Contacts of the helix formed by residues 338 - 351 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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331B VAL* 4.4 0.2 - - - -
336B GLU* 5.1 0.8 - - - +
337B GLY* 1.3 74.8 - - - +
339B ARG* 1.3 59.5 + - - +
340B ASP* 4.8 1.6 - - + +
341B ILE* 3.9 18.8 - - + +
342B THR* 2.7 37.0 + - - -
471B ALA* 3.6 27.1 - - + +
473B ASP* 3.4 26.8 + - - +
474B THR* 4.0 14.0 + - - +
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Residues in contact with ARG 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331B VAL* 4.1 22.2 - - + +
337B GLY 3.8 2.2 + - - -
338B GLU* 1.3 73.1 + - - +
340B ASP* 1.3 71.0 + - - +
342B THR* 3.2 2.8 + - - -
343B LEU* 2.9 50.1 + - + +
389B ALA* 6.2 0.2 - - - +
392B GLU* 3.1 36.8 + - - -
393B ILE* 3.3 41.4 - - + +
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Residues in contact with ASP 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338B GLU* 4.8 1.7 - - + +
339B ARG* 1.3 85.7 + - - +
341B ILE* 1.3 64.2 + - + +
343B LEU* 3.4 15.2 + - - +
344B GLY 3.0 17.3 + - - -
359B SER* 4.1 20.0 - - - +
360B ARG* 3.7 20.8 - - + +
475B VAL* 5.7 3.6 - - + -
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Residues in contact with ILE 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310B HIS* 3.5 33.7 - - + +
312B ARG* 4.1 9.3 + - - +
338B GLU* 3.6 18.4 + - + +
339B ARG 3.3 0.4 - - - -
340B ASP* 1.3 78.1 - - + +
342B THR* 1.3 63.6 + - - +
344B GLY* 3.2 9.5 + - - -
345B PHE* 3.2 20.4 + - + -
360B ARG 4.0 15.1 - - - +
473B ASP* 3.8 28.7 - - - +
474B THR* 3.9 2.5 - - - -
475B VAL* 3.4 46.0 - - + +
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Residues in contact with THR 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B SER 3.8 20.3 + - - +
329B GLY* 5.2 1.4 - - - +
331B VAL* 3.9 19.4 - - + +
337B GLY* 4.0 5.7 - - - -
338B GLU 2.7 30.2 + - - -
339B ARG 3.6 3.1 - - - -
341B ILE* 1.3 73.3 - - - +
343B LEU* 1.3 66.3 + - - +
344B GLY 3.0 1.7 + - - -
345B PHE* 3.3 20.8 + - + -
346B VAL* 3.0 37.4 + - + +
393B ILE* 5.5 3.1 - - + -
394B PHE* 4.2 15.3 - - + -
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Residues in contact with LEU 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B ARG* 2.9 51.7 + - + +
340B ASP* 3.7 13.2 - - - +
342B THR* 1.3 76.7 - - + +
344B GLY* 1.3 62.4 + - - +
346B VAL* 3.8 10.7 - - + +
347B ASP* 3.3 20.4 + - - +
360B ARG* 3.3 23.7 + - - +
393B ILE* 3.5 39.5 - - + +
394B PHE* 6.1 0.7 - - + -
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Residues in contact with GLY 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312B ARG* 6.2 0.4 - - - -
340B ASP 3.0 13.1 + - - -
341B ILE 3.2 5.1 + - - -
342B THR 3.0 1.0 - - - -
343B LEU* 1.3 80.5 - - - +
345B PHE* 1.3 60.6 + - - +
347B ASP* 3.4 4.9 + - - +
348B LEU* 3.4 23.4 + - - +
360B ARG* 3.9 18.3 - - - +
362B ILE* 3.8 20.6 - - - +
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Residues in contact with PHE 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295B ARG* 5.0 1.8 - - - -
