Contacts of the helix formed by residues 359 - 373 (chain F) in PDB entry 5ZR1
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 VAL 359 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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402E SER 6.2 1.8 - - - +
404E SER* 5.7 5.4 - - - +
347F VAL* 4.5 16.2 - - + +
348F SER* 5.6 2.0 - - - +
351F CYS* 3.7 26.5 - - - -
357F SER 5.6 0.2 - - - +
358F LYS* 1.3 76.2 - - + +
360F ASP* 1.3 76.5 + - - +
361F ASP 3.3 0.9 - - - -
362F VAL* 3.1 12.4 + - + +
363F ILE* 3.2 30.2 + - + +
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Residues in contact with ASP 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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402E SER* 6.1 1.6 - - - -
358F LYS* 3.3 33.9 - - + +
359F VAL* 1.3 90.4 - - - +
361F ASP* 1.3 64.9 + - - +
363F ILE* 3.8 7.8 + - - +
364F GLU* 3.2 22.3 + - - +
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Residues in contact with ASP 361 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273F LEU* 4.7 18.8 - - + +
274F VAL* 5.7 4.5 - - - +
356F THR* 4.2 17.8 + - - +
358F LYS* 4.1 6.0 + - - +
359F VAL 3.3 0.4 - - - -
360F ASP* 1.3 78.6 - - - +
362F VAL* 1.3 63.1 + - + +
363F ILE 3.4 0.2 - - - -
364F GLU* 3.4 20.1 + - - +
365F CYS* 3.1 35.2 + - - -
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Residues in contact with VAL 362 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273F LEU* 5.0 8.3 - - + -
321F CYS* 5.8 3.6 - - - -
325F LEU* 3.7 25.7 - - + +
347F VAL* 4.8 14.6 - - + -
350F MET* 3.9 18.8 - - + +
351F CYS* 3.6 31.6 - - - +
354F MET* 5.5 1.8 - - + -
356F THR* 3.9 18.2 - - + -
359F VAL* 3.1 9.5 + - + +
361F ASP* 1.3 77.3 - - - +
363F ILE* 1.3 64.8 + - + +
365F CYS* 3.4 6.7 + - - +
366F VAL* 3.3 22.7 + - + +
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Residues in contact with ILE 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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404E SER* 4.1 29.6 - - - +
407E ALA* 3.7 38.1 - - + +
408E LEU* 5.0 3.4 - - + +
347F VAL* 4.4 15.0 - - + -
359F VAL* 3.2 39.2 + - + +
360F ASP* 4.3 6.1 - - - +
362F VAL* 1.3 74.0 - - + +
364F GLU* 1.3 66.4 + - - +
366F VAL* 3.2 19.3 + - + +
367F LYS* 3.4 24.5 + - + +
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Residues in contact with GLU 364 (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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353E LYS* 5.8 1.7 - - - +
354E THR* 3.8 27.7 + - - +
360F ASP 3.2 17.1 + - - +
361F ASP* 3.4 25.8 - - - +
362F VAL 3.2 0.4 - - - -
363F ILE* 1.3 80.0 - - - +
365F CYS* 1.3 62.0 + - - +
366F VAL 3.5 0.2 + - - -
367F LYS* 3.6 7.1 + - - +
368F LEU* 3.3 32.8 + - + +
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Residues in contact with CYS 365 (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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273F LEU* 3.7 13.7 - - + -
318F GLN* 3.6 42.0 - - + +
321F CYS* 3.6 20.9 - - - -
322F GLY* 3.5 5.9 - - - -
361F ASP* 3.1 21.8 + - - +
362F VAL* 3.4 4.2 + - - +
363F ILE 3.3 0.4 - - - -
364F GLU* 1.3 78.3 - - - +
366F VAL* 1.3 63.3 + - - +
368F LEU* 4.1 12.6 - - - +
369F VAL* 3.3 25.9 + - - +
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Residues in contact with VAL 366 (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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408E LEU* 4.2 23.8 - - + -
322F GLY* 4.6 1.6 - - - -
325F LEU* 3.7 32.8 - - + -
326F ASN* 3.3 27.6 + - - +
329F PHE* 5.0 15.7 - - + -
362F VAL* 3.3 15.7 + - + +
363F ILE* 3.2 15.0 + - + +
365F CYS* 1.3 79.3 - - - +
367F LYS* 1.3 58.7 + - + +
369F VAL 3.4 1.2 + - - -
370F LYS* 2.9 28.4 + - + +
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Residues in contact with LYS 367 (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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407E ALA 3.0 28.5 + - - -
