Contacts of the strand formed by residues 470 - 476 (chain A) in PDB entry 1TKD
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 VAL 470 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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457A ALA* 3.2 8.5 - - - +
468A PRO 4.8 3.8 - - - +
469A TRP* 1.3 76.6 - - - +
471A GLN* 1.3 63.5 + - - +
660A CYS* 2.6 44.4 + - - +
661A ARG 5.2 0.9 - - - +
662A THR* 4.4 11.2 - - - +
663A GLU* 4.1 30.3 - - + +
666A ALA* 4.2 7.0 - - + -
696A MET* 3.6 30.3 - - + -
697A GLY* 3.6 13.5 - - - +
698A PRO* 5.3 1.6 - - + -
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Residues in contact with GLN 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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232A PHE* 4.3 2.0 - - - -
456A GLY* 2.9 33.4 - - - -
457A ALA* 2.9 8.4 + - + +
470A VAL* 1.3 78.5 - - - +
472A ALA* 1.3 65.1 + - - +
649A MET* 3.5 22.2 - - + +
657A GLN* 2.8 32.6 + - - +
658A VAL 3.5 2.2 - - - +
666A ALA* 4.9 0.4 - - - -
696A MET* 3.3 6.2 - - - +
697A GLY 2.7 43.1 + - - +
698A PRO 4.0 2.9 + - - +
699A ASN* 3.3 10.7 + - - -
700A TRP* 3.3 26.3 - - - +
703A CYS* 3.4 6.1 - - - +
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Residues in contact with ALA 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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470A VAL 4.2 0.2 + - - -
471A GLN* 1.3 73.1 - - - +
473A GLY* 1.3 59.5 + - - +
474A ILE* 3.6 8.1 - - + +
657A GLN* 3.6 2.9 - - - -
658A VAL 2.8 41.1 + - - +
660A CYS* 3.9 17.3 - - - -
666A ALA* 4.0 9.0 - - + +
669A VAL* 4.0 19.5 - - + -
670A ILE* 4.0 16.4 - - + -
695A LYS 3.6 4.9 - - - -
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Residues in contact with GLY 473 (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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471A GLN 4.0 0.8 - - - -
472A ALA* 1.3 73.5 - - - +
474A ILE* 1.3 61.1 + - - +
656A ILE 3.4 3.6 - - - -
657A GLN* 3.3 26.1 + - - -
693A GLU 3.8 0.9 - - - +
694A GLY* 3.1 3.5 - - - -
695A LYS* 2.7 44.9 + - - +
703A CYS* 3.8 10.8 - - - +
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Residues in contact with ILE 474 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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472A ALA 3.6 16.6 - - - +
473A GLY* 1.3 80.9 - - - +
475A ASP* 1.3 63.9 + - - +
625A TRP* 3.5 28.6 - - + -
655A GLU* 3.0 4.6 - - - +
656A ILE* 2.8 50.2 + - + -
657A GLN* 4.5 0.8 - - - +
658A VAL* 4.9 0.7 - - + -
669A VAL* 4.0 22.9 - - + -
670A ILE* 4.1 19.7 - - + +
673A ALA* 3.8 19.1 - - + -
692A THR* 3.6 21.8 - - - +
693A GLU 3.3 8.1 - - - +
694A GLY* 4.2 3.4 - - - -
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Residues in contact with ASP 475 (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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474A ILE* 1.3 77.1 - - - +
476A ALA* 1.3 78.3 + - - +
477A SER* 3.4 0.7 + - - -
625A TRP* 4.6 0.2 - - - -
654A ASP* 3.2 9.3 - - - +
655A GLU* 3.4 12.9 - - + +
692A THR* 3.4 3.3 - - - -
693A GLU* 2.9 37.5 + - + +
704A HIS* 3.6 16.1 - - + +
823A D3T 2.9 5.7 + - - -
901A MG 2.1 25.5 - - - -
902A MG 2.0 28.3 - - - -
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Residues in contact with ALA 476 (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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475A ASP* 1.3 70.4 - - - +
477A SER* 1.3 61.3 + - - +
479A LEU* 4.0 20.7 + - + -
622A CYS* 4.6 1.1 - - - -
625A TRP* 4.3 2.4 - - + -
654A ASP* 2.7 30.2 + - + +
677A MET* 3.9 25.4 - - + -
691A ASP 3.5 8.1 - - - +
692A THR* 4.2 3.6 - - - +
823A D3T 3.3 0.9 + - - -
901A MG 2.5 30.0 - - - -
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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