Contacts of the helix formed by residues 369 - 380 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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368B GLY* 1.3 75.2 - - - +
370B LEU* 1.3 67.9 + - + +
371B LEU* 3.7 16.0 + - - +
372B THR* 2.9 31.4 + - - -
373B THR* 2.8 27.6 + - - -
419B ASP* 4.2 4.7 - - - -
420B ASN* 4.1 1.8 - - - +
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Residues in contact with LEU 370 (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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369B ASP* 1.3 77.6 - - + +
371B LEU* 1.3 81.8 + - + +
374B ALA* 3.2 24.4 + - + +
398B GLN* 3.6 18.6 + - - +
400B ALA* 4.8 1.6 - - + -
401B ILE* 3.8 28.0 - - + -
405B TRP* 4.3 24.2 - - + -
419B ASP* 3.5 46.3 - - + +
96D ILE* 4.9 9.2 - - + -
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Residues in contact with LEU 371 (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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369B ASP* 3.2 14.3 + - - +
370B LEU* 1.3 96.5 - - + +
372B THR* 1.3 63.9 + - - +
374B ALA* 3.6 7.8 + - + +
375B LYS* 3.2 20.1 + - - +
96D ILE* 6.1 2.9 - - + -
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Residues in contact with THR 372 (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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366B VAL* 4.5 3.4 - - + -
367B ASP 4.7 0.2 - - - +
368B GLY* 3.8 19.0 - - - -
369B ASP* 2.9 28.5 + - - -
371B LEU* 1.3 73.2 - - - +
373B THR* 1.3 61.7 + - - +
374B ALA 3.0 1.1 - - - -
375B LYS* 2.7 36.5 + - + +
376B PHE* 3.1 5.2 + - - +
445B ILE* 4.0 33.2 - - + +
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Residues in contact with THR 373 (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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366B VAL* 3.7 14.6 - - + +
369B ASP 2.8 22.7 + - - -
372B THR* 1.3 74.5 - - - +
374B ALA* 1.3 60.7 + - - +
376B PHE* 3.1 14.9 + - - +
377B VAL* 3.1 14.6 - - - +
398B GLN* 3.4 22.4 - - - +
419B ASP 3.6 2.8 + - - -
420B ASN* 3.3 31.1 + - - +
422B VAL* 3.3 33.0 - - + -
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Residues in contact with ALA 374 (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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370B LEU* 3.2 19.6 + - + +
371B LEU* 3.6 10.1 - - + +
372B THR 3.0 0.4 - - - -
373B THR* 1.3 75.9 - - - +
375B LYS* 1.3 61.5 + - - +
376B PHE 3.1 0.2 + - - -
377B VAL* 3.1 4.0 + - - +
378B ASP* 2.9 36.4 + - - +
398B GLN* 3.3 12.1 + - - +
401B ILE* 5.1 0.2 - - + -
92D THR* 3.6 32.3 - - + -
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Residues in contact with LYS 375 (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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371B LEU 3.2 10.5 + - - +
372B THR* 2.7 22.0 + - + +
374B ALA* 1.3 75.8 - - - +
376B PHE* 1.3 58.4 + - - -
378B ASP* 3.6 7.9 + - - +
379B ALA* 3.3 21.7 + - - +
444B SER* 3.3 32.7 - - - +
445B ILE* 5.3 2.5 - - + -
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Residues in contact with PHE 376 (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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364B PHE* 3.6 36.8 - + - -
366B VAL* 3.8 16.4 - - + -
372B THR 3.1 3.6 + - - -
373B THR* 3.1 10.5 + - - +
374B ALA 3.0 0.6 - - - -
375B LYS* 1.3 75.1 - - - +
377B VAL* 1.3 69.8 + - + +
379B ALA* 3.0 21.7 + - - +
380B LEU* 3.4 25.0 + - + +
396B VAL* 5.6 0.4 - - + -
422B VAL* 4.4 9.2 - - + -
424B PHE* 5.4 1.8 - + - -
438B ILE* 3.9 14.8 - - + -
441B ALA* 3.6 35.7 - - + +
442B LEU* 3.8 22.2 - - + -
444B SER* 6.3 0.2 - - - -
445B ILE* 3.4 25.0 - - + +
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Residues in contact with VAL 377 (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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373B THR 3.1 15.7 - - - +
374B ALA* 3.1 3.3 + - - +
376B PHE* 1.3 84.7 - - + +
378B ASP* 1.3 67.7 + - - +
379B ALA 3.3 0.7 + - - -
380B LEU* 3.3 34.9 + - + +
385B ILE* 3.9 23.7 - - + +
396B VAL* 5.0 8.3 - - + -
397B ASP* 5.7 6.1 - - - +
398B GLN* 4.1 14.1 - - + +
422B VAL* 4.4 17.5 - - + -
92D THR* 3.1 27.4 - - - +
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Residues in contact with ASP 378 (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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374B ALA* 2.9 18.9 + - - +
375B LYS* 3.8 9.2 - - - +
376B PHE 3.2 0.2 - - - -
377B VAL* 1.3 80.1 - - - +
379B ALA* 1.3 59.7 + - - +
380B LEU 3.4 5.5 + - - +
385B ILE* 3.7 6.4 - - - +
90D ASN 5.6 2.3 - - - +
91D LYS* 3.6 16.2 - - + +
92D THR* 2.7 47.1 + - - -
93D SER* 4.4 3.5 + - - -
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Residues in contact with ALA 379 (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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375B LYS 3.3 12.0 + - - +
376B PHE 3.0 12.7 + - - +
378B ASP* 1.3 76.0 - - - +
380B LEU* 1.3 65.7 + - - +
381B LYS* 3.5 7.3 - - - +
440B GLN* 3.5 21.4 + - - +
441B ALA* 3.4 26.5 - - + +
444B SER* 4.4 9.4 - - - +
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Residues in contact with LEU 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376B PHE* 3.8 24.2 - - + +
377B VAL* 3.3 28.3 + - + +
378B ASP 3.8 7.3 - - - +
379B ALA* 1.3 81.5 - - - +
381B LYS* 1.3 60.1 + - - +
383B PRO* 3.8 16.4 - - + +
396B VAL* 3.6 38.1 - - + -
424B PHE* 4.1 12.6 - - + -
437B ASP* 3.9 14.8 - - - +
438B ILE* 4.0 15.5 - - + -
441B ALA* 4.0 15.3 - - + -
67C ARG* 5.1 2.9 + - - -
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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