Contacts of the helix formed by residues 382 - 396 (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 ASN 382 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380B ALA* 3.2 7.8 - - + +
381B ASP* 1.3 80.5 + - + +
383B TRP* 1.3 88.1 + - - +
384B ARG* 3.3 27.4 - - - +
385B ASN* 3.3 31.8 + - - +
386B ARG* 3.2 17.6 + - - +
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Residues in contact with TRP 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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336B GLN* 4.0 28.3 - - + -
337B ASN 3.8 11.2 - - - -
338B GLU* 4.1 27.1 + - - -
381B ASP 3.8 0.8 + - - -
382B ASN* 1.3 82.7 - - - +
384B ARG* 1.3 88.7 + - + +
386B ARG* 3.0 31.2 + - - +
387B GLU* 2.7 40.9 + - + +
424B SER* 3.5 30.5 - - - +
426B GLN* 3.3 45.3 - - + -
427B VAL* 3.6 1.6 - - + +
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Residues in contact with ARG 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334B THR* 3.1 22.9 + - - +
335B ARG* 3.5 2.8 - - - +
336B GLN* 2.9 74.6 + - - +
338B GLU* 3.5 43.8 + - - +
382B ASN* 3.3 21.7 - - - +
383B TRP* 1.3 101.5 - - + +
385B ASN* 1.3 62.6 + - - +
388B ALA* 2.9 28.2 + - - +
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Residues in contact with ASN 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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334B THR* 4.0 20.2 - - - +
373B PHE* 6.0 0.2 - - - -
377B ASN* 2.8 40.5 - - + +
380B ALA* 4.0 15.1 - - + +
382B ASN* 3.3 34.0 + - - +
383B TRP 3.1 0.6 - - - -
384B ARG* 1.3 77.1 - - - +
386B ARG* 1.3 64.8 + - - +
388B ALA* 3.4 2.1 + - - +
389B ALA* 3.0 18.2 + - - +
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Residues in contact with ARG 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377B ASN 3.4 11.0 - - - +
378B ILE* 3.7 21.9 - - - +
379B THR* 4.6 2.9 - - - +
380B ALA 2.9 33.7 + - - +
381B ASP* 2.9 19.2 + - - +
382B ASN 3.2 2.7 + - - +
383B TRP* 3.0 32.1 + - - +
385B ASN* 1.3 77.4 - - - +
387B GLU* 1.3 62.4 + - - +
389B ALA* 3.3 4.9 + - - +
390B VAL* 3.3 22.7 + - - +
419B LEU* 4.1 10.3 - - + +
422B ASP* 2.6 42.2 + - - -
423B GLN* 5.3 2.4 - - - +
424B SER* 4.4 2.2 - - - +
427B VAL* 4.0 10.1 - - + -
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Residues in contact with GLU 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333B LEU 4.1 1.7 - - - +
336B GLN* 2.6 42.0 + - - +
383B TRP* 2.7 23.3 + - + +
386B ARG* 1.3 71.7 - - - +
388B ALA* 1.3 62.7 + - - +
390B VAL* 3.3 8.5 + - - +
391B MET* 2.9 42.9 + - - +
426B GLN* 3.8 24.7 - - + +
427B VAL* 3.9 10.7 - - + +
430B THR* 2.5 37.8 + - - +
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Residues in contact with ALA 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333B LEU* 3.7 26.0 - - + +
334B THR* 3.6 21.8 - - + -
373B PHE* 3.9 10.8 - - + -
384B ARG 2.9 19.2 + - - +
385B ASN 3.4 3.6 + - - +
387B GLU* 1.3 83.1 + - - +
389B ALA* 1.3 52.8 + - - +
391B MET* 3.4 5.0 - - - +
392B ALA* 2.8 35.2 + - - +
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Residues in contact with ALA 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373B PHE* 3.8 10.5 - - - -
374B VAL* 3.6 22.8 - - - +
377B ASN* 4.0 4.9 - - + -
378B ILE* 3.8 31.9 - - + +
385B ASN 3.0 12.8 + - - +
386B ARG 3.5 9.9 - - - +
387B GLU 3.1 0.4 - - - -
388B ALA* 1.3 78.0 - - - +
390B VAL* 1.3 58.6 + - - +
392B ALA* 3.3 3.6 + - - +
393B PHE* 3.0 24.4 + - - +
