Contacts of the helix formed by residues 444 - 459 (chain F) in PDB entry 3ZXR
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 THR 444 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105F SER* 3.9 14.7 + - - -
114F LYS* 4.0 9.8 - - - +
438F THR* 4.8 1.3 - - - -
441F GLY* 3.7 20.2 - - - +
442F VAL 4.1 0.4 + - - -
443F PHE* 1.3 77.4 - - - +
445F ASN* 1.3 67.3 + - - +
446F ASP* 2.5 27.5 + - - -
447F LEU* 3.1 22.1 + - - +
448F ILE* 3.2 14.6 + - - +
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Residues in contact with ASN 445 (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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434F HIS* 3.5 23.7 + - - -
435F GLU* 5.7 0.5 - - - +
438F THR* 3.9 12.9 - - - +
444F THR* 1.3 73.8 - - - +
446F ASP* 1.3 57.3 + - - +
448F ILE* 3.3 6.2 + - - +
449F GLU* 2.9 48.6 + - - +
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Residues in contact with ASP 446 (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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105F SER* 2.6 27.6 + - - -
106F ARG* 2.8 26.2 + - - +
444F THR* 2.5 29.4 + - - -
445F ASN* 1.3 75.2 - - - +
447F LEU* 1.3 64.8 + - - +
449F GLU* 4.1 10.1 + - - +
450F THR* 2.8 31.4 + - - +
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Residues in contact with LEU 447 (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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28F LEU* 3.9 27.4 - - + -
105F SER 4.0 10.1 - - - +
106F ARG* 4.0 15.7 - - + +
111F ILE* 3.5 35.4 - - + -
319F PHE* 4.8 5.4 - - + -
378F LEU* 4.5 11.9 - - + -
443F PHE* 3.6 30.5 - - + -
444F THR* 3.1 18.0 + - - +
446F ASP* 1.3 81.3 - - - +
448F ILE* 1.3 57.9 + - + +
450F THR* 3.3 2.8 + - - -
451F TRP* 2.9 32.3 + - + +
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Residues in contact with ILE 448 (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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319F PHE* 4.6 8.7 - - + -
430F LEU* 4.1 15.0 - - + -
434F HIS* 3.8 44.4 - - + +
437F LEU* 4.3 7.6 - - + -
438F THR* 3.9 19.1 - - + -
443F PHE* 3.9 28.9 - - + -
444F THR 3.2 8.5 + - - +
445F ASN* 3.8 8.1 - - - +
447F LEU* 1.3 76.0 - - - +
449F GLU* 1.3 59.6 + - + +
451F TRP* 3.4 6.2 + - - +
452F ILE* 3.0 46.9 + - + +
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Residues in contact with GLU 449 (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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445F ASN* 2.9 34.3 + - + +
446F ASP* 4.1 7.6 - - - +
448F ILE* 1.3 76.5 - - + +
450F THR* 1.3 59.0 + - - +
452F ILE* 3.5 11.0 + - + +
453F SER* 2.9 32.1 + - - -
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Residues in contact with THR 450 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28F LEU* 3.7 20.2 - - + -
60F GLY* 3.8 23.6 - - - +
106F ARG* 3.6 18.1 + - - +
446F ASP* 2.8 22.3 + - - +
447F LEU 3.6 3.1 - - - -
449F GLU* 1.3 72.7 - - - +
451F TRP* 1.3 56.8 + - - +
453F SER* 3.7 5.2 - - - -
454F PHE* 2.7 39.8 + - + +
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Residues in contact with TRP 451 (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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28F LEU* 3.4 43.6 - - + +
29F PRO* 4.1 14.8 - - + -
318F ALA 2.9 29.5 + - - -
319F PHE* 3.4 34.8 - + + -
322F PRO* 3.6 13.7 - - + -
375F ASN* 4.7 4.9 - - + -
378F LEU* 3.5 22.4 - - + -
427F ILE* 4.2 8.4 - - + +
430F LEU* 3.9 15.9 - - + -
447F LEU* 2.9 17.9 + - + +
448F ILE* 3.5 6.7 - - - +
