Contacts of the helix formed by residues 472 - 479 (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 GLU 472 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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459A GLY* 4.6 4.8 + - - +
470A ILE* 3.5 7.4 + - - -
471A ASN* 1.3 70.3 + - - +
473A ASN* 1.3 67.0 + - - +
475A ASP* 3.2 9.2 + - - +
476A PHE* 3.1 38.3 + - + -
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Residues in contact with ASN 473 (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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421A ILE* 5.1 2.6 - - - +
425A VAL* 3.6 29.1 - - - +
430A ILE* 4.3 1.9 - - + +
455A ILE* 3.1 36.3 + - + +
456A ILE* 4.1 6.3 - - + -
458A MET* 5.1 1.4 - - - +
459A GLY* 3.0 32.3 - - - +
471A ASN* 3.2 6.5 + - - +
472A GLU* 1.3 75.6 - - - +
474A ALA* 1.3 65.8 + - - +
476A PHE* 3.1 14.4 + - - +
477A ILE* 3.0 26.0 + - - +
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Residues in contact with ALA 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 ILE* 3.6 17.9 - - + +
470A ILE* 5.5 2.7 - - + -
471A ASN* 2.7 39.7 + - + +
473A ASN* 1.3 72.2 - - - +
475A ASP* 1.3 61.9 + - - +
477A ILE* 3.3 2.6 + - - +
478A GLU* 3.2 18.5 + - - +
508A TYR* 4.5 11.7 - - + +
509A PHE* 3.6 25.8 - - + -
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Residues in contact with ASP 475 (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* 4.7 14.5 - - + +
471A ASN 3.1 6.0 + - - +
472A GLU* 3.6 11.2 - - - +
474A ALA* 1.3 80.3 - - - +
476A PHE* 1.3 61.3 + - + +
478A GLU* 3.5 8.0 + - - +
479A LYS* 2.9 39.8 + - - +
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Residues in contact with PHE 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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425A VAL* 4.1 15.9 - - + -
430A ILE* 3.8 23.8 - - + +
472A GLU* 3.1 31.7 + - + -
473A ASN* 3.1 25.7 + - - +
475A ASP* 1.3 79.9 - - + +
477A ILE* 1.3 61.4 + - - +
479A LYS* 3.2 12.7 + - + +
480A ALA* 3.2 22.7 + - - +
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Residues in contact with ILE 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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430A ILE* 3.7 26.7 - - + -
434A CYS* 3.8 6.3 - - - -
452A LEU* 3.7 23.6 - - + +
455A ILE* 5.3 3.4 - - + -
456A ILE* 3.5 38.1 - - + -
473A ASN 3.0 8.9 + - - +
474A ALA 3.7 7.0 - - - +
476A PHE* 1.3 74.6 - - - +
478A GLU* 1.3 59.8 + - - +
480A ALA* 3.6 0.7 + - - -
481A GLY 3.4 2.1 + - - -
482A GLY* 2.7 41.2 + - - -
483A MET 3.7 15.7 - - - +
486A ILE* 4.2 11.2 - - + -
509A PHE* 4.1 13.7 - - + -
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Residues in contact with GLU 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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474A ALA 3.2 12.7 + - - +
475A ASP* 3.7 11.2 - - - +
476A PHE 3.3 0.2 - - - -
477A ILE* 1.3 76.2 - - - +
479A LYS* 1.3 64.8 + - + +
481A GLY* 3.1 13.5 + - - -
483A MET* 3.5 39.5 + - + +
509A PHE* 4.6 0.9 - - + -
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Residues in contact with LYS 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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431A LYS* 5.0 1.0 + - - -
475A ASP* 2.9 32.3 - - - +
476A PHE* 3.3 14.4 - - + +
477A ILE 3.2 0.2 - - - -
478A GLU* 1.3 75.0 - - + +
480A ALA* 1.3 59.2 + - - +
481A GLY* 2.8 12.6 + - - -
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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