Contacts of the helix formed by residues 471 - 482 (chain A) in PDB entry 5Y7G
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 471 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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454A TYR* 4.0 3.4 - - - -
469A LEU 3.3 7.5 + - - -
470A LEU* 1.3 76.4 - - - +
472A GLU* 1.3 68.2 + - - -
473A GLU* 3.2 8.1 - - - -
474A LEU* 3.3 8.0 + - - +
475A LEU* 2.8 22.3 + - - +
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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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454A TYR* 3.9 23.1 + - - -
455A ARG* 2.8 33.8 + - - -
471A GLY* 1.3 71.0 - - - +
473A GLU* 1.3 66.8 + - + +
475A LEU* 3.8 5.3 - - - +
476A GLU* 2.9 44.7 + - + +
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Residues in contact with GLU 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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383A HIS* 4.9 8.6 - - + -
471A GLY* 3.2 4.4 - - - -
472A GLU* 1.3 81.3 + - + +
474A LEU* 1.3 56.8 + - - +
476A GLU* 5.6 0.7 - - - -
477A GLN* 2.8 47.0 + - + +
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Residues in contact with LEU 474 (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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383A HIS* 3.6 36.3 - - + +
385A VAL* 3.8 22.7 - - + -
389A LEU* 3.8 37.9 - - + -
469A LEU* 3.5 24.7 - - + +
470A LEU* 4.2 8.5 - - + -
471A GLY* 3.3 11.3 + - - +
473A GLU* 1.3 78.0 - - - +
475A LEU* 1.3 64.4 + - - +
477A GLN* 4.3 2.0 - - - -
478A ALA* 2.9 28.6 + - - +
509A ILE* 4.6 1.1 - - + -
511A PHE* 4.0 13.7 - - + -
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Residues in contact with LEU 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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393A LEU* 3.9 17.9 - - + -
396A LEU* 4.5 4.0 - - + -
450A ILE* 3.8 16.2 - - + -
451A ARG* 4.0 25.1 - - + -
454A TYR* 3.7 35.7 - - + -
470A LEU* 4.3 18.3 - - + +
471A GLY 2.8 21.7 + - - +
472A GLU* 3.8 8.1 - - - +
474A LEU* 1.3 75.3 - - - +
476A GLU* 1.3 64.9 + - - +
478A ALA* 3.9 1.9 - - - +
479A LEU* 2.9 40.8 + - + +
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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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451A ARG* 3.5 52.0 + - + +
455A ARG* 4.3 5.4 + - - -
472A GLU* 2.9 47.4 + - - +
473A GLU* 4.7 0.9 - - - +
475A LEU* 1.3 77.4 - - - +
477A GLN* 1.3 67.5 + - - +
479A LEU* 4.2 2.2 - - + -
480A ASP* 3.3 26.8 + - - +
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Residues in contact with GLN 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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381A ALA* 3.4 25.3 - - - +
383A HIS* 3.1 26.0 + - - -
473A GLU* 2.8 37.0 + - + +
474A LEU* 4.0 2.5 - - - +
476A GLU* 1.3 72.7 - - - +
478A ALA* 1.3 62.6 + - - +
480A ASP* 3.9 1.4 - - - +
481A CYS* 3.0 30.5 + - - +
511A PHE* 3.1 26.1 - - + +
513A PRO* 4.6 15.6 - - + +
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Residues in contact with ALA 478 (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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389A LEU* 4.0 18.6 - - + -
393A LEU* 4.7 6.7 - - + -
474A LEU 2.9 20.3 + - - +
475A LEU 3.9 2.7 - - - +
477A GLN* 1.3 77.0 - - - +
479A LEU* 1.3 59.4 + - - +
482A LEU* 2.8 48.9 + - + +
511A PHE* 3.5 25.2 - - + -
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Residues in contact with LEU 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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393A LEU* 5.0 7.2 - - + -
446A TYR* 3.5 40.4 + - + -
447A ARG* 3.2 43.9 + - + +
450A ILE* 3.9 24.0 - - + -
451A ARG* 3.9 20.2 - - + +
475A LEU* 2.9 42.1 + - + +
476A GLU* 3.8 6.1 - - - +
477A GLN 3.3 0.4 - - - -
478A ALA* 1.3 77.2 - - - +
480A ASP* 1.3 67.9 + - - +
482A LEU* 3.9 4.3 - - - +
487A LEU* 5.1 4.7 - - + -
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Residues in contact with ASP 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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447A ARG* 4.3 15.5 + - - +
451A ARG* 3.7 20.1 + - - -
476A GLU* 3.3 18.0 + - - +
477A GLN* 4.4 1.8 - - - +
478A ALA 3.2 0.4 - - - -
479A LEU* 1.3 81.3 - - - +
481A CYS* 1.3 60.5 + - - +
482A LEU 3.6 1.6 - - - -
516A ARG* 2.7 53.5 + - - +
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Residues in contact with CYS 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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477A GLN* 3.0 15.9 + - - +
480A ASP* 1.3 79.6 - - - +
482A LEU* 1.3 61.5 + - - +
483A PRO* 3.4 5.4 - - - +
511A PHE* 3.3 30.7 - - + -
513A PRO* 3.7 36.8 - - - -
516A ARG* 3.9 23.9 - - - +
517A ARG 3.7 15.7 - - - +
518A TYR* 3.2 19.2 - - - -
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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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389A LEU* 4.4 11.7 - - + -
390A ILE* 6.1 2.2 - - + -
393A LEU* 3.8 24.7 - - + -
446A TYR* 3.3 17.0 + - - -
447A ARG* 5.2 1.7 + - - -
478A ALA* 2.8 29.4 + - + +
479A LEU 3.9 4.5 - - - +
480A ASP 3.6 1.2 - - - -
481A CYS* 1.3 77.3 - - - +
483A PRO* 1.3 68.5 - - + +
487A LEU* 4.4 16.9 - - + +
490A TRP* 4.0 19.7 - - + -
509A ILE* 4.4 4.0 - - + -
511A PHE* 4.2 7.0 - - + -
518A TYR* 3.3 46.7 - - + -
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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