Contacts of the helix formed by residues 369 - 380 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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368L GLY* 1.3 75.1 - - - -
370L LEU* 1.3 69.0 + - - +
371L LEU* 3.6 17.2 + - - +
372L THR* 2.9 28.9 + - - -
373L THR* 2.7 25.6 + - - -
419L ASP* 4.2 3.8 - - - -
420L ASN* 4.0 1.6 - - - +
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Residues in contact with LEU 370 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96J ILE* 4.8 9.9 - - + -
369L ASP* 1.3 75.8 - - + +
371L LEU* 1.3 79.1 + - + +
374L ALA* 3.1 24.1 + - + +
398L GLN* 3.5 27.6 + - - +
400L ALA* 4.9 2.0 - - + -
401L ILE* 3.8 25.1 - - + -
405L TRP* 4.2 25.4 - - + -
419L ASP* 3.5 47.7 + - + +
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Residues in contact with LEU 371 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96J ILE* 6.2 1.8 - - + -
369L ASP* 3.1 15.0 + - - +
370L LEU* 1.3 94.2 - - + +
372L THR* 1.3 65.6 + - - +
374L ALA* 3.2 10.4 + - + +
375L LYS* 3.0 21.0 + - - +
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Residues in contact with THR 372 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366L VAL* 4.6 6.1 - - + -
367L ASP 4.5 2.0 - - - +
368L GLY* 3.9 18.6 - - - -
369L ASP* 2.9 23.9 + - - -
371L LEU* 1.3 75.9 - - - +
373L THR* 1.3 69.1 + - - +
375L LYS* 2.8 28.8 + - + +
376L PHE* 3.1 6.4 + - - +
445L ILE* 3.9 28.8 - - + +
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Residues in contact with THR 373 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366L VAL* 4.0 13.2 - - + +
368L GLY 4.4 0.2 - - - -
369L ASP 2.7 22.8 + - - -
372L THR* 1.3 75.4 - - - +
374L ALA* 1.3 61.8 + - - +
376L PHE* 3.1 15.6 + - - +
377L VAL* 3.2 13.3 + - - +
398L GLN* 3.2 24.7 - - - +
419L ASP 3.4 3.0 + - - +
420L ASN* 3.3 32.1 + - - +
422L VAL* 3.3 31.4 - - + -
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Residues in contact with ALA 374 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92J THR* 3.4 33.4 - - + +
96J ILE* 6.1 0.2 - - + -
370L LEU* 3.1 16.8 + - + +
371L LEU* 3.4 14.6 - - + +
372L THR 3.1 0.2 - - - -
373L THR* 1.3 75.3 - - - +
375L LYS* 1.3 59.0 + - - +
377L VAL* 3.2 6.4 + - - +
378L ASP* 2.8 33.4 + - - +
398L GLN* 3.4 11.6 + - - +
401L ILE* 5.2 0.7 - - + -
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Residues in contact with LYS 375 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371L LEU 3.0 12.3 + - - +
372L THR* 2.8 19.7 + - + +
374L ALA* 1.3 78.0 - - - +
376L PHE* 1.3 58.9 + - - +
378L ASP* 3.5 8.7 + - + +
379L ALA* 3.3 21.1 + - - +
444L SER* 4.4 29.9 - - - +
445L ILE* 4.8 7.9 - - + -
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Residues in contact with PHE 376 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364L PHE* 3.7 35.0 - + - -
366L VAL* 4.0 14.1 - - + -
372L THR 3.1 7.2 + - - +
373L THR* 3.4 8.7 - - - +
374L ALA 3.1 0.6 - - - -
375L LYS* 1.3 74.9 - - - +
377L VAL* 1.3 75.0 + - + +
379L ALA* 3.0 18.6 + - - +
380L LEU* 3.4 25.6 + - + +
396L VAL* 5.7 0.4 - - + -
422L VAL* 4.5 8.3 - - + -
424L PHE* 5.6 1.3 - + - -
438L ILE* 3.7 22.4 - - + -
441L ALA* 3.5 28.3 - - + -
442L LEU* 3.7 23.1 - - + -
444L SER* 6.2 0.2 - - - -
445L ILE* 3.7 25.3 - - + +
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Residues in contact with VAL 377 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92J THR* 3.0 28.0 - - - +
373L THR 3.2 15.7 - - - +
374L ALA* 3.2 3.8 + - - +
376L PHE* 1.3 86.2 - - + +
378L ASP* 1.3 68.8 + - - +
379L ALA 3.2 0.7 + - - -
380L LEU* 3.2 33.5 + - + +
385L ILE* 4.1 25.5 - - + +
396L VAL* 5.1 9.6 - - + +
397L ASP* 5.7 5.4 - - - +
398L GLN* 4.2 13.5 - - + +
422L VAL* 4.3 19.3 - - + -
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Residues in contact with ASP 378 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90J ASN 5.6 2.1 - - - +
91J LYS* 3.6 19.7 - - + +
92J THR* 2.7 47.0 + - - -
93J SER* 4.4 3.5 + - - -
374L ALA* 2.8 19.1 + - - +
375L LYS* 3.7 10.5 - - + +
377L VAL* 1.3 80.1 - - - +
379L ALA* 1.3 58.7 + - - +
380L LEU 4.1 4.6 - - - +
385L ILE* 3.9 4.7 - - - +
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Residues in contact with ALA 379 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375L LYS 3.3 11.8 + - - +
376L PHE 3.0 12.9 + - - +
378L ASP* 1.3 78.2 - - - +
380L LEU* 1.3 65.5 + - - +
381L LYS* 3.6 8.8 - - - +
440L GLN* 3.4 20.5 + - - +
441L ALA* 3.9 22.0 - - + +
444L SER* 4.0 16.4 - - - +
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Residues in contact with LEU 380 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67I ARG* 5.1 2.1 + - - -
376L PHE* 3.7 21.1 - - + +
377L VAL* 3.2 26.9 + - + +
378L ASP 4.1 5.5 - - - +
379L ALA* 1.3 81.0 - - - +
381L LYS* 1.3 60.5 + - - +
382L ILE 3.8 0.2 - - - -
383L PRO* 3.8 16.6 - - + +
396L VAL* 3.7 36.3 - - + -
424L PHE* 4.1 5.2 - - + -
437L ASP* 3.8 17.9 - - - +
438L ILE* 3.9 22.4 - - + +
441L ALA* 3.6 20.4 - - + -
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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