Contacts of the helix formed by residues 369 - 380 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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368A GLY* 1.3 75.0 - - - +
370A LEU* 1.3 69.5 + - - +
371A LEU* 3.0 19.4 + - - +
372A THR* 3.0 28.2 + - - -
373A THR* 2.7 26.9 + - - -
419A ASP* 4.3 3.6 - - - -
420A ASN* 4.1 2.0 - - - +
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Residues in contact with LEU 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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369A ASP* 1.3 74.9 - - + +
371A LEU* 1.3 79.5 - - + +
374A ALA* 3.2 21.3 + - + +
398A GLN* 3.5 25.2 + - - +
400A ALA* 4.8 2.2 - - + -
401A ILE* 3.8 29.2 - - + -
405A TRP* 4.4 23.1 - - + -
419A ASP* 3.5 47.4 + - + +
96C ILE* 5.0 8.1 - - + -
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Residues in contact with LEU 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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369A ASP* 3.1 14.3 + - - +
370A LEU* 1.3 95.7 - - + +
372A THR* 1.3 65.3 + - - +
374A ALA* 3.2 9.3 + - + +
375A LYS* 3.0 20.8 + - - +
96C ILE* 6.0 3.4 - - + -
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Residues in contact with THR 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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366A VAL* 4.7 3.8 - - + -
367A ASP 4.7 0.4 - - - +
368A GLY* 3.9 16.4 - - - -
369A ASP* 3.0 27.1 + - - -
371A LEU* 1.3 74.4 - - - +
373A THR* 1.3 59.7 + - - +
375A LYS* 2.7 39.8 + - + +
376A PHE* 3.1 5.5 + - - +
445A ILE* 3.7 33.3 + - + +
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Residues in contact with THR 373 (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 VAL* 3.9 16.4 - - + +
369A ASP 2.7 23.7 + - - -
372A THR* 1.3 76.2 - - - +
374A ALA* 1.3 61.6 + - - +
376A PHE* 3.0 21.2 + - - +
377A VAL* 3.2 7.4 + - - +
398A GLN* 3.4 23.1 - - + +
419A ASP 3.6 2.7 + - - -
420A ASN* 3.4 29.2 + - - +
422A VAL* 3.3 32.5 - - + -
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Residues in contact with ALA 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 LEU* 3.2 14.9 + - + +
371A LEU* 3.2 15.7 + - + +
372A THR 3.1 0.2 - - - -
373A THR* 1.3 78.3 - - - +
375A LYS* 1.3 66.1 + - - +
376A PHE 3.1 0.3 + - - -
377A VAL* 3.1 6.3 + - - +
378A ASP* 2.8 28.5 + - - +
398A GLN* 3.3 11.6 + - - +
92C THR* 3.5 33.0 - - + -
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Residues in contact with LYS 375 (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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371A LEU 3.0 11.2 + - - +
372A THR* 2.7 20.5 + - + +
374A ALA* 1.3 77.7 - - - +
376A PHE* 1.3 58.0 + - - +
378A ASP* 3.5 9.6 + - - +
379A ALA* 3.2 22.0 + - - +
444A SER* 4.0 30.4 - - - +
445A ILE* 4.9 7.2 - - + +
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Residues in contact with PHE 376 (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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364A PHE* 3.7 35.7 - + - -
366A VAL* 4.0 14.6 - - + -
372A THR 3.1 4.6 + - - +
373A THR* 3.0 12.4 + - - +
375A LYS* 1.3 74.4 - - - +
377A VAL* 1.3 77.0 + - + +
379A ALA* 2.9 21.4 + - - +
380A LEU* 3.4 25.8 + - + +
422A VAL* 4.4 9.0 - - + -
424A PHE* 5.5 1.6 - + - -
438A ILE* 3.7 13.5 - - + -
441A ALA* 3.4 29.2 - - + -
442A LEU* 3.7 24.5 - - + -
444A SER* 6.5 0.4 - - - -
445A ILE* 3.7 30.0 - - + +
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Residues in contact with VAL 377 (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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373A THR 3.3 13.9 - - - +
374A ALA* 3.1 6.4 + - - +
376A PHE* 1.3 86.0 - - + +
378A ASP* 1.3 68.9 + - - +
379A ALA 3.2 0.5 + - - -
380A LEU* 3.3 33.3 + - + +
385A ILE* 4.2 23.8 - - + +
396A VAL* 5.0 9.1 - - + +
397A ASP* 5.5 4.9 - - - +
398A GLN* 4.1 13.5 - - + +
422A VAL* 4.4 19.3 - - + -
92C THR* 2.9 28.5 - - - +
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Residues in contact with ASP 378 (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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374A ALA* 2.8 19.4 + - - +
375A LYS* 3.7 9.5 - - - +
377A VAL* 1.3 79.2 - - - +
379A ALA* 1.3 59.5 + - - +
380A LEU 3.7 5.4 - - - +
385A ILE* 4.0 5.4 - - - +
90C ASN 5.5 2.6 - - - +
91C LYS* 3.7 18.1 - - + +
92C THR* 2.8 46.5 + - - -
93C SER* 4.5 3.3 + - - -
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Residues in contact with ALA 379 (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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375A LYS 3.2 11.8 + - - +
376A PHE 2.9 13.5 + - - +
378A ASP* 1.3 75.9 - - - +
380A LEU* 1.3 67.4 + - - +
381A LYS* 3.5 8.7 - - - +
440A GLN* 3.4 21.0 + - - +
441A ALA* 3.9 21.3 - - + +
444A SER* 4.1 14.4 - - - +
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Residues in contact with LEU 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A PHE* 3.8 19.7 - - + +
377A VAL* 3.3 27.3 + - - +
378A ASP 3.7 7.6 - - - +
379A ALA* 1.3 82.9 - - - +
381A LYS* 1.3 60.6 + - - +
383A PRO* 3.9 13.9 - - + +
396A VAL* 3.7 37.7 - - + -
424A PHE* 4.2 13.0 - - + -
437A ASP* 3.8 17.5 - - - +
438A ILE* 3.9 17.9 - - + -
441A ALA* 3.8 18.8 - - + -
67D ARG* 5.2 2.1 + - - -
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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