3 - - - -
345D PHE* 3.0 27.8 + - + +
346D VAL* 3.5 10.3 - - - +
347D ASP 3.1 0.2 - - - -
348D LEU* 1.3 81.3 - - - +
350D ARG* 1.3 59.6 + - + +
374D VAL* 2.9 44.1 + - + +
376D PRO* 4.7 14.4 - - + -
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Residues in contact with ARG 350 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155D ILE* 4.0 11.5 - - + +
319D ARG* 3.9 1.9 + - - -
346D VAL* 3.0 37.3 + - - +
347D ASP* 4.4 10.9 + - - +
349D LEU* 1.3 78.9 - - + +
351D ASP* 1.3 73.5 + - - +
373D GLY* 3.8 17.6 + - - -
374D VAL 3.4 17.5 - - - +
376D PRO* 3.6 13.7 - - + +
393D ILE 5.4 1.8 + - - -
394D PHE* 2.8 30.7 + - - +
397D ASP* 2.9 43.4 + - - +
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Residues in contact with ASP 351 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319D ARG* 2.8 30.3 + - - -
347D ASP* 2.9 44.6 + - - +
350D ARG* 1.3 83.8 + - - +
352D ASP* 1.3 61.6 + - - +
353D TYR 3.4 19.7 - - - +
354D THR* 4.2 2.3 + - - +
368D TRP* 3.3 6.8 + - - -
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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