Contacts of the helix formed by residues 422 - 433 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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327B TYR* 3.7 14.3 - - + -
420B PRO 3.5 1.2 - - - -
421B THR* 1.3 90.9 - - + +
423B LEU* 1.3 67.0 + - - +
424B SER* 2.9 25.2 + - - +
425B ASP* 3.1 38.3 + - - +
426B VAL* 3.7 7.4 + - - +
464B ASN* 6.1 0.8 - - - +
507B CL 3.9 14.2 - - + +
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Residues in contact with LEU 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318B ALA* 5.0 0.4 - - - -
321B ASN 4.0 7.6 - - - +
322B PRO* 3.4 36.8 - - + +
323B THR* 3.7 17.3 - - - +
324B VAL* 3.8 10.4 - - + +
327B TYR* 3.4 18.1 - - + -
422B GLN* 1.3 73.1 - - - +
424B SER* 1.3 64.2 + - - +
426B VAL* 3.0 34.0 + - + +
427B ILE* 3.0 28.5 + - + +
455B LYS* 4.4 7.6 - - + -
459B GLU* 3.9 9.6 - - + +
460B ILE* 3.9 18.8 - - + -
507B CL 3.8 10.5 - - + +
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Residues in contact with SER 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422B GLN* 2.9 29.8 + - - -
423B LEU* 1.3 78.6 - - - +
425B ASP* 1.3 59.9 + - - +
427B ILE* 3.9 1.3 - - - -
428B ASP* 3.0 41.9 + - - +
460B ILE* 3.8 26.7 - - - +
464B ASN* 5.8 0.9 - - - -
507B CL 3.4 12.9 - - - +
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Residues in contact with ASP 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314B PRO 4.9 0.2 - - - -
420B PRO* 4.7 10.1 - - + -
421B THR* 4.0 12.3 + - - -
422B GLN* 3.1 35.8 + - - +
423B LEU 3.1 1.0 + - - -
424B SER* 1.3 88.4 + - - +
426B VAL* 1.3 56.6 + - - +
428B ASP* 3.5 9.4 + - - +
429B ARG* 3.0 28.1 + - - +
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Residues in contact with VAL 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B PRO 3.5 18.8 - - - +
315B SER* 4.3 0.3 - - - -
317B LEU* 4.1 5.2 - - + -
318B ALA* 3.6 30.4 - - + +
327B TYR* 3.4 31.0 - - + +
420B PRO* 3.5 35.4 - - + -
422B GLN 4.1 2.2 - - - +
423B LEU* 3.0 25.8 + - + +
425B ASP* 1.3 72.8 - - - +
427B ILE* 1.3 60.2 + - - +
429B ARG* 3.7 1.0 - - - +
430B LEU* 2.8 30.3 + - - +
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Residues in contact with ILE 427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B ALA* 4.0 21.3 - - + +
423B LEU* 3.0 37.7 + - + +
424B SER 4.0 3.6 - - - +
426B VAL* 1.3 75.1 - - - +
428B ASP* 1.3 65.8 + - - +
430B LEU* 3.2 5.6 + - + +
431B GLU* 2.9 23.4 + - - +
451B TRP* 4.1 12.6 - - + +
452B ILE* 3.7 37.3 - - + +
455B LYS* 3.9 24.0 - - + -
456B ARG* 3.7 17.9 - - + +
460B ILE* 4.1 9.9 - - + -
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Residues in contact with ASP 428 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424B SER* 3.0 30.8 + - - +
425B ASP* 3.7 9.7 - - - +
427B ILE* 1.3 75.2 - - - +
429B ARG* 1.3 58.4 + - - +
431B GLU* 3.3 5.7 + - - +
432B ALA* 3.0 27.6 + - - +
456B ARG* 2.9 30.2 + - - +
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Residues in contact with ARG 429 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311B HIS 5.3 3.0 + - - -
314B PRO* 3.5 57.2 - - + +
315B SER* 3.8 6.6 - - - +
425B ASP 3.0 18.1 + - - +
426B VAL 3.8 0.4 - - - +
428B ASP* 1.3 74.5 - - - +
430B LEU* 1.3 59.9 + - - +
432B ALA* 3.2 7.9 + - - +
433B ASP* 2.9 49.3 + - - +
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Residues in contact with LEU 430 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315B SER* 3.8 20.6 - - - +
318B ALA* 3.8 20.0 - - + -
319B PHE* 3.9 19.5 - - + -
426B VAL 2.8 19.3 + - - +
427B ILE* 3.2 6.0 + - + +
429B ARG* 1.3 75.1 - - - +
431B GLU* 1.3 53.9 + - - +
433B ASP 3.3 5.4 + - - -
434B HIS* 2.8 44.0 + - + +
437B LEU* 3.6 31.4 - - + -
448B ILE* 4.1 12.6 - - + -
451B TRP* 3.9 16.2 - - + -
452B ILE* 4.0 15.7 - - + -
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Residues in contact with GLU 431 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427B ILE 2.9 13.0 + - - +
428B ASP* 3.4 9.4 - - - +
430B LEU* 1.3 79.5 - - - +
432B ALA* 1.3 61.5 + - - +
434B HIS* 3.5 16.3 + - - -
452B ILE* 3.6 26.3 - - + +
456B ARG* 2.9 38.4 + - - +
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Residues in contact with ALA 432 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428B ASP 3.0 16.8 + - - +
429B ARG* 3.2 11.6 + - - +
431B GLU* 1.3 79.8 - - - +
433B ASP* 1.3 62.6 + - + +
434B HIS* 4.3 3.0 + - - -
435B GLU* 5.7 0.3 - - - +
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Residues in contact with ASP 433 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311B HIS* 5.7 1.6 + - - -
312B HIS* 4.6 16.7 + - - -
315B SER* 3.6 19.1 + - - -
429B ARG* 2.9 34.9 + - - +
430B LEU 3.3 5.1 + - - +
432B ALA* 1.3 82.9 - - + +
434B HIS* 1.3 64.1 + - - +
435B GLU* 4.1 13.5 + - - +
436B TYR* 4.1 4.0 + - - -
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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