Contacts of the strand formed by residues 381 - 388 (chain B) in PDB entry 3QEK
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 LYS 381 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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280B LEU* 6.1 0.2 - - - -
377B LEU* 3.4 6.6 - - - +
378B GLN* 2.9 75.0 + - - +
379B ASN* 4.0 16.6 + - + +
380B ARG* 1.3 79.3 - - - +
382B LEU* 1.3 61.8 + - - +
383B VAL* 3.6 18.6 + - + +
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Residues in contact with LEU 382 (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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275B ILE* 3.9 36.3 - - + +
280B LEU* 3.7 34.1 - - + -
287B ILE* 5.2 1.3 - - + -
289B GLY 6.0 0.2 - - - +
291B GLN* 3.7 25.8 - - - +
375B MSE 4.3 20.1 - - + +
376B ASN 3.7 0.7 - - - +
377B LEU* 3.6 28.3 - - + +
381B LYS* 1.3 75.1 - - - +
383B VAL* 1.3 62.0 + - - +
384B GLN 4.2 0.7 + - - -
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Residues in contact with VAL 383 (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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375B MSE 4.1 2.5 - - - -
376B ASN 2.7 41.0 + - - +
378B GLN* 3.9 27.4 - - + +
381B LYS* 3.9 39.0 - - - +
382B LEU* 1.3 79.1 - - - +
384B GLN* 1.3 67.1 + - - +
385B VAL* 3.3 7.6 + - + +
398B ARG* 3.6 31.0 - - + +
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Residues in contact with GLN 384 (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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293B ILE* 5.1 0.8 - - - +
373B SER* 2.9 27.8 + - - -
374B ILE 3.4 7.4 - - - +
375B MSE 3.6 17.1 - - + +
382B LEU 4.2 1.0 + - - -
383B VAL* 1.3 70.1 - - - +
385B VAL* 1.3 58.5 + - - +
386B GLY 3.6 18.4 - - - +
387B ILE* 3.1 20.3 - - - +
396B ASN* 3.0 9.7 + - - +
398B ARG* 2.9 47.6 + - - +
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Residues in contact with VAL 385 (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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288B ILE* 5.3 0.9 - - + -
374B ILE* 2.9 30.5 + - + +
376B ASN* 3.7 20.0 - - + -
378B GLN* 4.1 14.1 - - - +
383B VAL* 3.5 17.3 - - + +
384B GLN* 1.3 74.4 - - - +
386B GLY* 1.3 59.4 + - - +
395B GLN* 3.5 11.5 - - + +
396B ASN* 3.0 31.3 + - - +
398B ARG* 4.2 14.6 - - + +
400B ILE* 3.7 34.1 - - + -
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Residues in contact with GLY 386 (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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374B ILE* 2.9 33.3 + - - -
384B GLN* 3.6 8.2 - - - +
385B VAL* 1.3 84.1 - - - +
387B ILE* 1.3 72.1 + - - +
394B ILE 3.1 13.7 - - - -
395B GLN* 4.0 4.0 - - - -
396B ASN* 4.3 3.5 - - - +
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Residues in contact with ILE 387 (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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293B ILE* 3.6 13.9 - - + -
371B GLN* 4.2 10.8 - - - +
372B TYR 3.3 4.7 - - - +
373B SER* 3.4 17.9 - - - +
374B ILE* 3.7 6.2 - - - +
384B GLN* 3.1 28.7 - - - +
386B GLY* 1.3 83.8 - - - +
388B PHE* 1.3 78.3 + - - +
389B ASN* 3.7 11.8 + - + +
392B TYR 3.6 0.7 - - - +
393B ILE* 3.3 2.9 - - - -
394B ILE* 2.8 42.3 + - + +
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Residues in contact with PHE 388 (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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149B LEU* 4.6 21.1 - - + -
150B VAL* 3.8 41.3 - - + -
153B GLU* 3.7 22.7 - - + -
370B ALA 4.1 2.7 - - - -
371B GLN* 3.2 7.3 - - - -
372B TYR* 2.8 47.6 + + + +
374B ILE* 3.9 2.1 - - + +
387B ILE* 1.3 75.3 - - - +
389B ASN* 1.3 57.4 + - - +
390B GLY* 3.2 36.1 + - - -
391B SER* 3.4 23.1 - - - -
392B TYR 3.6 8.7 - - - -
393B ILE* 3.9 17.3 - - + +
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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