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Residues in contact with VAL 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378B ILE* 4.0 9.9 - - + -
386B ARG 3.3 15.7 - - - +
387B GLU* 3.3 17.0 - - - +
389B ALA* 1.3 73.8 - - - +
391B MET* 1.3 65.1 + - - +
393B PHE* 4.5 3.8 - - - -
394B GLY* 3.2 17.5 + - - -
416B ILE* 4.2 24.0 - - + -
419B LEU* 3.4 26.9 - - + -
427B VAL* 4.3 3.8 - - + +
430B THR* 4.0 14.4 - - + -
431B THR* 3.9 20.6 - - - +
433B TRP* 4.2 0.5 - - - -
434B CYS* 3.3 18.9 - - + +
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Residues in contact with MET 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333B LEU* 4.1 24.5 - - + -
348B SER 6.1 1.3 - - - +
349B MET* 6.1 7.2 - - + -
352B GLY* 5.0 7.0 - - - -
356B GLN* 5.4 2.0 - - - -
387B GLU* 2.9 40.4 + - - +
388B ALA* 3.4 8.3 - - - +
390B VAL* 1.3 78.5 - - - +
392B ALA* 1.3 62.5 + - - +
394B GLY 3.2 0.3 + - - -
395B SER* 2.8 32.9 + - - +
430B THR* 3.6 15.8 - - + +
433B TRP* 3.8 25.5 - - + -
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Residues in contact with ALA 392 (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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330B LEU* 3.8 27.8 - - + -
333B LEU* 4.1 4.0 - - + -
355B LEU* 4.1 11.1 - - - +
370B VAL* 4.1 6.4 - - + +
373B PHE* 4.3 4.3 - - + -
374B VAL* 4.1 12.1 - - + -
388B ALA 2.8 21.5 + - - +
389B ALA 3.3 6.3 + - - +
391B MET* 1.3 73.9 - - - +
393B PHE* 1.3 62.8 + - - +
395B SER* 3.1 12.6 + - - -
396B ILE* 3.4 16.1 + - - +
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Residues in contact with PHE 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371B LEU* 4.3 19.3 - - + -
374B VAL* 4.2 25.9 - - + +
389B ALA 3.0 16.5 + - - +
390B VAL* 3.9 6.5 - - - +
392B ALA* 1.3 76.2 - - - +
394B GLY* 1.3 63.4 + - - +
396B ILE* 3.1 26.5 + - + +
397B MET* 3.5 33.5 - - + +
408B TYR* 3.8 20.9 - - + -
409B VAL* 3.9 21.3 - - + -
412B ALA* 4.0 15.9 - - + -
416B ILE* 3.6 27.1 - - + -
434B CYS* 3.8 11.9 - - - -
438B ILE* 4.1 7.0 - - + -
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Residues in contact with GLY 394 (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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390B VAL 3.2 8.7 + - - -
391B MET 3.8 2.5 - - - -
393B PHE* 1.3 78.8 - - - +
395B SER* 1.3 62.2 + - - +
397B MET* 3.3 15.5 + - - +
433B TRP* 3.8 20.4 - - - -
434B CYS* 3.7 12.0 - - - -
437B ARG* 3.2 30.5 + - - -
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Residues in contact with SER 395 (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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352B GLY* 4.2 5.0 + - - -
355B LEU* 4.0 21.6 - - - +
356B GLN* 3.4 54.7 + - - +
359B ALA* 3.7 5.9 - - - +
391B MET* 2.8 26.9 + - - +
392B ALA* 3.1 10.6 + - - -
394B GLY* 1.3 77.7 - - - +
396B ILE* 1.3 59.9 + - - +
397B MET 3.4 1.0 + - - -
398B ASP 4.2 3.1 - - - +
433B TRP* 4.2 2.4 - - - -
437B ARG* 4.3 2.3 + - - -
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Residues in contact with ILE 396 (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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355B LEU* 4.8 6.1 - - + -
359B ALA* 4.0 8.5 - - + -
366B ILE* 3.9 29.4 - - + -
367B LEU* 4.2 23.3 - - + -
370B VAL* 3.8 35.2 - - + -
371B LEU* 4.8 8.5 - - + -
392B ALA 3.4 11.0 + - - +
393B PHE* 3.1 24.5 - - + +
395B SER* 1.3 81.3 - - - +
397B MET* 1.3 68.4 + - + +
398B ASP 3.1 5.8 - - - -
400B PRO* 3.1 24.9 - - + +
405B ARG* 4.2 1.2 - - - +
408B TYR* 6.4 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