Contacts of the helix formed by residues 448 - 456 (chain A) in PDB entry 3PRJ
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 LEU 448 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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421A LYS* 3.7 37.7 - - + +
425A TYR* 4.6 18.8 - - + -
444A VAL 5.0 1.1 - - - +
445A LEU* 3.7 17.7 - - + +
446A ASP 3.1 15.6 + - - +
447A GLY* 1.3 74.9 - - - +
449A HIS* 1.3 63.5 + - - +
450A ASN 3.6 1.3 - - - -
451A GLU* 3.7 17.4 + - + +
452A LEU* 3.2 35.1 + - + +
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Residues in contact with HIS 449 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440A ASP* 5.6 0.8 + - - -
445A LEU 3.7 18.2 + - - -
446A ASP* 3.7 27.8 + - + -
447A GLY* 3.0 8.8 + - - +
448A LEU* 1.3 80.3 - - - +
450A ASN* 1.3 69.4 + - - +
452A LEU* 3.4 5.8 + - + +
453A GLN* 3.3 26.2 + - - +
459A ILE* 3.6 38.0 - - + +
461A THR* 4.0 22.9 - - + +
464A LYS* 5.2 15.7 - - + -
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Residues in contact with ASN 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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447A GLY 5.1 1.4 + - - -
448A LEU 3.6 0.2 - - - -
449A HIS* 1.3 76.6 - - - +
451A GLU* 1.3 65.7 + - - +
453A GLN* 2.8 16.5 + - - +
454A THR* 2.7 40.3 + - - +
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Residues in contact with GLU 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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447A GLY 3.9 17.6 - - - +
448A LEU* 3.8 16.8 - - + +
449A HIS 3.4 0.2 - - - -
450A ASN* 1.3 89.0 + - - +
452A LEU* 1.3 59.7 + - + +
454A THR* 3.3 8.1 + - - -
455A ILE* 2.9 41.3 + - + +
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Residues in contact with LEU 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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425A TYR* 3.7 33.4 - - + -
438A ILE* 3.8 9.0 - - + -
445A LEU* 4.0 35.9 - - + +
448A LEU* 3.2 29.5 + - + +
449A HIS* 3.7 5.4 - - + +
450A ASN 3.1 0.8 - - - -
451A GLU* 1.3 77.2 - - + +
453A GLN* 1.3 63.1 + - - +
455A ILE* 3.5 5.5 + - + -
456A GLY 3.3 4.7 + - - -
457A PHE* 2.9 58.2 + - + +
459A ILE* 4.5 15.3 - - + -
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Residues in contact with GLN 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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449A HIS* 3.3 17.3 + - - +
450A ASN* 2.8 16.3 + - - +
452A LEU* 1.3 76.7 - - - +
454A THR* 1.3 67.1 + - - +
456A GLY* 2.8 16.5 + - - -
457A PHE 3.8 12.2 - - - +
458A GLN* 5.9 0.2 - - - -
459A ILE* 3.8 27.8 + - + +
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Residues in contact with THR 454 (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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450A ASN* 2.7 24.2 + - - +
451A GLU* 3.5 11.1 - - - -
453A GLN* 1.3 71.2 - - - +
455A ILE* 1.3 67.4 + - + +
456A GLY* 3.0 2.9 + - - -
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Residues in contact with ILE 455 (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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425A TYR* 4.3 13.9 - - + -
426A GLU* 3.8 46.9 - - + +
429A HIS* 3.0 45.1 + - + +
451A GLU* 2.9 30.7 + - + +
452A LEU* 3.7 10.3 - - + +
453A GLN 3.2 0.2 - - - -
454A THR* 1.3 74.9 - - + +
456A GLY* 1.3 58.2 + - - +
457A PHE* 4.3 4.3 - - + -
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Residues in contact with GLY 456 (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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429A HIS* 3.4 20.2 + - - -
434A LYS* 5.6 0.3 - - - +
436A ALA* 4.6 6.2 + - - +
453A GLN 2.8 12.4 + - - -
454A THR 3.0 2.2 + - - -
455A ILE* 1.3 79.2 - - - +
457A PHE* 1.3 65.7 + - - +
458A GLN* 3.8 2.3 + - - +
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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