Contacts of the helix formed by residues 475 - 486 (chain s) 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 s).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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461s ILE* 5.1 0.3 - - - +
462s LEU* 3.4 35.2 - - + +
471s ARG* 2.9 13.2 + - - +
472s ILE 3.3 13.8 + - - +
474s ASN* 1.3 75.1 - - - +
476s ASN* 1.3 58.6 + - - +
477s GLU* 2.9 34.5 + - - +
478s ILE* 3.1 22.3 + - + +
479s ARG* 3.1 30.2 + - - +
2013w G 5.5 1.0 + - - +
2014w T 4.2 14.3 + - - -
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Residues in contact with ASN 476 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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458s ARG* 4.2 15.5 - - - +
474s ASN 3.5 5.6 + - - +
475s ASN* 1.3 72.6 + - - +
477s GLU* 1.3 74.8 + - - +
479s ARG* 3.4 15.5 + - - +
480s GLN* 3.0 51.1 + - - +
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Residues in contact with GLU 477 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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456s PRO 4.9 2.4 - - - +
457s LEU* 4.3 18.2 - - + +
458s ARG* 3.0 68.2 + - + +
459s GLY 5.8 0.7 - - - +
460s LYS 6.1 0.4 - - - +
461s ILE* 4.0 22.0 - - + -
475s ASN* 2.9 10.1 + - - +
476s ASN* 1.3 78.8 + - - +
478s ILE* 1.3 63.9 + - - +
480s GLN* 3.5 23.0 + - - +
481s MET* 3.3 29.0 + - - +
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Residues in contact with ILE 478 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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461s ILE* 4.2 12.3 - - + -
462s LEU* 4.6 8.7 - - + +
464s VAL* 4.2 11.9 - - + -
472s ILE* 3.5 32.8 - - + +
473s LEU* 5.3 0.9 - - - -
475s ASN* 3.1 25.5 + - + +
477s GLU* 1.3 73.2 - - - +
479s ARG* 1.3 64.0 + - - +
481s MET* 3.3 19.0 + - + +
482s ILE* 3.1 36.0 + - + +
523s PHE* 3.7 43.0 - - + -
527s PHE* 6.1 0.2 - - + -
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Residues in contact with ARG 479 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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472s ILE 5.4 0.2 - - - +
473s LEU* 3.1 29.4 - - - +
474s ASN* 4.1 16.0 + - - +
475s ASN 3.1 18.2 + - - +
476s ASN* 3.6 16.5 + - - +
477s GLU 3.3 0.2 - - - -
478s ILE* 1.3 76.3 - - - +
480s GLN* 1.3 55.8 + - - +
482s ILE* 3.3 12.6 + - + +
483s THR* 2.9 35.4 + - - +
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Residues in contact with GLN 480 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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416s GLY* 2.9 39.0 + - - +
417s LYS* 3.4 13.8 + - - +
418s LEU* 5.5 1.2 - - - +
455s LEU* 3.7 23.5 - - + +
456s PRO 5.0 2.1 - - - +
457s LEU* 6.3 0.9 - - + -
476s ASN* 3.0 48.0 + - - +
477s GLU* 3.9 18.3 + - - +
478s ILE 3.4 0.4 - - - -
479s ARG* 1.3 74.4 - - + +
481s MET* 1.3 57.8 + - - +
483s THR* 3.5 7.4 + - - -
484s ALA* 3.0 28.9 + - - +
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Residues in contact with MET 481 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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433s LEU* 4.4 14.4 - - + -
455s LEU* 3.7 23.6 - - + -
457s LEU* 4.3 7.0 - - + -
461s ILE* 3.3 30.7 - - + -
477s GLU 3.3 13.5 + - - +
478s ILE* 3.7 12.1 - - + +
479s ARG 3.2 0.6 - - - -
480s GLN* 1.3 75.6 - - - +
482s ILE* 1.3 64.5 + - - +
484s ALA* 3.3 2.2 + - - +
485s PHE* 3.1 43.4 + - + -
520s LEU* 3.6 22.4 - - + -
523s PHE* 3.6 34.5 - - + -
524s PHE* 4.5 5.6 - - - -
528s MET* 5.0 0.2 - - - -
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Residues in contact with ILE 482 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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473s LEU* 5.3 5.6 - - + -
478s ILE* 3.1 33.3 + - + +
479s ARG* 3.6 12.8 - - + +
481s MET* 1.3 77.0 - - - +
483s THR* 1.3 58.0 + - - +
485s PHE* 3.5 1.4 + - - +
486s GLY* 2.9 28.4 + - - -
487s THR 4.2 2.4 + - - -
488s GLY* 4.3 21.9 + - - +
489s ILE* 3.7 39.3 - - + -
523s PHE* 4.0 4.9 - - + -
527s PHE* 6.0 0.2 - - + -
528s MET* 3.9 14.1 - - + -
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Residues in contact with THR 483 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418s LEU* 6.3 1.6 - - + -
479s ARG* 2.9 19.9 + - - +
480s GLN* 3.7 8.0 - - - -
482s ILE* 1.3 77.5 - - - +
484s ALA* 1.3 61.3 + - - +
486s GLY* 3.4 12.1 + - - +
499s ARG* 3.9 12.2 + - - +
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Residues in contact with ALA 484 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418s LEU* 3.9 16.1 - - + +
431s ILE* 3.9 25.6 - - + -
455s LEU* 4.3 8.5 - - + -
480s GLN 3.0 18.0 + - - +
481s MET* 3.3 6.0 + - - +
483s THR* 1.3 76.3 - - - +
485s PHE* 1.3 60.6 + - + +
499s ARG* 3.0 35.3 + - - +
500s TYR* 3.1 12.8 - - - -
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Residues in contact with PHE 485 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431s ILE* 3.8 22.4 - - + -
433s LEU* 4.4 9.0 - - + -
481s MET* 3.1 34.6 + - + +
482s ILE 4.1 1.8 - - - +
484s ALA* 1.3 79.1 - - + +
486s GLY* 1.3 62.7 + - - +
487s THR* 3.3 16.9 + - + +
497s LYS 3.6 0.2 - - - +
498s ALA* 3.5 5.6 - - + -
499s ARG* 3.0 28.0 + - - +
500s TYR* 4.5 8.1 - + - -
503s ILE* 3.6 44.9 - - + -
523s PHE* 4.9 0.2 - + - -
524s PHE* 3.4 28.9 - + - -
528s MET* 3.6 24.7 - - + -
531s LEU* 4.7 6.3 - - + -
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Residues in contact with GLY 486 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482s ILE 2.9 14.4 + - - -
483s THR* 3.8 9.2 - - - -
484s ALA 3.4 2.6 - - - -
485s PHE* 1.3 75.5 - - - +
487s THR* 1.3 58.1 + - - +
488s GLY 3.6 1.8 - - - -
497s LYS* 3.3 24.8 - - - +
499s ARG* 5.4 3.4 - - - -
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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