310B HIS* 4.2 13.9 - + - -
311B PHE* 3.8 37.5 - + + -
312B ARG* 3.8 27.5 - - + +
315B ALA* 4.8 3.8 - - + -
328B SER* 3.4 32.5 - - - -
341B ILE* 3.2 38.2 + - + -
342B THR* 3.3 25.5 + - + -
344B GLY* 1.3 73.3 - - - +
346B VAL* 1.3 69.4 + - + +
347B ASP 3.3 0.2 - - - -
348B LEU* 3.6 12.1 - - + +
349B LEU* 3.2 32.3 + - + +
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Residues in contact with VAL 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328B SER* 4.3 14.8 - - - -
342B THR* 3.0 38.0 + - + +
343B LEU* 3.8 12.3 - - + +
344B GLY 3.2 0.2 - - - -
345B PHE* 1.3 77.3 - - + +
347B ASP* 1.3 67.1 + - - +
349B LEU* 3.2 7.0 + - - +
350B ARG* 3.1 59.5 + - - +
376B PRO* 4.3 10.8 - - + -
393B ILE 6.1 0.4 - - - +
394B PHE* 4.2 21.1 - - + -
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Residues in contact with ASP 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343B LEU 3.3 8.8 + - - +
344B GLY 3.7 8.1 - - - +
345B PHE 3.3 0.2 - - - -
346B VAL* 1.3 81.8 - - - +
348B LEU* 1.3 57.1 + - - +
350B ARG* 4.4 13.7 + - - +
351B ASP* 2.9 55.1 + - - +
354B THR* 3.6 13.4 + - + +
360B ARG* 2.8 33.8 + - - +
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Residues in contact with LEU 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B ASP* 5.2 0.7 - - - +
312B ARG* 4.2 25.8 - - + +
315B ALA* 6.1 1.8 - - + -
316B LYS* 3.8 38.5 - - + +
319B ARG* 2.8 20.3 + - - -
344B GLY 3.4 16.8 + - - +
345B PHE* 3.6 16.6 - - + +
346B VAL 3.2 0.4 - - - -
347B ASP* 1.3 77.9 - - - +
349B LEU* 1.3 59.7 + - + +
354B THR* 3.7 29.8 - - + +
362B ILE* 4.6 15.0 - - + -
366B GLN* 4.2 14.4 - - + -
368B TRP* 3.4 17.0 + - - +
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Residues in contact with LEU 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311B PHE* 5.1 2.0 - - + -
315B ALA* 3.7 39.9 - - + +
316B LYS* 5.6 0.2 - - - -
318B LEU* 5.5 0.7 - - + -
319B ARG* 3.3 21.6 + - + +
326B ILE* 3.7 33.0 - - + -
328B SER* 5.0 4.3 - - - -
345B PHE* 3.2 33.3 + - + +
346B VAL* 3.6 9.0 - - - +
347B ASP 3.1 0.6 - - - -
348B LEU* 1.3 80.9 - - - +
350B ARG* 1.3 60.3 + - + +
374B VAL* 2.8 46.5 + - + +
376B PRO* 4.9 12.1 - - + -
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Residues in contact with ARG 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155B ILE* 4.0 11.3 - - + +
319B ARG* 3.9 1.5 + - - -
346B VAL* 3.1 33.2 + - - +
347B ASP* 4.4 9.9 + - - -
349B LEU* 1.3 78.4 - - + +
351B ASP* 1.3 74.8 + - - +
373B GLY* 3.7 18.1 + - - -
374B VAL 3.4 17.5 - - - +
376B PRO* 3.6 24.3 - - + +
393B ILE 5.4 1.6 + - - -
394B PHE* 2.8 30.5 + - - +
397B ASP* 2.8 43.9 + - - +
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Residues in contact with ASP 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319B ARG* 2.9 29.1 + - - -
347B ASP* 2.9 46.0 + - - +
350B ARG* 1.3 84.1 + - - +
352B ASP* 1.3 60.2 + - - +
353B TYR 3.4 18.5 - - - +
354B THR* 4.4 1.7 + - - +
368B TRP* 3.4 4.3 - - - -
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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