Contacts of the helix formed by residues 423 - 434 (chain B) in PDB entry 2PZD
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 ASN 423 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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368B THR* 3.6 18.2 - - + +
391B VAL* 3.4 15.9 - - - +
421B VAL* 3.7 0.9 - - - +
422B GLN* 1.3 89.2 - - - +
424B ALA* 1.3 63.6 + - - +
425B GLU* 3.3 12.7 + - - +
426B ASP* 3.1 42.8 + - - +
427B VAL* 3.7 2.6 + - - +
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Residues in contact with ALA 424 (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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465A PHE* 4.0 27.4 - - + -
10B EDO 4.6 6.1 - - - +
366B MET* 3.8 28.4 - - + +
368B THR* 3.0 16.5 + - - +
391B VAL* 3.7 5.2 - - + +
423B ASN* 1.3 74.1 - - - +
425B GLU* 1.3 61.7 + - - +
427B VAL* 3.0 6.2 + - - +
428B TYR* 2.9 29.2 + - + -
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Residues in contact with GLU 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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10B EDO 3.0 42.1 + - - +
423B ASN* 3.3 14.5 + - - +
424B ALA* 1.3 77.4 - - - +
426B ASP* 1.3 58.6 + - - +
428B TYR* 3.3 13.2 - - - +
429B GLU* 2.9 48.2 + - - +
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Residues in contact with ASP 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416B ILE* 4.7 2.4 - - - +
420B MET 4.2 5.0 - - - +
421B VAL* 3.7 18.1 - - + +
422B GLN* 2.9 33.4 + - - +
423B ASN* 3.1 26.0 + - - +
425B GLU* 1.3 78.5 - - - +
427B VAL* 1.3 60.3 - - - +
429B GLU* 3.8 5.4 + - - +
430B ALA* 3.2 22.0 + - - +
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Residues in contact with VAL 427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467A VAL* 4.3 5.4 - - + -
362B ILE* 4.7 7.4 - - + -
366B MET* 3.2 39.3 - - + -
391B VAL* 4.2 12.8 - - + -
413B ILE* 4.5 12.6 - - + -
416B ILE* 4.2 23.3 - - + -
421B VAL* 4.9 3.6 - - + -
423B ASN 3.9 12.8 - - - +
424B ALA 3.0 4.0 + - - +
426B ASP* 1.3 75.7 - - - +
428B TYR* 1.3 64.9 + - - +
430B ALA* 3.1 2.1 + - - +
431B VAL* 2.9 41.3 + - + +
437B LEU* 5.4 0.9 - - + -
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Residues in contact with TYR 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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465A PHE* 3.3 42.7 - + + +
466A TRP 2.7 32.6 + - - -
467A VAL* 3.2 27.1 - - + -
10B EDO 3.5 22.9 - - - -
366B MET* 4.8 2.2 - - - -
424B ALA* 2.9 26.0 + - + -
425B GLU* 3.3 17.9 - - - +
427B VAL* 1.3 77.5 - - - +
429B GLU* 1.3 61.3 + - - +
431B VAL* 3.5 3.5 + - - +
432B ARG* 3.1 28.0 + - + +
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Residues in contact with GLU 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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425B GLU* 2.9 35.7 + - - +
426B ASP* 4.1 5.2 - - - +
428B TYR* 1.3 70.5 - - - +
430B ALA* 1.3 58.2 + - - +
432B ARG* 3.4 19.2 + - - +
433B THR* 2.7 59.7 + - - +
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Residues in contact with ALA 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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416B ILE* 3.9 15.9 - - + -
426B ASP 3.2 15.5 + - - +
427B VAL 3.1 9.0 + - - +
429B GLU* 1.3 73.0 - - - +
431B VAL* 1.3 66.9 + - - +
432B ARG 3.2 0.2 + - - -
433B THR* 3.9 0.9 - - - -
434B GLN* 3.0 54.7 + - - +
437B LEU* 3.8 18.6 - - + +
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Residues in contact with VAL 431 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467A VAL* 4.0 18.8 - - + -
360B ARG* 2.6 62.2 + - + +
361B TYR* 4.0 5.6 - - - +
362B ILE* 3.9 39.3 - - + -
427B VAL* 2.9 21.6 + - + +
428B TYR 3.7 4.7 - - - +
430B ALA* 1.3 74.7 - - - +
432B ARG* 1.3 54.2 + - + +
437B LEU* 3.9 18.8 - - + -
454B PRO* 4.0 4.3 - - + +
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Residues in contact with ARG 432 (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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359B ARG* 5.9 5.3 - - - +
360B ARG* 3.5 25.2 + - + +
428B TYR* 3.1 19.0 + - + +
429B GLU* 3.7 22.3 + - - +
430B ALA 3.1 0.4 - - - -
431B VAL* 1.3 80.1 - - + +
433B THR* 1.3 60.9 + - + +
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Residues in contact with THR 433 (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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360B ARG* 4.3 1.3 - - - -
429B GLU* 2.7 46.6 + - - +
430B ALA* 3.6 3.5 + - - -
432B ARG* 1.3 84.2 - - + +
434B GLN* 1.3 70.8 + - - +
435B SER 4.3 0.3 + - - -
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Residues in contact with GLN 434 (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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360B ARG* 3.0 19.1 + - - +
416B ILE* 4.1 16.9 + - - +
417B GLY* 5.2 4.4 + - - -
430B ALA* 3.0 37.4 + - - +
433B THR* 1.3 87.6 + - - +
435B SER* 1.3 65.1 + - - +
436B GLN 3.5 16.7 + - - +
437B LEU* 3.6 25.5 - - + +
438B ALA 4.8 0.9 + - - -
454B PRO* 3.9 0.3 - - - +
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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