Contacts of the helix formed by residues 474 - 482 (chain A) in PDB entry 5TYZ
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 SER 474 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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428A PRO* 3.6 12.3 - - - +
472A ALA* 3.5 1.4 - - - +
473A ALA* 1.3 80.9 - - - +
475A GLU* 1.3 64.7 + - - +
476A GLU* 3.4 14.4 + - - +
477A ASP* 3.1 37.2 + - - +
478A ILE* 3.4 10.6 + - - +
480A ARG* 4.2 2.9 + - - -
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Residues in contact with GLU 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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322A ARG* 2.9 36.1 + - - -
428A PRO* 4.1 17.1 - - + +
431A LEU* 3.6 11.4 - - + +
432A LEU* 3.4 22.6 + - + -
474A SER* 1.3 70.7 - - - +
476A GLU* 1.3 67.9 + - - +
478A ILE* 2.9 21.3 + - - +
479A PHE* 3.1 22.0 + - + -
486A TYR* 3.8 9.8 + - + +
492A ARG* 2.9 46.9 + - - +
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Residues in contact with GLU 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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474A SER* 3.2 11.4 + - - +
475A GLU* 1.3 79.4 - - - +
477A ASP* 1.3 61.9 + - - +
479A PHE* 3.4 2.3 + - - +
480A ARG* 3.0 52.7 + - - +
486A TYR* 3.7 42.3 - - + +
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Residues in contact with ASP 477 (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 4.3 2.1 - - - +
472A ALA* 3.7 15.4 - - + -
473A ALA* 2.9 28.3 + - - +
474A SER* 3.1 22.7 + - - +
475A GLU 3.1 0.4 - - - -
476A GLU* 1.3 77.4 - - - +
478A ILE* 1.3 57.2 + - - +
480A ARG* 2.8 29.4 + - - +
481A HIS* 2.9 45.5 + - - +
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Residues in contact with ILE 478 (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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428A PRO* 3.5 39.9 - - + +
429A PHE* 3.7 28.3 - - + +
432A LEU* 3.6 30.3 - - + -
456A LEU* 4.6 6.3 - - + -
461A LEU* 5.1 4.3 - - + -
472A ALA* 3.7 13.7 - - + -
474A SER 3.6 9.4 - - - +
475A GLU* 2.9 10.5 + - - +
477A ASP* 1.3 73.7 - - - +
479A PHE* 1.3 66.5 + - + +
481A HIS* 3.2 9.5 + - + +
482A LEU* 3.1 38.5 + - + +
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Residues in contact with PHE 479 (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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143A CYS 4.7 2.5 - - - -
432A LEU* 3.9 17.9 - - + -
440A PHE* 4.0 25.4 - + - -
444A LEU* 5.0 4.3 - - + -
475A GLU* 3.1 25.7 + - + -
476A GLU 3.8 6.5 - - - +
478A ILE* 1.3 76.9 - - + +
480A ARG* 1.3 62.4 + - + +
482A LEU* 3.1 11.1 + - - +
484A LEU* 3.0 53.0 + - + +
485A GLU 3.4 18.8 - - - -
486A TYR* 3.6 21.3 - + + -
487A LEU* 3.8 30.3 - - + -
492A ARG* 3.9 27.6 - - - -
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Residues in contact with ARG 480 (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 SER* 4.2 2.8 + - - -
476A GLU* 3.0 48.2 + - - +
477A ASP* 2.8 41.5 + - - +
479A PHE* 1.3 76.6 - - + +
481A HIS* 1.3 65.9 + - + +
483A GLY* 3.0 14.1 + - - +
484A LEU 4.6 4.5 - - - +
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Residues in contact with HIS 481 (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 PHE* 5.6 1.1 - + - -
452A LYS* 5.6 1.0 - - - +
454A LEU* 4.4 11.0 - - - +
461A LEU* 4.0 17.3 - - + -
470A PHE* 3.8 41.3 - + + +
471A GLN 3.2 24.2 + - - -
472A ALA* 4.8 4.5 - - + -
477A ASP* 2.9 34.8 + - + +
478A ILE* 3.2 11.9 + - + +
480A ARG* 1.3 78.4 - - + +
482A LEU* 1.3 60.3 + - - +
483A GLY 3.5 0.7 + - - -
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Residues in contact with LEU 482 (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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444A LEU* 3.8 32.8 - - + -
447A PHE* 3.4 9.7 - - + -
448A SER* 3.4 33.7 - - - +
452A LYS* 3.2 29.2 - - + -
454A LEU* 4.1 9.2 - - + -
456A LEU* 4.5 8.3 - - + -
461A LEU* 3.9 21.8 - - + -
478A ILE* 3.1 29.7 + - + +
479A PHE* 3.7 5.2 - - - +
480A ARG 3.1 1.2 - - - -
481A HIS* 1.3 75.4 - - - +
483A GLY* 1.3 63.1 + - - +
484A LEU* 3.3 11.9 + - + -
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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