Contacts of the helix formed by residues 473 - 488 (chain A) in PDB entry 6WB2
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 THR 473 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446A ALA* 5.7 2.5 - - - -
472A THR* 1.3 75.0 - - - +
474A ASN* 1.3 62.5 + - - +
475A GLN* 3.2 12.1 - - - -
476A LYS* 3.0 11.9 + - - +
477A THR* 2.7 34.8 + - - -
196C G 5.7 5.8 - - - -
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Residues in contact with ASN 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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444A GLY 4.0 11.9 - - - +
445A ALA* 4.1 18.5 - - + +
446A ALA* 5.0 3.9 - - - +
473A THR* 1.3 72.0 - - - +
475A GLN* 1.3 92.3 + - - +
477A THR* 3.0 9.4 + - - -
478A GLN* 2.7 40.4 + - - +
56D C 5.7 2.8 + - - -
57D A 5.7 3.4 + - - -
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Residues in contact with GLN 475 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473A THR* 3.2 10.5 - - - -
474A ASN* 1.3 110.3 + - - +
476A LYS* 1.3 58.1 + - - +
478A GLN* 3.2 14.2 + - - +
479A LEU* 2.9 26.1 + - - +
499A SER* 6.1 0.9 - - - -
501A TYR* 3.8 47.7 - - + +
196C G 3.7 22.3 + - - -
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Residues in contact with LYS 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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469A LEU* 6.2 0.2 - - - -
472A THR* 4.7 8.3 - - - -
473A THR* 3.0 21.4 + - - +
475A GLN* 1.3 79.3 - - - +
477A THR* 1.3 56.0 + - - +
479A LEU* 3.6 8.8 - - - +
480A GLN* 2.9 33.6 + - + +
517A LEU* 4.3 14.1 - - + +
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Residues in contact with THR 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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444A GLY* 3.7 26.0 - - - -
445A ALA* 4.2 4.3 - - - -
446A ALA* 6.4 0.4 - - - -
453A GLY* 5.9 2.9 - - - -
454A LYS 4.4 9.6 - - - -
455A ALA* 3.7 6.9 - - - +
469A LEU* 5.5 5.4 - - - -
472A THR* 5.0 8.2 - - - -
473A THR 2.7 16.9 + - - -
474A ASN* 3.0 12.1 + - - -
476A LYS* 1.3 73.7 - - - +
478A GLN* 1.3 56.3 + - - +
480A GLN* 3.3 6.2 + - - +
481A ALA* 2.9 28.8 + - - +
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Residues in contact with GLN 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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442A VAL* 5.6 1.8 - - + -
443A ASP* 3.7 19.1 + - - +
444A GLY 2.7 32.3 + - - +
445A ALA* 5.2 0.6 - - - +
474A ASN* 2.7 38.7 + - - +
475A GLN* 3.2 11.4 + - - +
477A THR* 1.3 73.2 - - - +
479A LEU* 1.3 62.1 + - - +
481A ALA* 3.2 7.0 + - - +
482A ILE* 2.9 36.0 + - + +
497A THR* 4.7 11.2 - - - +
499A SER* 3.1 33.9 + - - +
502A ALA* 5.1 10.1 - - + -
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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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475A GLN 2.9 13.8 + - - +
476A LYS* 3.6 9.0 - - - +
477A THR 3.3 0.2 - - - -
478A GLN* 1.3 77.0 - - - +
480A GLN* 1.3 56.7 + - - +
482A ILE* 3.1 16.6 - - + +
483A TYR* 2.9 29.6 + - - +
502A ALA* 5.5 3.1 - - + +
517A LEU* 3.6 26.7 - - + -
518A VAL* 6.4 0.7 - - - -
521A ILE* 5.6 1.7 - - - +
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Residues in contact with GLN 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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455A ALA* 4.9 2.9 - - + -
467A VAL* 6.1 2.4 - - - +
469A LEU* 3.7 43.4 - - + +
476A LYS* 2.9 21.3 + - + +
477A THR* 3.7 4.0 - - - +
479A LEU* 1.3 75.5 - - - +
481A ALA* 1.3 58.5 + - - +
483A TYR* 3.3 13.0 + - - +
484A LEU* 2.9 31.2 + - - +
517A LEU* 3.3 28.8 - - + +
520A GLN* 3.7 10.4 + - - -
