Contacts of the helix formed by residues 456 - 460 (chain A) in PDB entry 1TK0
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 GLY 456 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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232A PHE* 3.5 4.9 - - - -
233A PRO* 3.1 25.5 + - - +
455A PHE* 1.3 75.2 - - - +
457A ALA* 1.3 67.1 + - - -
458A GLU 3.1 2.9 - - - -
459A HIS* 3.0 21.3 + - - +
471A GLN* 3.0 12.6 - - - -
698A PRO 3.6 8.1 - - - -
699A ASN* 3.6 4.9 - - - -
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Residues in contact with ALA 457 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A PRO* 4.4 4.7 - - - -
456A GLY* 1.3 71.2 - - - -
458A GLU* 1.3 62.7 + - - +
460A HIS* 2.9 21.6 + - - +
469A TRP* 3.4 14.7 + - + +
470A VAL 3.3 36.6 - - - +
471A GLN* 3.0 16.2 + - + +
642A TRP* 5.8 0.2 - - + -
649A MET* 4.2 9.2 - - + +
659A GLY* 3.9 15.7 - - - -
698A PRO 3.2 1.0 + - - -
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Residues in contact with GLU 458 (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 ALA* 1.3 77.6 - - - +
459A HIS* 1.3 91.4 + - + +
460A HIS 3.1 6.4 + - - +
461A LEU* 4.4 4.2 - - - +
468A PRO* 3.2 26.2 - - + +
469A TRP 3.4 11.1 + - - +
698A PRO* 2.9 36.3 + - + +
699A ASN* 2.8 29.8 + - - -
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Residues in contact with HIS 459 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A PRO* 4.0 17.2 - - + +
234A PHE 4.3 8.6 + - - +
235A ASP* 3.2 36.9 + - + +
414A GLY 5.2 2.6 - - - +
415A LYS* 5.9 0.3 - - - -
453A ALA 2.8 23.4 + - - -
454A ALA 3.4 19.7 - - - -
456A GLY* 3.0 29.7 + - - +
458A GLU* 1.3 100.5 + - + +
460A HIS* 1.3 56.6 + - - +
461A LEU* 4.2 4.8 + - - +
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Residues in contact with HIS 460 (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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233A PRO* 3.7 20.2 - - + -
415A LYS* 3.2 31.8 + - - +
457A ALA 2.9 9.6 + - - +
458A GLU 3.0 0.4 - - - -
459A HIS* 1.3 80.0 - - - +
461A LEU* 1.3 79.9 + - - +
462A ASP* 4.3 2.6 - - - -
463A GLY 4.7 2.8 + - - -
468A PRO* 3.3 2.6 - - - +
469A TRP* 3.0 50.1 + + + -
642A TRP* 3.4 48.2 + + + +
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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