Contacts of the helix formed by residues 346 - 363 (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 346 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280B ASP* 5.6 3.4 - - + +
284B SER* 4.5 2.0 - - - -
335B ARG 3.0 22.8 + - - -
336B GLN* 3.8 4.5 - - - +
337B ASN* 3.8 18.8 + - - +
344B ASP 3.5 3.6 - - - +
345B TRP* 1.3 84.3 + - - +
347B VAL* 1.3 65.3 + - + +
348B SER* 2.7 31.8 + - - +
349B MET* 3.0 41.7 + - - +
350B SER 3.1 9.0 + - - -
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Residues in contact with VAL 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B ASP* 3.7 33.2 - - + +
283B ALA* 3.9 14.4 - - + -
284B SER* 3.3 42.1 + - - +
287B VAL* 4.6 2.2 - - + -
332B LEU* 4.1 17.9 - - + +
335B ARG* 3.8 26.2 - - + -
346B ASN* 1.3 77.6 - - - +
348B SER* 1.3 59.8 + - - +
350B SER* 3.4 3.8 + - - -
351B ALA* 2.9 27.2 + - - +
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Residues in contact with SER 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332B LEU 3.2 25.4 - - - -
333B LEU* 3.5 23.5 - - - +
335B ARG 3.8 8.1 - - - -
336B GLN* 3.6 13.5 - - - +
346B ASN* 2.7 28.1 + - - +
347B VAL* 1.3 78.8 - - - +
349B MET* 1.3 66.7 + - - +
351B ALA* 3.2 3.3 + - - +
352B GLY* 3.0 19.1 + - - -
391B MET* 5.9 1.4 - - - +
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Residues in contact with MET 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337B ASN* 4.2 7.0 - - - +
343B ASP* 4.1 12.6 - - - +
344B ASP 2.9 36.6 - - - +
345B TRP* 3.6 42.1 - - + +
346B ASN* 3.0 23.0 + - - +
348B SER* 1.3 83.7 + - - +
350B SER* 1.3 63.4 + - - +
352B GLY* 3.2 2.6 + - - -
353B ALA* 3.1 19.9 + - - +
391B MET* 6.1 7.0 - - + -
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Residues in contact with SER 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A ARG* 5.1 1.6 + - - +
284B SER* 4.5 10.6 + - - -
287B VAL* 3.4 22.3 - - - +
288B GLU* 3.1 24.4 + - - +
291B SER* 4.7 0.9 + - - -
345B TRP* 3.5 23.0 + - - -
346B ASN 3.1 11.7 + - - -
347B VAL* 3.4 13.9 - - - -
349B MET* 1.3 76.7 - - - +
351B ALA* 1.3 60.0 + - - +
353B ALA* 3.5 4.8 + - - +
354B CYS* 3.1 17.3 + - - +
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Residues in contact with ALA 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B VAL* 4.0 2.0 - - - +
329B LEU* 3.7 41.7 - - + +
332B LEU* 3.8 14.6 - - + -
333B LEU* 3.8 7.6 - - + -
347B VAL 2.9 18.1 + - - +
348B SER 3.4 6.7 - - - +
350B SER* 1.3 74.0 - - - +
352B GLY* 1.3 61.9 + - - +
354B CYS* 3.2 2.9 + - - +
355B LEU* 2.9 29.6 + - - +
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Residues in contact with GLY 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333B LEU* 3.5 15.0 - - - +
348B SER 3.0 12.2 + - - -
349B MET* 3.2 4.2 + - - -
351B ALA* 1.3 73.6 - - - +
353B ALA* 1.3 64.5 + - - +
355B LEU* 3.1 7.7 + - - +
356B GLN* 3.0 32.8 + - - +
391B MET* 5.0 7.4 - - - -
395B SER* 4.2 8.3 + - - -
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Residues in contact with ALA 353 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A ARG* 3.8 32.5 - - - +
291B SER* 5.4 0.7 - - - +
345B TRP* 4.7 5.6 - - + -
349B MET 3.1 12.2 + - - +
350B SER* 3.6 9.6 - - - +
352B GLY* 1.3 74.7 - - - +
354B CYS* 1.3 61.6 + - - +
356B GLN* 3.4 11.9 + - - +
357B LEU* 3.2 28.3 + - - +
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Residues in contact with CYS 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B VAL* 3.5 22.4 - - + -
290B TRP* 4.1 11.4 - - - -
291B SER* 3.2 35.2 - - - +
329B LEU* 3.8 20.9 - - + -
350B SER 3.1 13.7 + - - +
351B ALA 3.5 8.3 - - - +
352B GLY 3.1 0.2 - - - -
353B ALA* 1.3 73.8 - - - +
355B LEU* 1.3 60.8 + - - +
357B LEU* 3.3 4.8 + - - +
358B PHE* 2.8 33.2 + - - +
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Residues in contact with LEU 355 (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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326B VAL* 4.0 26.7 - - + -
329B LEU* 4.6 14.3 - - + +
330B LEU* 3.7 25.4 - - + +
333B LEU* 4.3 9.2 - - + -
351B ALA 2.9 16.1 + - - +
352B GLY* 3.1 6.3 + - - +
354B CYS* 1.3 75.0 - - - +
