Contacts of the helix formed by residues 346 - 363 (chain F) in PDB entry 1ZUM
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 346 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40F VAL* 6.6 0.4 - - + -
196F GLN* 3.2 33.0 - - + +
344F GLN* 3.4 1.5 + - - +
345F VAL* 1.3 88.4 - - + +
347F GLU* 1.3 60.5 + - - +
348F THR* 3.5 14.2 + - - -
349F GLN* 2.9 29.6 + - - +
350F PHE* 3.0 24.8 + - - +
379F TYR* 3.8 18.4 - - + +
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Residues in contact with GLU 347 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346F ASP* 1.3 73.8 - - - +
348F THR* 1.3 70.6 + - - +
350F PHE* 3.2 6.1 - - + +
351F LYS* 2.9 67.0 + - + +
379F TYR* 3.7 35.7 + - + +
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Residues in contact with THR 348 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346F ASP* 3.2 15.2 + - - -
347F GLU* 1.3 84.7 + - - +
349F GLN* 1.3 66.9 + - - +
351F LYS* 3.5 13.0 + - - +
352F LYS* 3.1 33.1 + - + +
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Residues in contact with GLN 349 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168F TRP* 3.9 21.0 - - + -
300F GLN* 4.8 1.3 - - - +
344F GLN* 4.6 5.6 - - + -
345F VAL* 3.9 20.2 - - + -
346F ASP* 2.9 24.3 + - - +
348F THR* 1.3 76.3 - - - +
350F PHE* 1.3 58.1 + - - +
352F LYS* 3.1 24.4 + - - +
353F ILE* 2.8 48.1 + - + +
400F ILE 3.7 18.2 - - - +
401F PHE* 4.2 16.9 - - - +
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Residues in contact with PHE 350 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344F GLN* 4.6 3.7 - - - +
346F ASP 3.0 15.5 + - - +
347F GLU* 3.2 15.3 - - + +
349F GLN* 1.3 75.9 - - - +
351F LYS* 1.3 69.1 + - + +
353F ILE* 3.4 3.1 + - - +
354F LEU* 3.1 41.6 + - + +
373F ILE* 3.9 35.2 - - + -
378F GLY 4.7 4.9 - - - -
379F TYR* 3.5 45.5 - + + -
380F PHE 3.6 22.2 - - - -
381F ILE* 3.8 22.5 - - + +
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Residues in contact with LYS 351 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347F GLU* 2.9 59.8 + - + +
348F THR* 3.9 8.9 + - - +
350F PHE* 1.3 84.0 - - + +
352F LYS* 1.3 60.6 + - - +
354F LEU* 3.3 13.5 + - + +
355F GLY* 2.9 26.0 + - - -
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Residues in contact with LYS 352 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348F THR* 3.1 25.5 + - + +
349F GLN* 3.4 30.1 - - - +
351F LYS* 1.3 76.4 - - - +
353F ILE* 1.3 58.9 + - + +
355F GLY* 3.3 2.7 + - - -
356F TYR* 3.0 65.6 + - + -
399F GLU 5.1 3.6 + - - -
400F ILE* 5.8 1.5 - - - +
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Residues in contact with ILE 353 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344F GLN* 3.5 42.2 - - + +
349F GLN* 2.8 25.8 + - + +
350F PHE 3.7 0.2 - - - +
352F LYS* 1.3 75.0 - - + +
354F LEU* 1.3 64.4 + - - +
356F TYR* 3.1 8.9 + - - +
357F ILE* 2.9 29.0 + - + +
381F ILE* 3.3 23.8 - - + -
400F ILE* 3.9 33.0 - - + +
401F PHE 3.9 4.7 - - - +
402F GLY* 3.8 11.4 - - - -
403F PRO* 4.5 1.8 - - + -
404F VAL* 4.1 13.5 - - + -
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Residues in contact with LEU 354 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350F PHE* 3.1 43.5 + - + +
351F LYS* 3.3 14.1 + - + +
353F ILE* 1.3 75.8 - - - +
355F GLY* 1.3 63.8 + - - +
357F ILE* 3.4 14.9 + - + +
358F ASN* 3.1 22.2 + - - +
371F GLY 5.2 1.8 - - - +
372F GLY* 4.7 7.4 - - - -
373F ILE* 4.0 34.3 - - + +
381F ILE* 4.7 12.3 - - + -
