Contacts of the helix formed by residues 366 - 378 (chain B) in PDB entry 2BKU
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 ILE 366 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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322B ILE* 4.6 5.7 - - + +
326B VAL* 3.7 31.9 - - + -
355B LEU* 4.2 8.3 - - + -
358B PHE* 3.8 28.7 - - + +
359B ALA* 4.2 15.0 - - - +
362B CYS* 4.3 1.7 + - + +
363B GLY 3.0 21.9 + - - +
365B HIS* 1.3 79.1 - - - +
367B LEU* 1.3 67.6 + - - +
368B GLU 3.5 0.2 - - - -
369B PRO* 3.3 9.5 - - - +
370B VAL* 3.2 31.8 - - + +
396B ILE* 3.9 23.8 - - + -
400B PRO* 4.1 16.6 - - + -
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Residues in contact with LEU 367 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364B ASN* 2.9 33.0 + - + +
366B ILE* 1.3 78.9 - - + +
368B GLU* 1.3 64.9 + - - +
370B VAL* 3.3 3.3 + - - -
371B LEU* 2.9 39.7 + - + +
396B ILE* 4.2 17.3 - - + -
397B MET* 6.3 0.7 - - + -
400B PRO* 4.1 21.8 - - + -
404B GLN* 3.6 42.8 - - + +
405B ARG* 5.6 2.0 - - + +
408B TYR* 4.3 20.6 - - + +
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Residues in contact with GLU 368 (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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323B LYS* 5.8 6.5 - - - -
364B ASN 4.6 0.6 + - - -
365B HIS 4.5 2.3 + - - +
367B LEU* 1.3 78.1 - - - +
369B PRO* 1.3 74.7 - - + +
371B LEU* 4.0 4.1 - - - +
372B GLU* 3.0 43.0 + - - +
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Residues in contact with PRO 369 (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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322B ILE* 3.8 26.9 - - + +
323B LYS* 5.9 7.9 - - + -
326B VAL* 4.2 18.4 - - + -
327B PRO* 4.9 12.8 - - + -
330B LEU* 3.7 6.8 - - + +
365B HIS 3.9 7.0 - - - +
366B ILE 3.3 17.3 - - - +
368B GLU* 1.3 99.0 - - + +
370B VAL* 1.3 59.3 + - - +
372B GLU* 3.8 9.7 + - + +
373B PHE* 3.2 21.7 + - - +
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Residues in contact with VAL 370 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326B VAL* 4.2 14.1 - - + -
330B LEU* 4.3 8.5 - - + -
355B LEU* 4.4 7.9 - - + -
366B ILE* 3.2 35.9 - - + +
367B LEU 3.3 2.6 + - - +
368B GLU 3.2 0.6 - - - -
369B PRO* 1.3 75.6 - - - +
371B LEU* 1.3 61.4 + - - +
373B PHE* 3.2 2.9 + - - +
374B VAL* 2.8 46.2 + - + +
392B ALA* 4.1 17.5 - - + +
396B ILE* 3.8 36.1 - - + -
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Residues in contact with LEU 371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367B LEU* 2.9 35.9 + - + +
368B GLU* 4.1 3.4 - - - +
370B VAL* 1.3 73.8 - - - +
372B GLU* 1.3 65.8 + - - +
374B VAL* 4.0 6.0 - - + +
375B GLU* 3.0 30.5 + - - +
393B PHE* 4.3 21.3 - - + -
396B ILE* 4.8 8.5 - - + -
408B TYR* 3.4 63.9 - - + +
411B GLN* 5.9 0.2 - - - +
412B ALA* 6.0 1.8 - - + -
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Residues in contact with GLU 372 (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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368B GLU* 3.0 36.8 + - - +
369B PRO* 3.8 10.5 - - - +
371B LEU* 1.3 79.0 - - - +
373B PHE* 1.3 61.1 + - - +
375B GLU* 4.2 6.3 - - - +
376B GLN* 3.2 30.5 + - - +
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Residues in contact with PHE 373 (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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327B PRO 5.7 0.4 - - - -
330B LEU* 3.6 59.5 - - + -
331B ASN* 4.7 2.9 - - - -
333B LEU* 5.2 0.4 - - + -
334B THR* 4.7 6.1 - - + -
369B PRO 3.2 11.2 + - - +
370B VAL 3.2 7.7 + - - +
372B GLU* 1.3 76.4 - - - +
374B VAL* 1.3 70.5 + - - +
376B GLN* 3.2 3.8 + - - +
377B ASN* 2.9 57.3 + - - +
385B ASN* 6.0 0.2 - - - -
388B ALA* 3.9 18.6 - - + -
389B ALA* 3.8 25.4 - - - -
392B ALA* 4.3 7.0 - - + -
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Residues in contact with VAL 374 (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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370B VAL* 2.8 39.0 + - + +
371B LEU* 4.0 8.1 - - + +
373B PHE* 1.3 75.2 - - - +
375B GLU* 1.3 62.1 + - - +
376B GLN 3.1 0.3 + - - -
377B ASN 3.1 1.0 + - - -
378B ILE* 2.8 55.9 + - + +
389B ALA* 3.6 26.0 - - - +
392B ALA* 4.1 7.0 - - + -
393B PHE* 4.2 25.4 - - + +
412B ALA* 5.5 7.2 - - + -
416B ILE* 6.2 0.7 - - + -
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Residues in contact with GLU 375 (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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371B LEU 3.0 17.8 + - - +
372B GLU* 4.2 4.8 - - - +
374B VAL* 1.3 80.9 - - - +
376B GLN* 1.3 59.8 + - - +
378B ILE* 3.6 19.2 - - + +
379B THR* 5.0 2.6 + - - -
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Residues in contact with GLN 376 (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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372B GLU* 3.2 23.7 + - - +
373B PHE* 3.2 5.9 + - - +
374B VAL 3.1 0.8 - - - -
375B GLU* 1.3 79.6 - - + +
377B ASN* 1.3 65.1 + - - +
379B THR 5.3 1.5 - - - -
380B ALA* 4.4 7.6 - - - +
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Residues in contact with ASN 377 (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 PHE* 2.9 61.0 + - + +
376B GLN* 1.3 84.7 - - - +
378B ILE* 1.3 65.6 + - - +
379B THR 3.1 4.4 + - - -
380B ALA* 3.3 16.9 + - - +
385B ASN* 2.8 43.4 - - + +
386B ARG* 3.4 17.0 + - - -
389B ALA* 4.0 7.0 - - + -
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Residues in contact with ILE 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374B VAL* 2.8 35.0 + - + +
375B GLU* 3.6 18.2 - - + +
377B ASN* 1.3 76.9 - - - +
379B THR* 1.3 76.3 + - + +
386B ARG* 3.7 14.2 - - - +
389B ALA* 3.8 11.0 - - + +
390B VAL* 4.0 14.1 - - + +
393B PHE* 6.3 0.2 - - + -
412B ALA* 6.4 0.4 - - + -
415B SER* 4.1 23.8 - - - +
416B ILE* 4.4 13.7 - - + -
419B LEU* 3.8 36.7 - - + +
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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