Contacts of the helix formed by residues 338 - 350 (chain A) in PDB entry 4BKR
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 338 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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334A TYR* 2.9 26.1 + - - +
335A LYS* 3.5 28.7 - - - +
336A GLU 3.4 1.2 - - - -
337A LEU* 1.3 76.9 - - - +
339A PRO* 1.3 73.1 - - + +
340A GLU* 3.4 28.1 - - - +
341A VAL* 3.0 15.7 + - + +
342A GLN* 3.0 18.9 + - - +
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Residues in contact with PRO 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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337A LEU 3.3 6.9 - - - +
338A ASP* 1.3 85.1 - - + +
340A GLU* 1.3 64.3 + - - +
342A GLN* 3.4 8.7 + - + +
343A ASN* 2.9 30.8 + - - +
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Residues in contact with GLU 340 (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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299A LYS* 3.7 28.8 - - - +
338A ASP* 3.4 33.0 - - - +
339A PRO* 1.3 80.0 - - - +
341A VAL* 1.3 62.4 + - - +
343A ASN* 3.8 6.9 - - - +
344A GLN* 3.1 28.9 + - - +
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Residues in contact with VAL 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A GLU* 3.5 17.3 - - - +
292A LEU* 3.9 15.9 - - + -
295A VAL* 3.9 18.8 - - + -
296A MET* 4.2 7.6 - - + -
299A LYS* 3.6 29.8 - - + +
301A THR* 5.5 1.1 - - - +
335A LYS 3.7 17.5 - - - +
336A GLU 3.7 8.5 - - - +
338A ASP* 3.0 19.2 + - + +
340A GLU* 1.3 76.9 - - + +
342A GLN* 1.3 59.6 + - - +
344A GLN* 3.2 2.9 + - - +
345A VAL* 2.9 33.7 + - + +
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Residues in contact with GLN 342 (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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227A GLY 5.3 0.2 + - - -
228A GLU* 3.3 39.2 - - + +
229A LYS* 3.1 30.6 + - - +
230A ILE* 4.8 0.5 + - - +
337A LEU* 2.9 32.1 + - - +
338A ASP 3.0 16.7 + - - +
339A PRO* 3.7 9.5 - - + +
341A VAL* 1.3 76.9 - - - +
343A ASN* 1.3 56.9 + - - +
345A VAL* 3.4 1.7 + - - +
346A GLN* 2.9 30.9 + - - +
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Residues in contact with ASN 343 (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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339A PRO 2.9 18.7 + - - +
340A GLU* 3.8 8.0 - - - +
341A VAL 3.2 0.2 - - - -
342A GLN* 1.3 75.7 - - - +
344A GLN* 1.3 58.7 + - - +
346A GLN* 3.4 6.1 + - - +
347A GLN* 2.8 62.6 + - - +
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Residues in contact with GLN 344 (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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294A LYS* 5.9 1.2 - - - +
295A VAL* 3.6 34.3 - - + +
298A GLU* 3.3 28.0 + - - +
299A LYS* 4.3 13.5 + - - -
340A GLU 3.1 16.2 + - - +
341A VAL 3.2 3.8 + - - +
343A ASN* 1.3 75.3 + - - +
345A VAL* 1.3 68.4 + - - +
347A GLN* 3.3 11.5 + - + +
348A LEU* 3.0 39.9 + - + +
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Residues in contact with VAL 345 (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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228A GLU* 3.7 23.1 - - - +
230A ILE* 4.7 9.0 - - + -
288A TYR* 3.9 20.9 - - + -
291A LEU* 4.2 16.6 - - + +
292A LEU* 4.1 27.6 - - + +
295A VAL* 3.8 22.7 - - + -
341A VAL 2.9 20.0 + - - +
342A GLN 3.8 0.9 - - - +
344A GLN* 1.3 77.6 - - - +
346A GLN* 1.3 58.0 + - - +
348A LEU* 3.4 4.6 + - - +
349A TRP* 2.9 27.6 + - + +
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Residues in contact with GLN 346 (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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230A ILE* 3.5 37.5 - - + +
342A GLN 2.9 18.5 + - - +
343A ASN* 3.7 7.2 - - - +
344A GLN 3.2 0.2 - - - -
345A VAL* 1.3 77.4 - - - +
347A GLN* 1.3 64.0 + - + +
349A TRP* 3.2 14.7 + - - -
350A ASP* 3.0 38.4 + - - +
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Residues in contact with GLN 347 (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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343A ASN* 2.8 53.4 + - - +
344A GLN* 3.3 9.6 + - + +
346A GLN* 1.3 75.9 - - + +
348A LEU* 1.3 63.8 + - + +
350A ASP* 3.4 10.8 + - - +
351A GLN* 3.3 31.4 + - - +
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Residues in contact with LEU 348 (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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291A LEU* 3.5 21.5 - - + +
294A LYS* 5.2 4.0 - - + -
295A VAL* 3.8 24.7 - - + -
344A GLN* 3.0 33.5 + - + +
345A VAL* 3.8 2.2 - - - +
347A GLN* 1.3 74.5 - - + +
349A TRP* 1.3 67.1 + - - +
351A GLN* 2.9 26.4 + - - +
352A VAL* 3.1 17.2 + - - +
360A LEU* 4.0 39.9 - - + +
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Residues in contact with TRP 349 (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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166A LEU* 5.3 2.2 - - + -
167A ARG* 2.9 88.8 + - + +
230A ILE* 3.4 29.6 - - + +
284A MET* 3.5 34.5 - - + -
287A LEU* 3.5 24.5 - - + -
288A TYR* 3.6 23.1 - + + -
291A LEU* 3.6 25.8 - - + +
345A VAL* 2.9 19.2 + - + +
346A GLN* 3.2 10.7 + - - +
348A LEU* 1.3 76.8 - - - +
350A ASP* 1.3 67.0 + - - +
351A GLN 3.5 0.2 + - - -
352A VAL* 3.6 15.3 + - - +
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Residues in contact with ASP 350 (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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167A ARG* 3.2 23.3 + - - +
346A GLN* 3.0 30.8 + - - +
347A GLN* 3.9 8.2 - - - +
348A LEU 3.1 1.0 - - - -
349A TRP* 1.3 84.5 - - - +
351A GLN* 1.3 61.8 + - + +
352A VAL 5.3 0.4 - - - -
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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