Contacts of the helix formed by residues 361 - 374 (chain A) in PDB entry 2IHU
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 ILE 361 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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265A TYR* 3.6 58.2 + - + +
283A THR* 3.8 21.1 - - + +
284A MET* 4.0 14.1 - - - -
359A HIS* 3.6 24.4 + - - +
360A ASP* 1.3 78.4 + - - +
362A GLU* 1.3 66.4 + - - +
363A PRO* 3.3 4.5 - - - -
364A LEU* 3.0 22.6 + - + +
365A ARG* 3.0 43.1 + - + +
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Residues in contact with GLU 362 (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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265A TYR* 5.7 0.3 + - - -
358A ARG* 5.4 2.1 + - - -
360A ASP* 2.9 20.7 + - - +
361A ILE* 1.3 80.6 + - - +
363A PRO* 1.4 57.8 - - + +
365A ARG* 2.8 46.6 + - - +
366A ALA* 2.8 31.8 + - - +
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Residues in contact with PRO 363 (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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278A PHE* 3.5 23.2 - - + -
283A THR* 4.3 10.8 - - + +
360A ASP* 3.4 20.0 - - - +
361A ILE* 3.3 6.3 - - - -
362A GLU* 1.4 91.2 - - + +
364A LEU* 1.3 54.4 + - - +
366A ALA* 3.8 7.0 - - + +
367A ARG* 3.1 27.9 + - - +
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Residues in contact with LEU 364 (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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265A TYR 5.2 0.2 - - - +
272A MET* 4.3 6.3 - - + -
276A LEU* 3.7 17.7 - - + -
278A PHE* 3.8 10.6 - - + -
280A ALA* 3.5 46.2 - - + +
283A THR* 3.7 14.3 - - + +
284A MET* 3.9 35.2 - - + +
361A ILE* 3.0 18.6 + - + +
363A PRO* 1.3 77.7 - - - +
365A ARG* 1.3 59.3 + - - +
367A ARG* 3.2 2.1 + - + +
368A ILE* 2.9 46.4 + - + +
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Residues in contact with ARG 365 (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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261A HIS 4.1 3.8 + - - -
262A GLU* 2.9 34.7 + - - +
264A ASN 3.0 24.7 + - - -
265A TYR* 3.5 18.0 + - - -
358A ARG* 4.6 6.3 - - - +
361A ILE* 3.0 30.3 + - + +
362A GLU* 2.8 52.2 + - - +
364A LEU* 1.3 76.6 - - + +
366A ALA* 1.3 57.5 + - - +
368A ILE* 3.4 10.7 + - + +
369A ALA* 2.9 31.1 + - - +
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Residues in contact with ALA 366 (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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362A GLU 2.8 18.1 + - - +
363A PRO* 3.8 7.2 - - + +
365A ARG* 1.3 75.6 - - - +
367A ARG* 1.3 57.8 + - - +
369A ALA* 3.4 7.0 + - - +
370A GLU* 2.9 30.0 + - - +
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Residues in contact with ARG 367 (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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276A LEU* 2.8 31.0 + - + +
277A ASN* 3.0 36.6 + - - +
278A PHE* 3.8 36.3 - - + +
363A PRO 3.1 19.0 + - - +
364A LEU* 3.2 6.7 + - + +
366A ALA* 1.3 75.3 - - - +
368A ILE* 1.3 65.3 + - - +
370A GLU* 3.3 32.2 + - - +
371A PHE* 3.1 40.5 + - - -
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Residues in contact with ILE 368 (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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272A MET* 5.6 1.1 - - + -
276A LEU* 4.0 22.4 - - + -
364A LEU* 2.9 39.2 + - + +
365A ARG* 3.7 8.5 - - + +
367A ARG* 1.3 74.0 - - - +
369A ALA* 1.3 62.9 + - - +
371A PHE* 3.2 5.2 + - - +
372A LEU* 3.1 31.4 + - + +
419A LEU* 4.3 24.7 - - + +
420A PHE* 3.8 26.9 - - + -
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Residues in contact with ALA 369 (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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365A ARG 2.9 17.5 + - - +
366A ALA* 3.7 8.1 - - - +
368A ILE* 1.3 76.4 - - - +
370A GLU* 1.3 62.7 + - - +
372A LEU* 3.4 10.9 + - - +
373A ALA* 3.1 25.5 + - - +
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Residues in contact with GLU 370 (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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366A ALA 2.9 16.9 + - - +
367A ARG* 3.4 40.3 + - - +
368A ILE 3.2 0.2 - - - -
369A ALA* 1.3 77.4 - - - +
371A PHE* 1.3 64.3 + - + +
373A ALA* 3.4 5.3 + - - +
374A ASP* 3.1 21.7 + - - +
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Residues in contact with PHE 371 (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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275A ILE* 3.3 31.6 - - + -
276A LEU* 3.6 27.6 - - + -
277A ASN* 5.5 1.6 - - + -
367A ARG* 3.1 35.1 + - - +
368A ILE 3.2 8.7 + - - +
370A GLU* 1.3 83.8 - - + +
372A LEU* 1.3 61.7 + - - +
373A ALA 3.2 0.9 + - - -
374A ASP* 3.2 10.1 + - - +
385A HIS* 3.0 58.1 - + + -
416A TYR* 5.2 1.6 - + - -
420A PHE* 3.7 25.1 - + + -
536A ARG* 4.5 0.3 + - - -
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Residues in contact with LEU 372 (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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368A ILE* 3.1 33.1 + - + +
369A ALA* 3.8 9.0 - - - +
370A GLU 3.4 0.2 - - - -
371A PHE* 1.3 76.4 - - - +
373A ALA* 1.3 56.4 + - - +
385A HIS 3.9 14.6 - - - +
389A ASP* 2.9 52.3 - - + +
392A ASN* 4.3 5.4 - - - +
420A PHE* 3.6 46.0 - - + +
536A ARG* 2.9 12.3 + - - -
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Residues in contact with ALA 373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A ALA 3.1 17.8 + - - +
370A GLU* 3.4 5.6 + - - +
371A PHE 3.2 0.2 - - - -
372A LEU* 1.3 76.8 - - + +
374A ASP* 1.3 67.2 + - - +
375A PRO* 2.9 13.4 - - - +
389A ASP* 5.0 1.1 - - - -
536A ARG* 3.6 4.0 + - - +
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Residues in contact with ASP 374 (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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370A GLU 3.1 11.2 + - - +
371A PHE* 3.2 17.4 + - - +
372A LEU 3.4 0.8 - - - -
373A ALA* 1.3 72.4 - - - +
375A PRO* 1.3 66.4 - - - +
376A GLU* 3.0 22.7 + - - +
378A TYR* 2.5 25.9 + - - -
385A HIS* 3.1 23.2 + - + -
386A GLN* 3.1 14.3 + - + +
536A ARG* 2.8 27.5 + - - -
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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