Contacts of the helix formed by residues 482 - 491 (chain A) in PDB entry 1BK6
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 482 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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434A CYS* 3.2 34.7 - - - -
437A LEU* 4.8 0.4 - - - +
477A ILE* 2.7 15.8 + - - -
480A ALA 3.2 3.2 - - - -
481A GLY* 1.3 79.6 - - - +
483A MET* 1.3 51.0 + - - -
485A LYS* 3.1 6.4 + - - +
486A ILE* 2.8 38.6 + - - +
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Residues in contact with MET 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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477A ILE* 3.4 10.3 + - - +
478A GLU* 3.5 32.8 - - + +
481A GLY* 3.4 0.6 - - - -
482A GLY* 1.3 75.8 - - - +
484A GLU* 1.3 64.1 + - - +
486A ILE* 3.4 9.4 + - - +
487A PHE* 3.0 23.1 + - + +
505A ILE* 4.0 10.2 - - + +
509A PHE* 3.5 43.5 - - + -
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Residues in contact with GLU 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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481A GLY* 3.6 11.5 + - - +
482A GLY 3.3 0.8 - - - -
483A MET* 1.3 80.3 - - - +
485A LYS* 1.3 60.3 + - + +
487A PHE* 3.1 12.2 + - + +
488A ASN* 3.0 43.2 + - - +
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Residues in contact with LYS 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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434A CYS 3.3 24.5 - - - +
435A ASP* 4.3 17.0 + - - +
437A LEU* 4.2 16.6 - - + -
438A GLU* 3.3 47.6 - - + +
480A ALA 4.5 2.8 + - - -
481A GLY* 3.5 21.1 + - - +
482A GLY 3.1 7.3 + - - +
484A GLU* 1.3 77.6 - - + +
486A ILE* 1.3 64.2 + - - +
488A ASN* 3.1 20.9 + - - +
489A CYS* 3.3 16.8 + - - -
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Residues in contact with ILE 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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437A LEU* 4.0 19.7 - - + +
449A LEU* 4.3 13.2 - - + -
452A LEU* 4.3 17.5 - - + -
456A ILE* 6.5 0.2 - - + -
477A ILE* 4.2 21.8 - - + -
482A GLY 2.8 23.8 + - - +
483A MET* 3.8 7.2 - - - +
485A LYS* 1.3 70.8 - - - +
487A PHE* 1.3 62.3 + - - +
489A CYS* 3.2 20.4 + - - +
501A ALA* 3.6 19.8 - - - +
504A ILE* 4.1 34.3 - - + -
505A ILE* 4.2 14.1 - - + -
509A PHE* 5.0 5.4 - - + -
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Residues in contact with PHE 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 MET* 3.0 15.1 + - + +
484A GLU* 3.1 15.5 - - + +
486A ILE* 1.3 78.3 - - - +
488A ASN* 1.3 68.2 + - - +
490A GLN* 2.9 57.8 + - - +
491A GLN* 5.5 1.2 - - - +
505A ILE* 4.3 25.3 - - + +
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Residues in contact with ASN 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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438A GLU* 5.2 4.5 - - - +
484A GLU* 3.0 26.6 + - - +
485A LYS* 3.1 14.2 + - - +
487A PHE* 1.3 84.8 - - - +
489A CYS* 1.3 57.2 + - - +
490A GLN 2.9 11.4 + - - -
491A GLN* 3.0 24.6 + - - +
492A ASN 4.2 1.0 + - - -
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Residues in contact with CYS 489 (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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437A LEU* 4.6 16.2 - - - -
445A ILE* 4.0 30.1 - - - -
449A LEU* 4.8 4.7 - - + -
485A LYS 3.3 18.6 + - - -
486A ILE* 3.2 15.9 + - - +
488A ASN* 1.3 75.4 - - - +
490A GLN* 1.3 60.5 + - - +
491A GLN 3.1 1.3 - - - -
492A ASN* 3.4 18.8 - - - +
497A ILE* 3.8 13.9 - - + -
498A TYR* 3.3 17.7 + - - -
501A ALA* 3.9 9.6 - - + -
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Residues in contact with GLN 490 (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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486A ILE 4.1 0.7 - - - +
487A PHE* 2.9 53.2 - - - +
488A ASN 2.9 1.4 + - - -
489A CYS* 1.3 78.9 - - - +
491A GLN* 1.3 59.7 + - + +
492A ASN 3.3 1.6 - - - -
498A TYR* 3.4 12.9 - - - +
501A ALA* 3.8 14.8 - - + -
502A TYR* 3.0 63.5 + - + +
505A ILE* 4.0 15.6 - - - +
244B ARG* 3.0 26.7 + - - -
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Residues in contact with GLN 491 (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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487A PHE 5.5 0.7 - - - +
488A ASN* 3.0 15.0 + - - +
490A GLN* 1.3 83.8 - - + +
492A ASN* 1.3 58.7 + - - -
244B ARG* 5.0 1.8 - - - +
279B TRP* 3.8 42.2 - - + +
314B LEU* 5.9 5.9 - - - +
317B THR* 4.5 9.5 - - + +
321B ARG* 3.1 22.7 + - - -
127E LYS* 6.0 2.4 - - - +
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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