408E LEU* 4.1 28.0 - - + +
410E GLU* 3.6 22.2 + - - +
411E GLU* 4.7 5.5 - - - +
412E SER* 4.9 4.8 - - - +
363F ILE* 3.4 21.1 + - + +
364F GLU* 3.6 8.0 + - - +
365F CYS 3.5 0.2 - - - -
366F VAL* 1.3 77.4 - - - +
368F LEU* 1.3 65.0 + - + +
370F LYS* 3.5 8.0 + - - +
371F GLU* 3.3 21.3 + - - +
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Residues in contact with LEU 368 (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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239B PHE* 5.5 1.1 - - + -
353E LYS* 3.9 40.2 - - + +
354E THR* 3.4 29.2 - - - +
356E ILE* 3.6 35.8 - - + +
318F GLN* 5.1 2.0 - - - +
364F GLU* 3.3 31.2 + - + +
365F CYS* 4.5 7.0 - - - +
366F VAL 3.3 0.6 - - - -
367F LYS* 1.3 80.8 - - + +
369F VAL* 1.3 60.6 + - - +
371F GLU* 3.7 15.3 + - - +
372F LEU* 3.5 20.3 - - - +
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Residues in contact with VAL 369 (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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356E ILE* 5.0 5.2 - - + -
318F GLN 3.5 20.9 - - - +
319F LEU* 3.8 17.0 - - + +
322F GLY* 3.6 26.0 - - - +
323F LEU* 3.6 26.5 - - + +
326F ASN* 4.0 5.2 - - - +
365F CYS 3.3 18.8 + - - +
366F VAL 3.4 1.4 + - - -
367F LYS 3.4 0.2 - - - -
368F LEU* 1.3 79.0 - - + +
370F LYS* 1.3 65.1 + - - +
371F GLU 3.2 0.7 - - - -
372F LEU* 3.0 21.5 + - + +
373F ILE* 3.3 15.7 + - + +
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Residues in contact with LYS 370 (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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408E LEU* 5.8 8.5 - - + -
326F ASN* 3.6 19.0 + - - +
330F ILE* 5.4 0.6 - - - +
366F VAL* 2.9 18.9 + - + +
367F LYS* 3.6 10.8 - - - +
368F LEU 3.4 0.2 - - - -
369F VAL* 1.3 78.3 - - - +
371F GLU* 1.3 59.8 + - - +
373F ILE* 4.5 2.2 - - - -
374F ILE* 3.3 45.9 + - + +
379F PHE* 3.3 38.1 - - + -
383F GLN* 3.6 11.1 - - - +
390F ASP* 4.6 16.8 - - - +
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Residues in contact with GLU 371 (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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238B SER 5.5 0.7 - - - -
239B PHE* 3.8 9.8 - - - +
240B LEU* 2.8 34.6 + - + +
241B ASP* 3.0 32.8 + - - +
529C ARG* 3.4 25.2 + - - +
614C ARG* 6.1 0.9 - - - +
353E LYS* 3.3 23.6 + - - -
367F LYS 3.3 9.9 + - - +
368F LEU* 3.7 17.4 - - - +
369F VAL 3.2 0.2 - - - -
370F LYS* 1.3 79.4 - - - +
372F LEU* 1.3 67.3 + - + +
374F ILE* 3.4 7.6 - - - +
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Residues in contact with LEU 372 (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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238B SER 4.3 11.2 - - - +
240B LEU* 4.6 19.7 - - + +
529C ARG* 5.6 0.8 + - - -
530C GLU* 5.1 5.0 - - - +
356E ILE* 4.0 29.2 - - + -
357E ILE* 3.8 28.7 - - + -
305F GLU* 5.1 4.7 - - - +
309F ASN* 5.4 2.7 - - - +
319F LEU* 4.5 13.9 - - + -
368F LEU 3.5 17.5 - - - +
369F VAL* 3.0 15.4 + - + +
371F GLU* 1.3 86.5 - - + +
373F ILE* 1.3 63.2 + - + +
374F ILE 3.6 0.2 - - - -
375F GLY 5.2 1.3 + - - -
376F GLU* 3.5 17.2 - - - +
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Residues in contact with ILE 373 (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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305F GLU* 4.0 11.0 - - - +
323F LEU* 3.8 34.3 - - + +
326F ASN* 4.3 16.8 - - + +
327F CYS* 5.8 0.7 - - - -
369F VAL* 3.3 18.1 + - + +
370F LYS* 4.4 4.3 - - - +
372F LEU* 1.3 83.3 - - + +
374F ILE* 1.3 64.9 + - - +
375F GLY 3.3 3.8 + - - -
376F GLU* 3.5 30.3 + - - +
378F TRP* 4.1 9.0 - - + -
379F PHE* 3.2 55.2 - - + +
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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