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Residues in contact with GLY 355 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351F LYS 2.9 14.5 + - - -
352F LYS* 3.6 4.7 - - - -
354F LEU* 1.3 78.7 - - - +
356F TYR* 1.3 51.5 + - - +
358F ASN* 3.3 6.8 + - - +
359F THR* 2.7 36.9 + - - -
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Residues in contact with TYR 356 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352F LYS* 3.0 59.8 + - + -
353F ILE* 3.1 8.5 + - - +
355F GLY* 1.3 74.1 - - - +
357F ILE* 1.3 60.4 + - + +
359F THR* 3.1 10.0 + - - -
360F GLY 2.9 24.4 + - - -
386F PHE* 5.4 0.2 - - - -
394F THR* 4.6 9.2 - - + -
395F ILE* 3.6 19.3 - - + +
398F GLU* 2.7 42.2 + - + +
399F GLU 3.9 5.4 + - - -
400F ILE* 3.2 51.4 - - + -
404F VAL* 6.1 2.7 - - + -
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Residues in contact with ILE 357 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353F ILE* 2.9 26.9 + - + +
354F LEU* 3.6 14.8 - - + +
355F GLY 3.3 0.2 - - - -
356F TYR* 1.3 74.5 - - - +
358F ASN* 1.3 63.8 + - - +
360F GLY 3.2 1.7 + - - -
361F LYS* 3.1 37.0 + - + +
367F LEU* 5.4 0.2 - - + -
371F GLY* 3.3 37.5 - - - +
381F ILE* 4.2 10.8 - - + -
384F THR* 3.9 22.4 - - + +
386F PHE* 3.4 16.4 - - + -
404F VAL* 3.9 25.6 - - + -
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Residues in contact with ASN 358 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354F LEU 3.1 14.0 + - - +
355F GLY* 3.7 9.6 - - - +
357F ILE* 1.3 77.4 - - - +
359F THR* 1.3 56.3 + - - +
361F LYS* 3.2 23.0 + - - +
362F GLN* 2.9 57.6 + - - +
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Residues in contact with THR 359 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355F GLY 2.7 21.0 + - - -
356F TYR* 3.1 15.9 + - + -
358F ASN* 1.3 76.9 + - - +
360F GLY* 1.3 60.7 + - - +
362F GLN* 3.4 6.7 + - - +
363F GLU* 3.0 38.7 + - + +
394F THR* 4.0 32.5 - - + -
395F ILE* 4.7 2.5 - - + -
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Residues in contact with GLY 360 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356F TYR 2.9 11.7 + - - -
357F ILE 3.2 3.7 + - - -
359F THR* 1.3 76.8 - - - +
361F LYS* 1.3 60.8 + - - +
363F GLU* 3.3 12.1 + - - +
364F GLY 3.5 0.2 + - - -
365F ALA* 3.2 24.1 + - - +
386F PHE* 4.0 14.4 - - - -
395F ILE* 3.6 26.0 - - - +
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Residues in contact with LYS 361 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357F ILE* 3.1 31.8 + - + +
358F ASN* 3.6 21.2 - - - +
360F GLY* 1.3 75.6 - - - +
362F GLN* 1.3 61.8 - - + +
364F GLY* 3.3 12.8 + - - -
365F ALA 4.5 6.3 - - - +
367F LEU* 4.4 25.9 - - + +
371F GLY 5.0 6.7 + - - -
386F PHE* 4.0 15.0 - - + -
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Residues in contact with GLN 362 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358F ASN* 2.9 48.2 + - - +
359F THR* 3.8 7.4 - - - +
360F GLY 3.4 0.2 - - - -
361F LYS* 1.3 76.8 - - + +
363F GLU* 1.3 60.7 + - + +
364F GLY 3.5 0.5 + - - -
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Residues in contact with GLU 363 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359F THR* 3.0 29.8 + - + +
360F GLY* 3.6 5.7 - - - +
361F LYS 3.2 0.6 - - - -
362F GLN* 1.3 77.2 - - + +
364F GLY* 1.3 58.5 + - - +
365F ALA 4.6 0.7 - - - +
392F GLY 4.5 0.7 - - - +
393F MET* 3.2 33.4 - - + +
394F THR* 2.5 46.4 + - - -
395F ILE* 3.3 21.8 + - - +
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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