Contacts of the helix formed by residues 376 - 386 (chain B) in PDB entry 1Z6T
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 ARG 376 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44B ARG* 5.4 5.3 - - - +
374B MET 3.5 4.2 + - - -
375B LEU* 1.3 74.1 - - - +
377B GLU* 1.3 66.5 + - - +
378B ASP* 3.0 24.6 + - - +
379B ILE* 3.1 41.4 + - + +
380B LYS 3.5 3.6 + - - -
414B ILE* 5.4 4.0 - - - +
417B GLU* 2.7 45.4 + - - +
421B LYS* 6.1 0.4 - - - +
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Residues in contact with GLU 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 GLU 4.9 0.3 - - - +
375B LEU 4.0 2.0 - - - +
376B ARG* 1.3 73.9 - - - +
378B ASP* 1.3 59.1 + - - +
379B ILE 3.2 1.9 + - - -
380B LYS* 3.0 53.8 + - - +
381B ASP* 4.7 4.9 + - - +
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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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376B ARG* 3.0 37.1 + - - +
377B GLU* 1.3 75.2 - - - +
379B ILE* 1.3 62.7 + - - +
381B ASP* 5.3 2.9 - - - +
382B TYR* 3.2 22.9 + - - -
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Residues in contact with ILE 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375B LEU* 4.1 17.7 - - + -
376B ARG* 3.4 40.6 - - + +
378B ASP* 1.3 93.2 + - - +
380B LYS* 1.3 63.8 + - - +
381B ASP 3.3 2.2 - - - -
382B TYR* 3.3 21.3 + - + +
383B TYR* 3.1 17.7 + - - +
414B ILE* 4.3 13.9 - - + +
417B GLU* 3.9 30.3 - - + +
418B PHE* 3.6 28.7 - - + -
421B LYS* 6.0 1.6 - - + -
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Residues in contact with LYS 380 (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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372B VAL* 3.7 15.7 - - + +
373B GLU* 3.2 42.6 + - - +
375B LEU* 3.1 39.3 - - + +
376B ARG 3.5 5.2 + - - +
377B GLU* 3.0 44.6 + - - +
379B ILE* 1.3 78.3 - - - +
381B ASP* 1.3 65.5 + - - +
383B TYR* 3.2 5.0 + - - +
384B THR* 3.0 26.0 + - - +
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Residues in contact with ASP 381 (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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377B GLU 4.7 4.3 + - - +
378B ASP 5.8 2.5 - - - +
379B ILE 3.3 0.4 - - - -
380B LYS* 1.3 78.9 - - - +
382B TYR* 1.3 70.4 + - + +
384B THR* 3.1 10.6 + - - +
385B ASP* 2.9 30.0 + - - +
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Residues in contact with TYR 382 (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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378B ASP 3.2 27.4 - - - -
379B ILE* 3.3 15.5 + - + +
381B ASP* 1.3 81.7 - - + +
383B TYR* 1.3 60.5 + - - +
385B ASP* 3.3 12.4 + - - +
386B LEU* 3.6 3.6 + - - +
404B TRP* 3.3 72.4 - + + +
406B MET* 4.2 12.8 - - - +
414B ILE* 3.9 36.6 - - + -
418B PHE* 4.3 2.0 - - + -
459B LYS* 6.0 0.4 - - - -
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Residues in contact with TYR 383 (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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368B MET* 3.5 19.0 - - + +
372B VAL* 3.6 35.9 - - + -
375B LEU* 3.8 14.6 - - + -
379B ILE 3.1 7.0 + - - +
380B LYS 3.6 7.4 - - - +
381B ASP 3.2 0.2 - - - -
382B TYR* 1.3 73.2 - - - +
384B THR* 1.3 66.5 + - - +
386B LEU* 3.0 34.2 + - + +
387B SER* 3.9 2.9 + - - -
418B PHE* 3.7 36.2 - + + -
423B LEU* 2.6 45.3 + - + +
437B LEU* 3.7 8.9 - - + +
445B LEU* 3.8 29.1 - - + +
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Residues in contact with THR 384 (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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372B VAL* 5.8 2.4 - - - +
380B LYS* 3.0 14.3 + - - +
381B ASP* 3.4 15.3 + - - +
383B TYR* 1.3 76.4 - - - +
385B ASP* 1.3 61.5 + - - +
387B SER* 2.6 30.7 + - - -
445B LEU* 5.3 0.4 - - - -
448B LYS* 4.5 9.4 + - - -
449B ASN* 3.8 27.7 + - - +
452B GLN* 3.8 25.4 - - - +
456B LEU* 3.5 12.9 - - + +
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Residues in contact with ASP 385 (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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381B ASP* 2.9 19.4 + - - +
382B TYR* 3.3 12.9 - - - +
383B TYR 3.2 0.2 - - - -
384B THR* 1.3 78.1 - - - +
386B LEU* 1.3 57.9 + - - +
387B SER 3.0 4.9 + - - -
388B ILE* 3.1 27.4 + - - +
403B LEU* 3.9 11.8 - - + +
404B TRP* 2.9 22.9 + - + +
456B LEU* 3.2 27.9 - - - +
459B LYS* 2.5 35.8 + - - +
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Residues in contact with LEU 386 (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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382B TYR 3.7 9.4 - - - +
383B TYR* 3.0 33.2 + - + +
385B ASP* 1.3 72.9 - - - +
387B SER* 1.3 55.1 + - - +
388B ILE 3.1 5.8 - - - -
389B LEU* 3.0 45.8 + - + +
400B LEU* 3.5 34.5 - - + -
403B LEU* 5.0 0.4 - - + -
404B TRP* 3.9 10.8 - - + -
415B LEU* 4.3 2.0 - - + -
418B PHE* 4.1 11.0 - - + -
424B LEU* 4.1 33.4 - - + -
437B LEU* 3.7 13.5 - - + +
445B LEU* 4.3 4.3 - - + -
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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