Contacts of the helix formed by residues 475 - 486 (chain u) in PDB entry 6QX2
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 475 (chain u).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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461u ILE* 5.8 0.4 - - - +
462u LEU* 3.4 34.9 + - + +
471u ARG 2.9 12.1 + - - +
472u ILE 3.3 14.9 + - - +
473u LEU 4.2 0.9 - - - +
474u ASN* 1.3 76.0 - - - +
476u ASN* 1.3 58.2 + - - +
477u GLU* 2.9 34.0 + - - +
478u ILE* 3.1 22.2 + - + +
479u ARG* 3.1 28.2 + - - +
2013v G 5.6 0.2 + - - -
2014v T 4.2 17.4 + - - -
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Residues in contact with ASN 476 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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474u ASN 3.5 5.1 + - - +
475u ASN* 1.3 70.6 + - - +
477u GLU* 1.3 70.7 + - - +
479u ARG* 3.4 7.4 + - - +
480u GLN* 3.0 39.4 + - - +
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Residues in contact with GLU 477 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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456u PRO 5.1 1.6 - - - +
457u LEU* 4.4 19.4 - - + +
458u ARG* 3.3 57.5 + - + +
459u GLY 5.9 0.2 - - - +
460u LYS 6.1 0.7 - - - +
461u ILE* 4.9 19.3 - - + -
475u ASN* 2.9 9.6 + - - +
476u ASN* 1.3 84.0 - - - +
478u ILE* 1.3 64.1 + - + +
480u GLN* 3.5 21.4 + - - +
481u MET* 3.3 29.6 + - - +
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Residues in contact with ILE 478 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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461u ILE* 4.2 13.9 - - + -
462u LEU* 4.6 8.7 - - + +
464u VAL* 4.1 11.4 - - + -
472u ILE* 3.5 33.0 - - + +
473u LEU* 5.4 1.3 - - + -
475u ASN* 3.1 25.2 + - + +
477u GLU* 1.3 74.0 - - + +
479u ARG* 1.3 64.7 + - - +
481u MET* 3.3 19.0 + - + +
482u ILE* 3.1 34.8 + - + +
523u PHE* 3.7 41.3 - - + -
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Residues in contact with ARG 479 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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472u ILE 5.2 0.2 + - - -
473u LEU* 3.2 48.6 + - - +
474u ASN 5.7 0.4 - - - +
475u ASN 3.1 19.3 + - - +
476u ASN* 3.6 8.7 - - - +
477u GLU 3.3 0.2 - - - -
478u ILE* 1.3 76.9 - - - +
480u GLN* 1.3 57.8 + - + +
482u ILE* 3.3 37.1 + - - +
483u THR* 2.9 43.1 + - - +
489u ILE* 5.5 1.2 - - - +
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Residues in contact with GLN 480 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417u LYS* 3.3 36.1 + - - +
418u LEU* 4.9 0.5 + - - +
455u LEU* 3.7 20.4 - - + +
456u PRO 4.9 0.9 - - - +
457u LEU* 6.3 0.7 - - + -
458u ARG* 5.4 7.9 - - - +
476u ASN* 3.0 26.4 + - - +
477u GLU* 3.9 23.4 + - - +
478u ILE 3.4 0.2 - - - -
479u ARG* 1.3 76.1 - - + +
481u MET* 1.3 57.6 + - - +
483u THR* 3.5 7.2 + - - -
484u ALA* 3.0 29.5 + - - +
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Residues in contact with MET 481 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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433u LEU* 4.4 12.8 - - + -
455u LEU* 3.7 23.1 - - + -
457u LEU* 4.2 13.2 - - + -
461u ILE* 4.3 6.7 - - + -
477u GLU 3.3 17.5 + - - +
478u ILE* 3.7 20.6 - - + +
479u ARG 3.2 0.8 - - - -
480u GLN* 1.3 76.1 - - - +
482u ILE* 1.3 65.2 + - - +
484u ALA* 3.3 2.6 + - - +
485u PHE* 3.1 42.4 + - + -
520u LEU* 3.6 30.7 - - + -
523u PHE* 3.6 32.3 - - + -
524u PHE* 4.6 4.9 - - - -
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Residues in contact with ILE 482 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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473u LEU* 5.2 1.1 - - + -
478u ILE* 3.1 32.2 + - + +
479u ARG* 3.6 39.9 - - - +
481u MET* 1.3 78.2 - - - +
483u THR* 1.3 56.7 + - - +
485u PHE* 3.9 1.4 - - - +
486u GLY* 2.9 28.2 + - - -
487u THR 4.2 2.1 + - - -
488u GLY* 4.4 21.5 - - - +
489u ILE* 3.7 37.2 - - + -
523u PHE* 4.0 5.4 - - + -
527u PHE* 5.9 0.2 - - + -
528u MET* 3.9 14.3 - - + +
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Residues in contact with THR 483 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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479u ARG* 2.9 31.1 + - - +
480u GLN* 3.7 7.6 - - - -
482u ILE* 1.3 77.0 - - - +
484u ALA* 1.3 63.1 + - - +
486u GLY* 3.4 12.5 + - - -
499u ARG* 4.5 6.4 + - - -
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Residues in contact with ALA 484 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418u LEU* 4.3 20.9 - - + -
431u ILE* 3.9 24.5 - - + -
455u LEU* 4.3 10.5 - - + -
480u GLN 3.0 18.7 + - - +
481u MET 3.3 5.1 + - - +
483u THR* 1.3 77.0 - - - +
485u PHE* 1.3 58.1 + - + +
499u ARG* 3.0 26.8 + - - +
500u TYR* 3.1 13.9 - - - -
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Residues in contact with PHE 485 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431u ILE* 3.9 21.8 - - + -
433u LEU* 4.3 11.4 - - + -
481u MET* 3.1 30.6 + - + +
482u ILE 4.1 2.2 - - - +
484u ALA* 1.3 79.9 - - + +
486u GLY* 1.3 62.6 + - - +
487u THR* 3.3 17.3 + - + +
498u ALA* 3.5 5.6 - - + -
499u ARG* 3.0 27.9 + - - +
500u TYR* 4.6 7.0 - + - +
503u ILE* 3.6 46.4 - - + -
523u PHE* 4.9 0.2 - + - -
524u PHE* 3.4 29.4 - + - -
528u MET* 3.6 24.5 - - + -
531u LEU* 4.5 7.0 - - + -
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Residues in contact with GLY 486 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482u ILE 2.9 14.5 + - - -
483u THR* 3.8 8.7 - - - -
484u ALA 3.4 1.8 - - - -
485u PHE* 1.3 76.6 - - - +
487u THR* 1.3 57.2 + - - +
488u GLY 3.6 1.6 - - - -
497u LYS* 3.3 25.6 - - - +
499u ARG* 4.5 8.1 - - - -
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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