356B GLN* 1.3 59.4 + - - +
358B PHE* 3.1 7.5 + - + +
359B ALA* 2.8 28.2 + - - +
366B ILE* 4.2 14.4 - - + -
370B VAL* 4.4 7.6 - - + -
392B ALA* 4.1 16.6 - - + +
395B SER* 4.0 20.0 - - - +
396B ILE* 4.8 4.7 - - + -
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Residues in contact with GLN 356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352B GLY* 3.0 19.1 + - - +
353B ALA* 3.7 11.3 - - - +
354B CYS 3.3 0.2 - - - -
355B LEU* 1.3 74.2 - - - +
357B LEU* 1.3 57.9 + - + +
359B ALA* 3.2 3.3 + - - +
360B GLN* 2.9 42.4 + - + +
391B MET* 5.4 2.4 - - - -
395B SER* 3.4 44.0 + - - +
398B ASP 4.4 0.2 - - - +
433B TRP* 4.0 21.8 - - - -
437B ARG* 4.3 14.5 + - - +
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Residues in contact with LEU 357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A ARG* 4.1 10.5 - - - +
291B SER* 3.6 37.5 - - - +
294B CYS* 3.7 13.5 - - + -
295B GLU* 3.9 27.1 - - + +
298B ILE* 3.6 22.9 - - + +
353B ALA 3.2 16.9 + - - +
354B CYS* 3.5 7.9 - - - +
355B LEU 3.2 0.4 - - - -
356B GLN* 1.3 77.3 - - + +
358B PHE* 1.3 55.7 + - - +
360B GLN* 3.4 12.0 + - - +
361B ASN* 2.9 32.7 + - - +
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Residues in contact with PHE 358 (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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290B TRP* 4.2 13.0 - + + -
294B CYS* 3.6 22.3 - - - -
318B ALA* 3.5 39.3 - - + -
322B ILE* 3.9 6.3 - - + -
325B VAL* 3.8 33.4 - - + -
326B VAL* 3.7 23.6 - - + -
329B LEU* 4.0 12.8 - - + -
354B CYS* 2.8 24.5 + - - +
355B LEU* 3.1 12.8 + - + +
357B LEU* 1.3 76.7 - - - +
359B ALA* 1.3 56.5 + - - +
361B ASN* 4.5 1.1 - - - -
362B CYS* 2.8 50.3 + - - +
366B ILE* 3.8 14.9 - - + +
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Residues in contact with ALA 359 (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 2.8 15.8 + - - +
356B GLN 3.4 7.0 - - - +
358B PHE* 1.3 72.0 - - - +
360B GLN* 1.3 58.1 + - - +
363B GLY* 2.7 34.0 + - - -
366B ILE* 4.2 16.5 - - + +
395B SER 3.7 12.8 - - - +
396B ILE* 4.0 17.9 - - + -
398B ASP 3.3 17.3 - - - +
399B GLY* 3.6 5.2 - - - -
400B PRO* 4.5 2.0 - - + -
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Residues in contact with GLN 360 (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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134A LYS* 2.7 34.5 + - - +
298B ILE* 3.9 17.0 - - + +
356B GLN* 2.9 31.7 + - + +
357B LEU* 3.4 18.6 + - - +
359B ALA* 1.3 75.3 - - - +
361B ASN* 1.3 58.9 + - - +
363B GLY* 4.5 1.3 + - - -
398B ASP* 3.0 39.6 + - + +
399B GLY* 3.9 9.5 - - - +
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Residues in contact with ASN 361 (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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294B CYS* 3.6 11.5 - - + +
297B GLU* 2.9 53.1 + - - +
298B ILE* 3.6 16.4 - - + +
301B ALA* 6.0 0.7 - - - +
318B ALA* 3.4 17.1 - - - +
357B LEU 2.9 18.6 + - - +
358B PHE 4.0 2.7 - - - +
360B GLN* 1.3 79.4 - - - +
362B CYS* 1.3 62.4 + - - +
363B GLY 3.5 0.4 - - - -
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Residues in contact with CYS 362 (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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318B ALA* 3.8 15.0 - - - -
319B LEU* 3.7 36.1 - - + -
322B ILE* 3.7 26.9 - - + -
358B PHE* 2.8 26.9 + - + +
361B ASN* 1.3 78.1 - - - +
363B GLY* 1.3 67.4 + - - +
364B ASN 3.3 0.3 + - - -
365B HIS* 3.2 26.2 + - + -
366B ILE* 4.6 3.6 - - + +
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Residues in contact with GLY 363 (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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359B ALA 2.7 22.9 + - - -
360B GLN 4.5 1.2 + - - -
361B ASN 3.5 1.2 - - - -
362B CYS* 1.3 70.8 - - - +
364B ASN* 1.3 64.2 + - - -
366B ILE* 3.0 27.0 + - - +
399B GLY 3.6 18.6 - - - -
400B PRO* 4.0 7.2 - - - -
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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
------------------------------------------------------------
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