Contacts of the helix formed by residues 495 - 508 (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 ASP 495 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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493A GLU 3.5 8.0 + - - +
494A ASN* 1.3 72.6 + - - +
496A LYS* 1.3 64.6 + - - +
498A TYR* 3.3 29.9 + - + -
499A GLU* 2.9 36.2 + - + +
245B GLY* 4.2 1.6 - - - -
246B LYS* 3.3 38.3 + - - +
247B LYS* 3.4 25.0 + - + +
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Residues in contact with LYS 496 (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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446A GLU* 4.3 23.6 - - - +
494A ASN* 2.9 19.3 + - - +
495A ASP* 1.3 74.0 - - - +
497A ILE* 1.3 56.2 + - - +
499A GLU* 4.4 2.3 - - - +
500A LYS* 3.2 26.7 + - - +
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Residues in contact with ILE 497 (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 ASN* 3.6 34.3 - - + +
445A ILE* 3.9 18.8 - - + -
446A GLU* 4.0 18.4 - - + -
449A LEU* 4.1 5.5 - - + +
489A CYS* 3.7 29.4 - - + +
492A ASN* 3.6 32.3 - - + +
494A ASN* 2.9 23.7 + - + +
495A ASP 3.1 0.4 - - - -
496A LYS* 1.3 73.7 - - - +
498A TYR* 1.3 69.1 + - - +
499A GLU 3.2 1.1 - - - -
500A LYS* 3.0 7.3 + - - +
501A ALA* 2.8 20.6 + - - +
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Residues in contact with TYR 498 (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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489A CYS 3.3 14.4 - - - +
490A GLN* 3.4 22.4 - - - +
492A ASN* 3.3 22.0 - - - +
493A GLU 4.4 4.9 - - - -
494A ASN 3.1 15.5 + - - -
495A ASP* 3.3 36.4 + - - -
497A ILE* 1.3 78.6 - - - +
499A GLU* 1.3 96.6 + - + +
501A ALA* 3.2 1.6 + - - +
502A TYR* 2.9 37.0 + + + -
244B ARG* 3.6 45.6 + - + +
245B GLY* 4.2 7.6 - - - -
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Residues in contact with GLU 499 (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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495A ASP* 2.9 25.8 + - + +
496A LYS* 4.4 2.9 - - - +
498A TYR* 1.3 102.7 - - + +
500A LYS* 1.3 62.6 + - - +
502A TYR* 3.5 5.9 + - - +
503A LYS* 3.2 22.5 + - - +
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Residues in contact with LYS 500 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446A GLU* 5.9 1.1 - - - +
449A LEU* 3.9 35.4 - - + -
450A ASP* 3.4 20.4 - - - +
453A GLU* 3.1 43.5 - - - +
496A LYS 3.2 19.5 + - - +
497A ILE* 3.0 6.1 + - - +
499A GLU* 1.3 78.4 - - - +
501A ALA* 1.3 61.2 - - - +
503A LYS* 3.5 6.9 + - + +
504A ILE* 3.1 32.5 + - + +
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Residues in contact with ALA 501 (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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449A LEU* 4.7 4.9 - - + +
486A ILE* 3.6 31.3 - - + +
489A CYS* 3.9 15.5 - - + -
490A GLN* 3.8 14.1 - - + -
497A ILE 2.8 12.2 + - - +
498A TYR 3.2 8.5 + - - +
500A LYS* 1.3 74.9 - - - +
502A TYR* 1.3 65.9 + - - +
504A ILE* 3.2 4.9 + - - +
505A ILE* 3.0 26.0 + - - +
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Residues in contact with TYR 502 (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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490A GLN* 3.0 60.0 + - + +
498A TYR* 2.9 47.7 + + - +
499A GLU* 4.0 5.2 - - - +
501A ALA* 1.3 75.0 - - - +
503A LYS* 1.3 58.2 + - - +
505A ILE* 3.4 1.2 + - - +
506A GLU* 2.8 34.2 + - - +
244B ARG* 3.3 26.0 + - - -
127E LYS* 3.9 37.8 - - + +
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Residues in contact with LYS 503 (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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453A GLU* 5.7 4.5 - - - +
499A GLU 3.2 15.1 + - - +
500A LYS* 3.7 7.2 - - + +
501A ALA 3.2 0.4 - - - -
502A TYR* 1.3 79.2 - - - +
504A ILE* 1.3 58.4 + - + +
506A GLU* 3.8 7.1 - - - +
507A THR* 2.8 40.8 + - - +
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Residues in contact with ILE 504 (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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449A LEU* 4.0 36.3 - - + +
452A LEU* 5.4 2.7 - - + -
453A GLU* 4.2 28.7 - - + +
456A ILE* 5.6 5.8 - - + -
486A ILE* 4.1 28.7 - - + -
500A LYS* 3.1 26.0 + - + +
501A ALA 3.6 6.1 - - - +
503A LYS* 1.3 76.6 - - + +
505A ILE* 1.3 59.1 + - - +
507A THR* 4.7 0.2 - - - -
508A TYR* 2.8 47.1 + - + +
509A PHE* 3.9 13.4 - - + -
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Residues in contact with ILE 505 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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483A MET* 4.0 34.3 - - + +
486A ILE* 4.2 15.7 - - + -
487A PHE* 4.3 26.9 - - + +
490A GLN* 4.0 15.9 - - - +
501A ALA 3.0 19.2 + - - +
502A TYR 3.9 2.5 - - - +
504A ILE* 1.3 75.3 - - - +
506A GLU* 1.3 62.2 + - - +
509A PHE* 2.8 52.6 + - + +
510A GLY* 4.6 0.2 - - - -
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Residues in contact with GLU 506 (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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502A TYR* 2.8 22.6 + - + +
503A LYS* 3.8 6.7 - - - +
505A ILE* 1.3 79.3 - - - +
507A THR* 1.3 71.7 + - - +
509A PHE 4.0 2.3 + - - -
510A GLY* 4.2 10.3 + - - -
161B GLY 3.2 24.1 - - - +
162B THR* 3.7 29.5 - - + +
163B SER 4.9 1.9 + - - -
128E LYS* 5.1 3.5 + - - +
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Residues in contact with THR 507 (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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460A GLU* 5.2 1.7 - - - +
503A LYS* 2.8 25.8 + - - +
506A GLU* 1.3 81.3 + - - +
508A TYR* 1.3 96.0 + - + +
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Residues in contact with TYR 508 (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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453A GLU* 5.1 11.9 - - + -
456A ILE* 3.0 37.9 - - + -
457A LYS* 3.5 26.9 - - - +
460A GLU* 3.4 39.2 - - + +
471A ASN* 4.5 1.3 - - - -
474A ALA* 4.5 9.8 - - + +
504A ILE* 2.8 36.0 + - + +
507A THR* 1.3 103.1 - - + +
509A PHE* 1.3 82.0 + - + +
510A GLY 3.9 1.8 - - - -
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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