Contacts of the helix formed by residues 445 - 453 (chain A) in PDB entry 2PZI
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 445 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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443A LYS* 3.3 17.7 + - + +
444A LEU* 1.3 77.9 - - - +
446A ALA* 1.3 64.2 + - - +
447A ASN* 4.2 8.0 + - - +
448A GLU* 3.2 31.0 + - - +
449A ILE* 3.4 15.3 + - - +
582A LEU* 4.2 3.4 - - - -
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Residues in contact with ALA 446 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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445A THR* 1.3 72.3 - - - +
447A ASN* 1.3 56.0 + - - +
449A ILE* 3.3 6.5 + - - +
450A VAL* 2.9 33.1 + - - +
547A LEU* 3.4 36.3 - - + +
548A LEU* 4.0 13.2 - - + +
552A TYR* 5.2 2.0 - - - +
582A LEU* 4.0 22.5 - - + +
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Residues in contact with ASN 447 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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445A THR* 3.2 8.0 + - - +
446A ALA* 1.3 80.6 - - - +
448A GLU* 1.3 62.9 + - - +
450A VAL* 3.4 3.5 + - - +
451A THR* 3.3 27.2 + - - +
513A LEU 5.3 2.6 + - - -
514A ASP 4.1 18.6 + - - -
515A LEU 5.7 1.0 - - - -
516A GLY* 5.5 4.4 - - - +
548A LEU* 4.0 15.6 - - + +
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Residues in contact with GLU 448 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421A THR 4.1 6.8 - - - +
422A PHE* 3.6 11.9 - - + +
423A GLY* 2.9 33.1 + - - -
424A VAL 4.9 2.6 + - - -
425A ASP* 5.4 3.8 - - - +
426A LEU* 5.1 5.0 - - - +
444A LEU* 4.2 5.5 - - - +
445A THR* 3.2 22.1 + - - +
447A ASN* 1.3 81.0 + - - +
449A ILE* 1.3 61.8 + - + +
451A THR* 3.3 15.8 + - - +
452A ALA* 3.5 13.3 + - - +
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Residues in contact with ILE 449 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422A PHE* 4.0 28.0 - - + -
444A LEU* 3.9 14.6 - - + -
445A THR 3.4 14.4 - - - +
446A ALA* 3.3 6.9 + - - +
448A GLU* 1.3 75.4 - - - +
450A VAL* 1.3 65.6 + - - +
452A ALA* 3.1 3.8 + - - +
453A LEU* 3.0 49.7 + - + +
547A LEU* 4.1 12.1 - - + -
575A ALA* 5.7 0.2 - - - -
578A ALA* 3.7 32.5 - - + -
582A LEU* 3.8 31.6 - - + -
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Residues in contact with VAL 450 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419A ARG* 2.9 19.2 + - - -
446A ALA 2.9 20.0 + - - +
447A ASN* 3.8 8.1 - - - +
448A GLU 3.4 0.4 - - - -
449A ILE* 1.3 77.2 - - - +
451A THR* 1.3 60.9 + - + +
452A ALA 3.4 0.3 + - - -
453A LEU* 3.5 15.8 + - + +
513A LEU* 3.7 27.1 - - + +
514A ASP* 3.9 13.9 - - - +
544A VAL* 3.8 32.9 - - + +
547A LEU* 4.7 10.5 - - + -
548A LEU* 3.7 21.1 - - + -
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Residues in contact with THR 451 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419A ARG* 3.5 32.0 + - - +
420A SER* 4.4 6.9 - - - -
447A ASN* 3.3 23.6 + - - +
448A GLU* 3.3 11.1 + - - +
450A VAL* 1.3 77.6 - - + +
452A ALA* 1.3 56.2 + - - +
514A ASP* 3.8 36.3 - - + +
475B GLN* 5.4 4.6 + - - +
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Residues in contact with ALA 452 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418A SER* 3.7 4.5 - - - -
419A ARG 3.0 18.3 + - - -
420A SER* 3.4 36.4 + - - +
421A THR 3.7 15.3 - - - +
422A PHE* 3.9 11.4 - - + -
448A GLU 3.5 15.7 + - - +
449A ILE 3.1 4.6 + - - +
451A THR* 1.3 78.9 + - - +
453A LEU* 1.3 66.5 + - - +
454A SER 3.6 0.7 + - - -
574A LEU* 6.0 1.3 - - - +
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Residues in contact with LEU 453 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419A ARG* 2.8 31.4 + - - +
422A PHE* 4.9 8.5 - - + -
449A ILE* 3.0 39.4 + - + +
450A VAL* 3.5 16.8 + - - +
452A ALA* 1.3 77.0 - - - +
454A SER* 1.3 68.9 + - - +
455A VAL* 6.0 0.2 - - + -
540A TRP* 4.7 6.7 - - + +
544A VAL* 4.2 25.4 - - + -
547A LEU* 4.6 4.7 - - + -
559A PHE* 4.5 11.9 - - + -
571A ALA* 4.8 4.7 - - + +
574A LEU* 4.9 10.3 - - + -
575A ALA* 4.0 30.5 - - + +
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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