Contacts of the helix formed by residues 473 - 483 (chain A) in PDB entry 4Z4Q
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 473 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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460A ILE* 3.6 30.5 + - + +
469A ASP 3.3 9.4 + - - +
470A ILE 3.5 16.4 - - - +
471A LEU 3.1 3.0 - - - -
472A LYS* 1.3 76.5 - - - +
474A GLU* 1.3 70.2 + - - +
475A GLU* 3.5 16.6 + - - +
476A ILE* 3.2 32.3 + - + +
477A ASN* 3.1 27.7 + - - +
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Residues in contact with GLU 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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456A ARG* 3.8 28.1 + - - +
472A LYS 3.6 4.3 + - - -
473A ASN* 1.3 78.9 - - - +
475A GLU* 1.3 74.5 + - + +
477A ASN* 3.7 2.0 - - - +
478A THR* 3.1 35.1 + - + +
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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
----------------------------------------------------------
453A LEU* 5.1 3.4 - - + +
454A PRO 4.0 2.9 - - - +
455A LEU* 3.8 22.0 - - + +
456A ARG* 3.2 54.4 + - - +
457A GLY 5.0 3.8 - - - +
458A LYS 5.7 1.2 - - - +
459A VAL* 4.9 16.2 - - + -
460A ILE 5.8 0.4 - - - +
473A ASN* 3.5 14.1 - - - +
474A GLU* 1.3 85.5 - - + +
476A ILE* 1.3 62.9 + - + +
478A THR* 3.5 7.7 + - - -
479A MET* 3.3 28.4 + - - +
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Residues in contact with ILE 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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459A VAL* 5.0 9.4 - - + -
460A ILE* 3.6 17.7 - - + -
462A THR* 3.9 9.9 - - + -
470A ILE* 3.7 22.0 - - + +
471A LEU* 5.7 0.4 - - - -
473A ASN* 3.2 20.4 + - + +
475A GLU* 1.3 74.0 - - + +
477A ASN* 1.3 68.8 + - - +
479A MET* 3.1 14.6 + - - +
480A ILE* 3.0 23.5 + - + +
518A LEU* 6.4 0.2 - - + -
521A PHE* 3.3 53.7 - - + -
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Residues in contact with ASN 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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470A ILE 4.8 0.6 + - - -
471A LEU* 2.2 35.4 + - - +
472A LYS 4.3 1.4 - - - -
473A ASN 3.1 22.0 + - - +
474A GLU* 3.7 4.0 - - - +
476A ILE* 1.3 76.4 - - - +
478A THR* 1.3 63.0 + - + +
480A ILE* 2.9 24.3 + - - +
481A TYR* 2.9 16.0 + - - +
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Residues in contact with THR 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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415A LYS* 5.3 16.5 - - + +
416A LEU* 6.1 4.9 - - - -
453A LEU* 4.0 20.8 - - - +
474A GLU* 3.1 27.3 + - + +
475A GLU* 3.5 9.9 + - - -
477A ASN* 1.3 76.7 - - + +
479A MET* 1.3 58.3 + - - +
481A TYR* 3.8 7.0 - - - -
482A THR* 2.9 32.2 + - - -
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Residues in contact with MET 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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429A LEU* 5.7 1.3 - - + -
431A LEU* 3.6 22.2 - - + -
453A LEU* 3.6 24.2 - - + -
455A LEU* 4.4 11.2 - - - -
459A VAL* 6.0 1.1 - - - -
475A GLU* 3.3 19.6 + - - +
476A ILE* 3.1 14.2 + - - +
478A THR* 1.3 73.6 - - - +
480A ILE* 1.3 62.8 + - - +
481A TYR 3.1 2.2 - - - -
482A THR* 4.5 1.6 - - - +
483A ILE* 3.1 41.0 + - + +
518A LEU* 4.0 17.7 - - + -
521A PHE* 4.6 15.0 - - + -
522A PHE* 3.0 40.4 - - + -
526A MET* 6.0 0.4 - - - -
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Residues in contact with ILE 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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476A ILE* 3.0 13.4 + - + +
477A ASN* 2.9 12.2 + - - +
479A MET* 1.3 75.8 - - - +
481A TYR* 1.3 57.2 + - - +
483A ILE* 4.9 1.7 - - - +
484A GLY* 3.6 17.1 + - - -
485A ALA 4.3 3.6 + - - -
486A GLY* 4.3 10.0 + - - +
487A VAL* 4.7 22.7 - - + +
521A PHE* 5.3 9.4 - - + -
526A MET* 5.8 6.3 - - - -
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Residues in contact with TYR 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 ASN* 2.9 14.1 + - - +
478A THR* 4.2 7.0 - - - +
480A ILE* 1.3 78.1 - - - +
482A THR* 1.3 62.1 + - - +
483A ILE 3.4 1.1 - - - -
484A GLY* 3.7 9.4 + - - -
497A ASN* 5.0 1.4 + - - -
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Residues in contact with THR 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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416A LEU* 3.7 34.5 - - - -
429A LEU* 5.1 4.9 - - - -
453A LEU* 5.0 4.9 - - - -
478A THR 2.9 20.5 + - - -
479A MET* 4.5 3.1 - - - -
481A TYR* 1.3 74.8 - - - +
483A ILE* 1.3 60.6 + - - +
484A GLY 3.3 0.2 - - - -
497A ASN* 3.0 19.9 + - - -
498A TYR* 3.5 22.9 + - - -
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Residues in contact with ILE 483 (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 LEU* 3.8 18.8 - - + -
479A MET* 3.1 24.9 + - + +
480A ILE* 4.9 1.8 - - - +
482A THR* 1.3 77.4 - - - +
484A GLY* 1.3 63.6 + - - +
485A ALA* 4.2 15.3 - - + +
491A PHE* 4.9 0.7 - - + -
496A ALA* 3.6 9.5 - - + -
497A ASN* 3.2 26.4 + - - +
498A TYR* 4.1 9.0 - - + +
501A ILE* 3.2 35.9 - - + -
522A PHE* 4.4 10.5 - - + -
526A MET* 3.6 34.5 - - + -
529A LEU* 5.1 2.5 - - + -
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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