Contacts of the helix formed by residues 369 - 380 (chain J) in PDB entry 1I43
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 ASP 369 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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368J GLY* 1.3 75.8 - - - -
370J LEU* 1.3 68.3 + - + +
371J LEU* 3.5 21.7 + - - +
372J THR* 3.0 23.7 + - - -
373J THR* 2.7 26.6 + - - -
419J ASP* 4.4 1.3 - - - -
420J ASN* 3.9 4.5 - - - +
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Residues in contact with LEU 370 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369J ASP* 1.3 75.3 - - + +
371J LEU* 1.3 78.8 + - + +
374J ALA* 3.1 23.2 + - + +
398J GLN* 3.5 24.9 + - - +
400J ALA* 4.7 2.7 - - + -
401J ILE* 3.7 28.0 - - + -
405J TRP* 4.2 24.7 - - + -
419J ASP* 3.5 49.1 + - + +
96L ILE* 5.0 9.0 - - + -
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Residues in contact with LEU 371 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369J ASP* 3.2 15.0 + - - +
370J LEU* 1.3 95.9 - - + +
372J THR* 1.3 62.5 + - - +
374J ALA* 3.4 8.4 + - + +
375J LYS* 3.2 19.9 + - - +
96L ILE* 6.3 2.0 - - + -
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Residues in contact with THR 372 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366J VAL* 4.5 2.5 - - + -
367J ASP 4.5 0.2 - - - +
368J GLY* 3.9 16.3 - - - -
369J ASP* 3.0 23.9 + - - -
371J LEU* 1.3 76.4 - - - +
373J THR* 1.3 71.0 + - - +
375J LYS* 2.9 27.6 + - + +
376J PHE* 3.2 7.3 + - - +
445J ILE* 3.5 38.7 + - + +
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Residues in contact with THR 373 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366J VAL* 3.8 15.0 - - + +
369J ASP 2.7 21.8 + - - -
372J THR* 1.3 75.1 - - - +
374J ALA* 1.3 61.9 - - - +
376J PHE* 3.2 16.5 + - - +
377J VAL* 3.2 12.5 - - - +
398J GLN* 3.2 24.5 - - + +
419J ASP 3.6 2.7 + - - +
420J ASN* 3.3 31.6 + - - +
422J VAL* 3.3 31.6 - - + -
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Residues in contact with ALA 374 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370J LEU* 3.1 18.4 + - + +
371J LEU* 3.6 9.6 - - + +
372J THR 3.1 0.2 - - - -
373J THR* 1.3 76.6 - - - +
375J LYS* 1.3 53.6 + - - +
376J PHE 3.1 0.3 + - - -
377J VAL* 3.1 6.1 + - - +
378J ASP* 2.8 37.0 + - - +
398J GLN* 3.2 12.9 + - - +
401J ILE* 5.1 0.9 - - + -
92L THR* 3.5 33.9 - - + +
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Residues in contact with LYS 375 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371J LEU 3.2 9.6 + - - +
372J THR* 2.9 19.3 + - + +
374J ALA* 1.3 78.7 - - - +
376J PHE* 1.3 60.7 + - - +
378J ASP* 3.9 9.0 - - + +
379J ALA* 3.3 21.0 + - - +
444J SER* 3.6 35.7 + - - +
445J ILE* 5.1 4.7 - - + -
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Residues in contact with PHE 376 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364J PHE* 3.7 34.3 - + - -
366J VAL* 4.0 14.8 - - + -
372J THR 3.2 5.6 + - - +
373J THR* 3.2 9.7 + - - +
374J ALA 3.0 0.4 - - - -
375J LYS* 1.3 75.1 - - - +
377J VAL* 1.3 80.0 + - + +
379J ALA* 3.0 18.4 + - - +
380J LEU* 3.3 28.0 + - + +
396J VAL* 5.6 0.2 - - + -
422J VAL* 4.4 8.7 - - + -
424J PHE* 5.5 2.0 - + - -
438J ILE* 3.8 11.9 - - + -
441J ALA* 3.1 40.7 - - + +
442J LEU* 3.6 24.0 - - + -
444J SER* 5.0 0.2 - - - -
445J ILE* 3.4 27.3 - - + +
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Residues in contact with VAL 377 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373J THR 3.2 16.4 - - - +
374J ALA* 3.1 4.2 + - - +
376J PHE* 1.3 86.1 - - + +
378J ASP* 1.3 67.9 + - - +
380J LEU* 3.1 36.3 + - + +
385J ILE* 4.2 25.3 - - + +
396J VAL* 5.0 8.7 - - + -
397J ASP* 5.6 5.6 - - - +
398J GLN* 4.1 13.7 - - + +
422J VAL* 4.4 15.9 - - + -
92L THR* 3.1 26.9 - - - +
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Residues in contact with ASP 378 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374J ALA* 2.8 18.4 + - - +
375J LYS* 3.9 11.2 - - + +
377J VAL* 1.3 80.1 - - - +
379J ALA* 1.3 60.0 + - - +
380J LEU 3.8 4.9 - - - +
385J ILE* 4.0 5.6 - - - +
90L ASN 5.6 1.5 - - - +
91L LYS* 3.7 17.7 - - + +
92L THR* 2.8 46.3 + - - -
93L SER* 4.6 2.8 + - - -
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Residues in contact with ALA 379 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375J LYS 3.3 11.3 + - - +
376J PHE 3.0 14.2 + - - +
378J ASP* 1.3 78.3 - - - +
380J LEU* 1.3 68.7 + - - +
381J LYS* 3.5 14.9 - - - +
440J GLN* 3.5 13.1 + - - +
441J ALA* 3.4 22.2 - - + -
444J SER* 4.1 10.8 - - - +
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Residues in contact with LEU 380 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376J PHE* 3.6 25.1 - - + +
377J VAL* 3.1 28.4 + - + +
378J ASP 3.8 6.9 - - - +
379J ALA* 1.3 82.9 - - - +
381J LYS* 1.3 59.6 + - - +
383J PRO* 4.1 11.7 - - + +
396J VAL* 3.6 37.5 - - + -
424J PHE* 4.1 12.8 - - + -
437J ASP* 3.9 14.4 - - - +
438J ILE* 4.0 16.6 - - - -
441J ALA* 3.7 18.8 - - + -
67K ARG* 5.2 2.4 + - - -
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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