Contacts of the helix formed by residues 422 - 433 (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 GLN 422 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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327F TYR* 3.7 14.6 - - + -
420F PRO* 3.5 1.2 - - - +
421F THR* 1.3 90.5 - - + +
423F LEU* 1.3 64.0 + - - +
424F SER* 2.9 25.9 + - - +
425F ASP* 3.1 38.3 + - - +
426F VAL* 3.6 7.6 + - - +
507F CL 3.8 14.1 - - + +
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Residues in contact with LEU 423 (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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318F ALA* 5.0 0.4 - - - -
321F ASN 4.0 7.0 - - - +
322F PRO* 3.4 38.1 - - + +
323F THR* 3.7 15.3 - - - +
324F VAL* 3.8 11.1 - - + +
327F TYR* 3.4 19.7 - - + -
422F GLN* 1.3 70.1 - - - +
424F SER* 1.3 64.9 + - - +
426F VAL* 3.1 23.2 + - + +
427F ILE* 3.0 38.2 + - + +
455F LYS* 4.4 7.9 - - + -
459F GLU* 3.9 9.6 - - + +
460F ILE* 3.9 19.7 - - + -
507F CL 3.8 8.9 - - + +
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Residues in contact with SER 424 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422F GLN* 2.9 29.1 + - - -
423F LEU* 1.3 77.8 - - - +
425F ASP* 1.3 60.1 + - - +
427F ILE* 3.9 1.6 - - - +
428F ASP* 3.0 42.4 + - - +
460F ILE* 3.9 26.2 - - - +
464F ASN* 5.7 1.3 - - - -
507F CL 3.4 15.2 - - - +
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Residues in contact with ASP 425 (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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314F PRO 5.0 0.2 - - - -
420F PRO* 4.7 9.9 - - + -
421F THR* 4.0 13.3 + - - -
422F GLN* 3.1 38.1 + - - +
424F SER* 1.3 88.7 + - - +
426F VAL* 1.3 58.8 + - - +
428F ASP* 3.5 9.7 + - - +
429F ARG* 3.0 27.5 + - - +
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Residues in contact with VAL 426 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314F PRO 3.5 18.3 - - - +
315F SER* 4.3 0.3 - - - -
317F LEU* 4.1 5.2 - - + -
318F ALA* 3.6 29.6 - - + +
327F TYR* 3.3 30.5 - - + +
420F PRO* 3.5 35.4 - - + -
422F GLN 3.6 1.8 + - - +
423F LEU* 3.1 25.5 + - + +
425F ASP* 1.3 73.1 - - - +
427F ILE* 1.3 56.9 + - - +
429F ARG* 3.4 1.2 + - - +
430F LEU* 2.8 35.0 + - - +
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Residues in contact with ILE 427 (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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318F ALA* 3.9 21.1 - - + -
423F LEU* 3.0 37.8 + - + +
424F SER 4.0 3.1 - - - +
426F VAL* 1.3 74.7 - - - +
428F ASP* 1.3 64.9 + - - +
430F LEU* 3.3 5.3 + - + +
431F GLU* 2.9 23.9 + - - +
451F TRP* 4.2 13.5 - - + +
452F ILE* 3.7 37.0 - - + +
455F LYS* 4.0 22.7 - - + -
456F ARG* 3.7 19.5 - - + +
460F ILE* 4.1 10.1 - - + -
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Residues in contact with ASP 428 (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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424F SER* 3.0 31.3 + - - +
425F ASP* 3.6 9.0 - - - +
427F ILE* 1.3 75.0 - - - +
429F ARG* 1.3 57.5 + - - +
431F GLU* 3.3 6.4 + - - +
432F ALA* 3.1 27.8 + - - +
456F ARG* 2.9 29.9 + - - +
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Residues in contact with ARG 429 (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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311F HIS 5.4 2.6 + - - -
314F PRO* 3.5 56.0 - - + +
315F SER* 3.8 7.0 - - - +
425F ASP 3.0 17.9 + - - +
426F VAL 3.8 0.2 - - - +
427F ILE 3.2 0.2 - - - -
428F ASP* 1.3 74.5 - - - +
430F LEU* 1.3 59.8 + - - +
432F ALA* 3.2 9.2 + - - +
433F ASP* 2.8 50.7 + - - +
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Residues in contact with LEU 430 (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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315F SER* 3.8 20.8 - - - +
318F ALA* 3.8 20.0 - - + -
319F PHE* 3.8 19.7 - - + -
426F VAL 2.8 21.6 + - - +
427F ILE* 3.3 5.6 + - + +
429F ARG* 1.3 73.2 - - - +
431F GLU* 1.3 54.3 + - - +
432F ALA 3.4 0.2 + - - -
433F ASP 3.4 1.4 + - - -
434F HIS* 2.7 45.7 + - + +
437F LEU* 3.6 31.6 - - + -
448F ILE* 4.1 12.6 - - + +
451F TRP* 3.9 16.2 - - + -
452F ILE* 3.9 15.3 - - + -
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Residues in contact with GLU 431 (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 2.9 16.4 + - - +
428F ASP* 3.5 6.0 - - - +
429F ARG 3.2 0.2 - - - -
430F LEU* 1.3 77.2 - - - +
432F ALA* 1.3 61.7 + - - +
434F HIS* 3.4 17.7 + - + -
452F ILE* 3.6 23.9 - - + +
456F ARG* 2.9 39.7 + - - +
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Residues in contact with ALA 432 (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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428F ASP 3.1 16.0 + - - +
429F ARG* 3.6 12.3 - - - +
431F GLU* 1.3 80.2 - - - +
433F ASP* 1.3 61.9 + - + +
434F HIS* 4.3 2.1 + - - -
435F GLU* 5.7 0.9 - - - +
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Residues in contact with ASP 433 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311F HIS* 5.8 0.9 + - - -
312F HIS* 4.6 16.3 + - - -
315F SER* 3.6 19.2 + - - -
429F ARG* 2.8 38.5 + - - +
430F LEU 3.4 2.7 + - - +
432F ALA* 1.3 83.0 - - + +
434F HIS* 1.3 64.8 + - - +
435F GLU* 4.1 14.3 + - - +
436F TYR* 4.1 3.8 + - - -
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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