Contacts of the helix formed by residues 331 - 339 (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 331 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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330A ASN* 1.3 74.3 - - - +
332A LEU* 1.3 67.4 + - + +
334A THR* 3.1 4.4 + - - -
335A GLN* 2.8 27.8 + - - +
370A ALA 5.3 0.3 - - - +
371A GLY* 4.1 12.8 - - - -
372A ASN* 3.8 33.4 + - - +
375A GLN* 3.3 22.6 + - - +
128D LYS* 4.7 6.8 - - - +
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Residues in contact with LEU 332 (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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330A ASN* 3.0 11.3 + - - +
331A ASP* 1.3 85.7 - - + +
333A GLN* 1.3 63.3 + - + +
335A GLN* 3.2 16.6 + - - +
336A VAL* 3.3 17.6 + - - +
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Residues in contact with GLN 333 (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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289A GLN* 3.5 33.3 + - - +
292A ILE* 3.6 22.2 - - + +
293A GLN* 3.2 29.9 + - - +
296A ILE* 3.7 20.3 - - + +
326A ILE* 4.0 3.8 - - - +
329A GLY* 3.3 12.4 - - - -
330A ASN* 2.9 48.7 + - - +
332A LEU* 1.3 76.0 - - + +
334A THR* 1.3 61.7 + - - +
336A VAL* 3.5 17.3 + - - +
337A VAL* 3.8 10.9 - - - +
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Residues in contact with THR 334 (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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327A VAL* 3.3 41.4 + - + +
329A GLY 3.3 12.5 + - - -
330A ASN 2.9 14.6 + - - -
331A ASP* 3.1 9.6 + - - -
333A GLN* 1.3 76.4 - - - +
335A GLN* 1.3 62.2 + - - +
337A VAL* 3.2 4.9 + - - +
338A ILE* 3.1 20.1 + - + +
368A ILE* 4.2 22.2 - - + -
375A GLN* 3.9 14.4 - - - +
128D LYS* 3.3 10.3 + - - +
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Residues in contact with GLN 335 (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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331A ASP 2.8 13.2 + - - +
332A LEU* 3.2 9.1 + - - +
334A THR* 1.3 73.8 - - - +
336A VAL* 1.3 65.9 - - - +
338A ILE* 3.7 18.1 - - - +
339A ASN* 2.8 63.1 + - - +
372A ASN* 5.2 3.3 + - - +
374A GLU* 5.3 4.7 - - - +
375A GLN* 3.3 36.7 + - - +
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Residues in contact with VAL 336 (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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296A ILE* 4.1 32.3 - - + +
301A PRO* 4.4 18.4 - - + -
332A LEU 3.5 14.6 - - - +
333A GLN* 3.6 12.1 - - - +
334A THR 3.2 0.6 - - - -
335A GLN* 1.3 79.1 - - - +
337A VAL* 1.3 57.6 + - + +
339A ASN* 3.6 9.5 + - - +
340A ALA* 3.2 23.9 + - - +
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Residues in contact with VAL 337 (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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296A ILE* 5.8 0.2 - - + -
301A PRO* 4.7 10.8 - - + -
305A VAL* 4.8 7.2 - - + -
323A VAL* 4.1 16.2 - - + -
326A ILE* 3.3 40.8 - - + -
327A VAL* 4.1 14.8 - - + -
333A GLN 3.8 6.7 - - - +
334A THR 3.2 6.6 + - - +
335A GLN 3.1 0.4 - - - -
336A VAL* 1.3 78.1 - - + +
338A ILE* 1.3 64.2 + - - +
339A ASN 3.2 1.3 - - - -
340A ALA* 3.3 13.0 + - - +
342A VAL* 2.9 47.7 + - + +
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Residues in contact with ILE 338 (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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334A THR* 3.1 12.8 + - + +
335A GLN* 3.2 26.4 + - - +
337A VAL* 1.3 75.1 - - - +
339A ASN* 1.3 61.2 + - - +
341A GLY* 3.1 19.8 + - - -
342A VAL* 3.9 8.2 + - - -
343A LEU* 4.2 21.6 + - + +
368A ILE* 3.8 36.1 - - + -
375A GLN* 3.9 32.1 - - + +
378A ALA* 4.5 12.8 - - + -
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Residues in contact with ASN 339 (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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302A LYS* 5.4 0.3 + - - -
335A GLN* 2.8 49.8 + - - +
336A VAL* 3.8 8.1 - - - +
338A ILE* 1.3 75.3 - - - +
340A ALA* 1.3 56.4 + - - +
341A GLY 3.0 9.4 + - - -
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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