450F THR* 1.3 73.6 - - - +
452F ILE* 1.3 65.4 + - - +
454F PHE* 3.2 7.2 + + + +
455F LYS* 3.0 58.9 + - - +
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Residues in contact with ILE 452 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427F ILE* 3.7 21.9 - - + +
430F LEU* 3.9 15.9 - - + -
431F GLU* 3.6 38.1 - - + +
434F HIS* 5.7 0.4 - - + -
448F ILE* 3.0 37.3 + - + +
449F GLU* 3.8 10.1 - - + +
451F TRP* 1.3 75.8 - - - +
453F SER* 1.3 64.9 + - - +
455F LYS* 3.4 2.1 + - - +
456F ARG* 3.0 62.2 + - - +
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Residues in contact with SER 453 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449F GLU 2.9 18.9 + - - -
450F THR* 3.7 5.8 - - - -
452F ILE* 1.3 79.8 - - - +
454F PHE* 1.3 63.4 + - - +
456F ARG* 3.3 5.8 + - - +
457F GLU* 3.1 49.3 + - - +
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Residues in contact with PHE 454 (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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28F LEU* 5.8 3.8 - - + -
29F PRO* 3.8 28.0 - - + -
59F ARG* 3.9 40.6 - - + -
60F GLY* 4.9 8.7 - - - -
450F THR* 2.7 27.6 + - + +
451F TRP* 3.7 7.6 - + + +
453F SER* 1.3 72.9 - - - +
455F LYS* 1.3 69.8 + - + +
457F GLU* 5.7 0.4 - - - -
458F ASN* 2.9 74.4 + - + +
459F GLU* 3.4 24.0 - - - -
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Residues in contact with LYS 455 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29F PRO* 5.4 7.4 + - - +
322F PRO* 2.8 36.7 + - - +
323F THR* 4.4 5.1 - - - +
373F SER 5.4 1.2 + - - -
374F GLY* 5.8 0.2 - - - -
423F LEU* 4.4 3.1 - - + -
427F ILE* 4.0 30.1 - - + -
451F TRP* 3.0 54.4 + - - +
452F ILE 3.9 3.4 - - - +
454F PHE* 1.3 87.0 - - + +
456F ARG* 1.3 58.0 + - - +
459F GLU* 2.8 39.7 + - - +
460F ILE* 2.9 31.5 + - + +
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Residues in contact with ARG 456 (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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427F ILE* 3.7 8.3 - - + +
428F ASP* 2.9 35.6 + - - +
431F GLU* 2.9 41.8 + - - -
452F ILE* 3.0 35.8 + - - +
453F SER* 3.8 6.1 - - - +
455F LYS* 1.3 77.9 - - - +
457F GLU* 1.3 63.1 + - + +
460F ILE* 3.8 21.0 - - + +
461F GLU* 3.0 33.8 + - - +
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Residues in contact with GLU 457 (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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453F SER* 3.1 36.5 + - - +
454F PHE* 5.7 0.5 - - - -
456F ARG* 1.3 79.3 - - + +
458F ASN* 1.3 69.9 + - - +
461F GLU* 4.6 13.9 - - - +
462F PRO* 3.4 17.6 - - - +
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Residues in contact with ASN 458 (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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454F PHE* 2.9 63.4 + - + +
457F GLU* 1.3 86.9 + - - +
459F GLU* 1.3 63.6 + - + +
462F PRO* 3.5 16.3 - - - +
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Residues in contact with GLU 459 (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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29F PRO* 5.5 1.2 - - - +
322F PRO 3.4 10.4 - - - +
323F THR* 3.7 18.2 - - - +
324F VAL* 4.3 11.2 + - + -
423F LEU* 3.9 3.6 - - + +
454F PHE* 3.4 16.3 - - + -
455F LYS* 2.8 49.4 + - + +
458F ASN* 1.3 89.9 - - + +
460F ILE* 1.3 68.0 + - - +
461F GLU 3.5 0.9 - - - -
462F PRO* 3.5 2.6 - - - +
463F VAL* 3.2 29.5 + - + +
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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