Contacts of the helix formed by residues 422 - 433 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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327E TYR* 3.7 14.5 - - + -
420E PRO 3.5 1.2 - - - -
421E THR* 1.3 89.5 - - - +
423E LEU* 1.3 66.6 + - - +
424E SER* 3.0 25.5 + - - +
425E ASP* 3.1 37.5 + - - +
426E VAL* 3.6 8.1 + - - +
507E CL 4.0 12.0 - - + +
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Residues in contact with LEU 423 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318E ALA* 5.0 0.4 - - - -
321E ASN 3.9 7.4 - - - +
322E PRO* 3.4 37.0 - - + +
323E THR 3.7 16.8 - - - +
324E VAL* 3.8 10.2 - - + +
327E TYR* 3.5 16.6 - - + -
422E GLN* 1.3 73.4 - - - +
424E SER* 1.3 64.0 + - - +
426E VAL* 3.0 33.7 + - + +
427E ILE* 3.0 28.0 + - + +
455E LYS* 4.4 7.6 - - + -
459E GLU* 3.8 10.5 - - + +
460E ILE* 4.0 18.6 - - + -
507E CL 3.7 9.8 - - + +
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Residues in contact with SER 424 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422E GLN* 3.0 27.4 + - - -
423E LEU* 1.3 77.9 - - - +
425E ASP* 1.3 60.4 + - - +
427E ILE* 4.0 1.2 - - - +
428E ASP* 3.0 42.3 + - - +
460E ILE* 3.9 26.7 - - - -
464E ASN* 5.8 0.7 - - - -
507E CL 3.4 14.4 - - - +
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Residues in contact with ASP 425 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314E PRO 5.0 0.2 - - - -
420E PRO* 4.7 10.7 - - + +
421E THR* 4.0 12.3 + - - -
422E GLN* 3.1 37.7 + - - +
423E LEU 3.1 0.6 - - - -
424E SER* 1.3 88.9 + - - +
426E VAL* 1.3 56.6 + - - +
428E ASP* 3.6 9.2 - - - +
429E ARG* 3.0 27.9 + - - +
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Residues in contact with VAL 426 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314E PRO 3.5 17.7 - - - +
315E SER* 4.3 0.3 - - - -
317E LEU* 4.1 4.9 - - + -
318E ALA* 3.7 24.9 - - + +
327E TYR* 3.3 29.6 - - + +
420E PRO* 3.5 37.5 - - + -
422E GLN 4.1 1.1 - - - +
423E LEU* 3.0 32.5 + - + +
425E ASP* 1.3 74.1 - - - +
427E ILE* 1.3 55.4 + - - +
429E ARG* 3.4 1.6 + - - +
430E LEU* 2.8 34.3 + - - +
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Residues in contact with ILE 427 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318E ALA* 4.0 20.6 - - + -
423E LEU* 3.0 31.5 + - + +
424E SER* 4.0 4.0 - - - +
426E VAL* 1.3 73.8 - - - +
428E ASP* 1.3 64.1 + - - +
430E LEU* 3.2 6.6 + - + +
431E GLU* 2.9 23.7 + - - +
451E TRP* 4.2 12.8 - - + +
452E ILE* 3.7 36.3 - - + +
455E LYS* 4.0 23.3 - - + -
456E ARG* 3.7 20.2 - - + +
460E ILE* 4.0 14.4 - - + -
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Residues in contact with ASP 428 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424E SER* 3.0 32.1 + - - +
425E ASP* 3.6 10.3 - - - +
427E ILE* 1.3 74.7 - - - +
429E ARG* 1.3 57.8 + - - +
431E GLU* 3.4 5.4 + - - +
432E ALA* 3.0 27.4 + - - +
456E ARG* 2.9 29.7 + - - +
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Residues in contact with ARG 429 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311E HIS* 5.3 3.2 + - - -
314E PRO* 3.5 58.7 - - + +
315E SER* 3.9 6.5 - - - +
425E ASP 3.0 18.3 + - - +
426E VAL 3.7 0.4 - - - +
428E ASP* 1.3 75.2 - - - +
430E LEU* 1.3 59.0 + - - +
432E ALA* 3.2 8.5 + - - +
433E ASP* 2.8 49.4 + - - +
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Residues in contact with LEU 430 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315E SER* 3.8 21.0 - - - +
318E ALA* 3.8 19.7 - - + -
319E PHE* 3.9 13.5 - - + -
426E VAL 2.8 21.0 + - - +
427E ILE* 3.6 4.9 - - + +
429E ARG* 1.3 72.1 - - - +
431E GLU* 1.3 53.4 + - - +
433E ASP 3.3 4.1 + - - -
434E HIS* 2.7 45.2 + - + +
437E LEU* 3.6 31.0 - - + -
448E ILE* 4.1 14.8 - - + -
451E TRP* 3.9 17.9 - - + -
452E ILE* 3.9 20.4 - - + -
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Residues in contact with GLU 431 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427E ILE 2.9 13.1 + - - +
428E ASP* 3.4 9.3 - - - +
430E LEU* 1.3 78.1 - - - +
432E ALA* 1.3 61.2 + - - +
434E HIS* 3.5 17.7 + - - -
452E ILE* 3.5 25.2 - - + +
456E ARG* 2.9 38.0 + - - +
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Residues in contact with ALA 432 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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428E ASP 3.0 16.8 + - - +
429E ARG* 3.2 11.6 + - - +
431E GLU* 1.3 79.3 - - - +
433E ASP* 1.3 62.0 + - + +
434E HIS* 4.7 2.2 + - - -
435E GLU* 5.7 0.5 - - - +
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Residues in contact with ASP 433 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311E HIS* 5.8 1.2 + - - -
312E HIS* 4.6 16.2 + - - -
315E SER* 3.6 19.2 + - - -
429E ARG* 2.8 37.0 + - - +
430E LEU 3.3 2.5 + - - +
432E ALA* 1.3 82.1 - - + +
434E HIS* 1.3 64.6 + - - +
435E GLU* 4.1 14.6 + - - +
436E TYR* 4.1 3.7 - - - -
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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