Contacts of the helix formed by residues 418 - 426 (chain B) 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 PRO 418 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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414B GLY* 3.4 13.6 - - - +
415B LEU 4.5 2.9 - - - +
416B GLN 3.3 12.6 - - - +
417B ARG* 1.3 82.8 - - - +
419B ASP* 1.3 67.3 + - - +
421B ILE* 3.3 11.3 + - + +
422B ARG* 3.3 47.4 + - - +
458B MET* 5.1 8.0 - - + +
462B ASP* 5.5 2.5 - - - +
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Residues in contact with ASP 419 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417B ARG* 2.9 6.4 + - + +
418B PRO* 1.3 82.9 - - - +
420B ILE* 1.3 55.9 + - - +
422B ARG* 2.7 40.4 + - + +
423B TYR* 2.7 36.3 + - - +
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Residues in contact with ILE 420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373B THR* 4.5 6.5 - - + +
376B ILE* 3.6 27.8 - - + -
377B GLN* 4.5 7.4 - - - +
380B ILE* 3.9 27.4 - - + -
410B ALA* 3.7 20.0 - - + +
413B GLY* 3.3 26.7 - - - +
414B GLY* 4.7 0.9 - - - +
417B ARG* 2.9 34.6 + - + +
419B ASP* 1.3 77.5 - - - +
421B ILE* 1.3 57.5 + - + +
423B TYR* 3.2 2.3 + - - +
424B LEU* 2.9 45.9 + - + +
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Residues in contact with ILE 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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411B SER* 3.3 45.5 - - - +
414B GLY* 3.6 21.5 - - - +
418B PRO 3.3 9.3 + - - +
420B ILE* 1.3 77.9 - - + +
422B ARG* 1.3 58.5 + - + +
424B LEU* 3.3 8.1 + - + +
425B VAL* 2.8 38.8 + - + +
454B ASN* 4.6 11.4 - - + +
455B ILE* 3.9 23.1 - - + +
458B MET* 3.8 28.9 - - + -
473B ASN* 5.0 2.7 - - - +
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Residues in contact with ARG 422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418B PRO* 3.3 37.4 + - - +
419B ASP* 2.7 47.4 + - + +
421B ILE* 1.3 78.9 - - + +
423B TYR* 1.3 58.6 + - - +
425B VAL* 3.3 6.2 + - - +
426B SER* 2.8 31.9 + - - -
458B MET* 5.7 3.0 - - + +
462B ASP* 3.6 30.0 + - - +
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Residues in contact with TYR 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380B ILE* 3.5 49.5 + - + -
383B ASN* 4.5 6.4 + - - -
385B ILE* 3.6 22.6 - - + +
386B PRO* 3.9 24.6 - - - +
419B ASP 2.7 16.1 + - - +
420B ILE* 3.4 9.4 - - - +
422B ARG* 1.3 71.9 - - - +
424B LEU* 1.3 70.0 + - + +
426B SER* 2.6 28.9 + - - -
427B GLN* 3.0 34.6 + - + +
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Residues in contact with LEU 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380B ILE* 4.4 2.5 - - + -
385B ILE* 4.3 25.7 - - + +
407B ILE* 4.1 17.5 - - + +
410B ALA* 4.1 11.2 - - + -
411B SER* 4.0 34.1 - - - +
420B ILE* 2.9 37.2 + - + +
421B ILE* 3.6 8.5 - - + +
423B TYR* 1.3 89.2 - - + +
425B VAL* 1.3 63.4 + - + +
427B GLN* 3.2 15.6 + - - +
428B GLY 3.5 6.6 + - - -
429B CYS* 3.5 24.1 + - + +
455B ILE* 6.0 3.6 - - + -
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Residues in contact with VAL 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421B ILE* 2.8 27.5 + - + +
422B ARG* 3.8 6.1 - - - +
424B LEU* 1.3 72.9 - - - +
426B SER* 1.3 60.2 + - - +
428B GLY* 3.0 19.6 + - - -
429B CYS* 4.5 4.0 - - - -
430B ILE* 3.7 20.6 - - + +
455B ILE* 3.6 35.7 - - + -
473B ASN* 3.5 21.3 - - - +
476B PHE* 4.1 15.7 - - + -
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Residues in contact with SER 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422B ARG 2.8 14.3 + - - -
423B TYR* 2.6 26.4 + - - -
425B VAL* 1.3 77.5 - - - +
427B GLN* 1.3 74.7 + - - +
428B GLY 3.3 1.6 + - - -
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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