Contacts of the helix formed by residues 463 - 472 (chain A) in PDB entry 1TF5
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 463 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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462A LYS* 1.3 77.9 - - + +
464A HIS* 1.3 60.4 + - - +
465A GLU* 3.2 20.0 - - - +
466A ARG* 3.1 36.1 + - + +
467A GLU* 2.9 36.6 + - + +
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Residues in contact with HIS 464 (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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130A ASN* 3.6 40.8 + - + +
132A TYR* 3.9 23.7 - - + -
461A ALA* 4.0 35.2 + - + -
462A LYS 4.9 5.1 + - - -
463A ASN* 1.3 70.6 - - - +
465A GLU* 1.3 61.8 + - - +
467A GLU* 3.8 5.9 + - - +
468A ALA* 2.9 31.7 + - - +
486A MET 4.8 6.2 + - - -
488A GLY 5.7 3.6 + - - -
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Residues in contact with GLU 465 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A TYR* 3.7 36.1 + - + +
463A ASN* 3.2 9.6 - - - +
464A HIS* 1.3 77.2 - - - +
466A ARG* 1.3 64.5 + - - +
468A ALA* 3.3 3.6 + - - +
469A GLN* 3.2 41.5 + - + +
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Residues in contact with ARG 466 (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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457A GLN* 5.8 2.0 + - - -
458A VAL 3.4 24.4 + - - +
459A LEU* 4.3 5.7 - - - +
460A ASN 5.6 0.2 - - - +
462A LYS* 6.4 0.2 - - - +
463A ASN* 3.1 34.7 - - - +
465A GLU* 1.3 80.2 - - - +
467A GLU* 1.3 78.5 + - - +
469A GLN* 3.2 23.8 + - + +
470A ILE* 3.3 27.8 + - + +
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Residues in contact with GLU 467 (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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459A LEU* 4.1 24.3 - - + +
460A ASN* 3.5 10.2 + - - +
461A ALA* 2.8 32.3 + - - -
462A LYS* 2.8 24.3 + - - +
463A ASN 2.9 22.0 + - - +
464A HIS* 4.0 7.1 + - - +
466A ARG* 1.3 89.3 + - - +
468A ALA* 1.3 59.8 + - - +
470A ILE* 3.2 3.5 + - - +
471A ILE* 2.9 33.3 + - - +
487A ALA* 3.5 13.7 - - - +
488A GLY* 4.1 6.7 + - - +
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Residues in contact with ALA 468 (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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132A TYR* 3.6 30.5 - - + +
464A HIS 2.9 18.8 + - - +
465A GLU 3.6 4.5 - - - +
466A ARG 3.3 0.2 - - - -
467A GLU* 1.3 76.5 - - - +
469A GLN* 1.3 57.7 + - + +
471A ILE* 4.4 4.0 - - - -
472A GLU* 3.0 30.8 + - - +
488A GLY* 5.5 3.8 - - - -
491A THR* 3.6 25.7 - - + +
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Residues in contact with GLN 469 (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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132A TYR* 6.1 0.2 - - - +
465A GLU* 3.2 32.8 + - + +
466A ARG* 3.2 13.3 + - - +
467A GLU 3.1 0.4 - - - -
468A ALA* 1.3 80.3 - - + +
470A ILE* 1.3 65.0 + - + +
472A GLU* 3.6 17.6 + - - +
473A GLU* 3.6 17.0 + - - +
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Residues in contact with ILE 470 (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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457A GLN* 2.9 64.8 - - + +
459A LEU* 3.8 21.5 - - + -
466A ARG* 3.4 29.6 - - + +
467A GLU* 3.2 7.4 + - - +
469A GLN* 1.3 76.5 - - + +
471A ILE* 1.3 57.2 + - - +
473A GLU* 2.8 28.4 + - - +
474A ALA* 3.1 9.5 + - - -
481A THR* 4.4 11.2 - - + +
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Residues in contact with ILE 471 (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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433A LEU* 4.5 13.7 - - + -
459A LEU* 3.3 30.3 - - + -
467A GLU 2.9 11.6 + - - +
468A ALA* 3.9 5.4 - - - +
470A ILE* 1.3 75.7 - - - +
472A GLU* 1.3 60.0 + - - +
474A ALA* 2.9 27.4 + - + +
481A THR* 4.7 0.9 - - + -
483A ALA* 5.2 0.7 - - + -
487A ALA 5.1 0.4 - - - +
488A GLY* 3.6 19.5 - - - +
491A THR* 3.2 38.6 - - + +
493A ILE* 3.5 28.3 - - + +
525A ARG* 4.0 18.2 - - - +
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Residues in contact with GLU 472 (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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468A ALA 3.0 18.4 + - - +
469A GLN* 3.7 13.0 - - - +
470A ILE 3.1 0.2 - - - -
471A ILE* 1.3 76.9 - - - +
473A GLU* 1.3 69.8 + - + +
474A ALA 3.5 0.4 + - - -
475A GLY 5.1 0.2 - - - -
476A GLN* 4.7 5.4 + - - -
491A THR* 4.2 11.9 - - + +
492A ASP 4.1 14.2 - - - +
493A ILE* 5.4 0.2 - - - -
494A LYS* 4.7 14.4 + - + +
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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