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Residues in contact with ALA 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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442A VAL* 4.0 23.1 - - + +
443A ASP 4.2 4.9 - - - +
455A ALA* 3.7 21.0 - - + +
456A GLY 4.2 8.5 - - - +
457A TYR* 5.2 3.7 - - - -
477A THR 2.9 18.3 + - - +
478A GLN* 3.5 8.7 - - - +
479A LEU 3.2 0.2 - - - -
480A GLN* 1.3 77.5 - - - +
482A ILE* 1.3 58.5 + - - +
484A LEU* 3.4 4.1 + - - +
485A ALA* 2.9 28.3 + - - +
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Residues in contact with ILE 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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442A VAL* 3.7 24.0 - - + -
478A GLN* 2.9 16.5 + - + +
479A LEU* 3.1 22.9 - - + +
481A ALA* 1.3 74.9 - - - +
483A TYR* 1.3 55.7 + - - +
485A ALA* 3.5 8.2 - - - +
486A LEU* 2.9 30.8 + - - +
497A THR* 5.1 8.5 - - + +
502A ALA* 4.5 20.0 - - + -
506A ILE* 4.5 22.9 - - + -
521A ILE* 5.7 8.3 - - + -
533A LEU* 6.2 5.4 - - + -
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Residues in contact with TYR 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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479A LEU 2.9 18.3 + - - +
480A GLN* 3.4 19.5 - - - +
482A ILE* 1.3 80.4 - - - +
484A LEU* 1.3 56.4 + - + +
486A LEU* 3.2 3.8 + - + -
487A GLN* 2.9 57.3 + - + +
517A LEU* 5.4 2.2 - - + -
520A GLN* 3.2 64.1 + - + +
521A ILE* 3.8 21.1 - - + -
524A GLN* 3.6 21.1 - - + +
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Residues in contact with LEU 484 (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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457A TYR* 4.8 14.7 + - + -
465A LYS* 5.9 2.9 - - + +
467A VAL* 6.1 5.6 - - + -
480A GLN 2.9 16.2 + - - +
481A ALA* 4.0 4.3 - - - +
483A TYR* 1.3 76.4 - - + +
485A ALA* 1.3 61.8 + - - +
487A GLN* 3.4 27.2 + - - +
488A ASP* 3.5 13.9 + - - +
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Residues in contact with ALA 485 (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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440A PHE* 4.2 30.5 - - + -
442A VAL* 4.5 11.9 - - + -
457A TYR* 4.9 11.4 - - + -
481A ALA 2.9 18.1 + - - +
482A ILE* 3.5 10.8 - - - +
483A TYR 3.1 0.2 - - - -
484A LEU* 1.3 78.4 - - - +
486A LEU* 1.3 62.1 + - - +
487A GLN 3.3 0.2 + - - -
488A ASP* 3.6 1.6 + - - +
489A SER* 3.3 23.4 + - - -
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Residues in contact with LEU 486 (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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482A ILE 2.9 16.7 + - - +
483A TYR* 3.9 5.4 - - + +
485A ALA* 1.3 73.6 - - - +
487A GLN* 1.3 63.4 + - - +
489A SER* 2.8 22.4 + - - +
521A ILE 6.0 0.7 - - - +
524A GLN* 5.3 12.9 - - + +
525A LEU* 5.4 15.5 - - + -
527A LYS* 6.0 2.3 - - - -
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Residues in contact with GLN 487 (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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483A TYR* 2.9 58.8 + - + +
484A LEU* 3.6 21.5 - - - +
485A ALA 3.1 0.6 - - - -
486A LEU* 1.3 80.4 - - - +
488A ASP* 1.3 59.5 + - + +
489A SER 3.8 1.9 + - - +
524A GLN* 5.4 5.6 - - + -
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Residues in contact with ASP 488 (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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440A PHE* 5.7 2.0 - - - -
457A TYR* 4.7 12.8 - - + +
484A LEU 3.5 11.6 + - - +
485A ALA 3.9 2.0 - - - +
486A LEU 3.4 0.2 - - - -
487A GLN* 1.3 77.4 - - + +
489A SER* 1.3 65.1 + - - +
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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