Contacts of the helix formed by residues 346 - 363 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280D ASP* 5.5 3.8 - - - +
284D SER* 4.5 2.5 - - - -
335D ARG 3.0 22.7 + - - +
336D GLN* 3.9 2.0 - - - +
337D ASN* 3.6 23.4 + - - +
344D ASP* 3.4 3.0 - - + +
345D TRP* 1.3 80.6 + - - +
347D VAL* 1.3 65.4 + - + +
348D SER* 2.7 36.2 + - - +
349D MET* 3.0 42.4 + - - +
350D SER* 3.2 11.8 + - - -
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Residues in contact with VAL 347 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280D ASP* 3.8 35.6 - - + +
283D ALA* 3.9 7.9 - - + +
284D SER* 3.4 40.3 + - - +
287D VAL* 4.6 1.8 - - + -
332D LEU* 3.8 26.2 - - + +
335D ARG* 3.8 26.7 - - + +
346D ASN* 1.3 74.9 - - - +
348D SER* 1.3 60.0 + - - +
350D SER* 3.5 3.1 + - - -
351D ALA* 3.0 26.9 + - - +
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Residues in contact with SER 348 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332D LEU 3.4 25.1 - - - -
333D LEU* 3.4 22.4 - - - +
335D ARG 3.7 12.8 - - - -
336D GLN* 3.5 14.5 - - - +
346D ASN* 2.7 28.0 + - - +
347D VAL* 1.3 78.2 - - - +
349D MET* 1.3 60.9 + - - +
351D ALA 3.4 0.7 + - - -
352D GLY* 3.1 21.3 + - - -
391D MET* 5.9 1.8 - - - +
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Residues in contact with MET 349 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337D ASN* 4.2 6.7 - - - +
343D ASP* 4.1 13.5 - - - +
344D ASP 3.1 31.0 - - - +
345D TRP* 3.5 43.9 - - + -
346D ASN* 3.0 23.0 + - - +
348D SER* 1.3 77.8 + - - +
350D SER* 1.3 60.1 + - - +
352D GLY* 3.2 2.5 + - - +
353D ALA* 3.0 28.4 + - - +
391D MET* 6.2 7.0 - - + -
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Residues in contact with SER 350 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140C ARG* 5.1 1.5 + - - -
143C ASN* 5.2 2.1 + - - -
284D SER* 4.2 12.6 + - - -
287D VAL* 3.5 18.1 - - - +
288D GLU* 3.8 16.8 + - - +
291D SER* 4.7 0.9 + - - -
345D TRP* 3.0 31.0 + - - -
346D ASN 3.2 5.7 + - - -
347D VAL* 3.6 12.6 - - - -
348D SER 3.4 0.2 - - - -
349D MET* 1.3 79.1 - - - +
351D ALA* 1.3 55.9 + - - -
353D ALA* 3.4 4.9 + - - +
354D CYS* 2.9 29.3 + - - +
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Residues in contact with ALA 351 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287D VAL* 4.0 2.1 - - - +
329D LEU* 3.6 44.4 - - + +
332D LEU* 3.7 15.9 - - + -
333D LEU* 3.9 7.0 - - + +
347D VAL 3.0 17.6 + - - +
348D SER 3.6 6.1 - - - +
349D MET 3.3 0.4 - - - -
350D SER* 1.3 72.5 - - - +
352D GLY* 1.3 61.5 - - - +
354D CYS* 3.5 2.3 + - - +
355D LEU* 2.9 29.1 + - - +
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Residues in contact with GLY 352 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333D LEU* 3.6 15.0 - - - +
348D SER 3.1 12.0 + - - -
349D MET* 3.2 4.6 + - - -
351D ALA* 1.3 73.6 - - - +
353D ALA* 1.3 64.1 + - - +
355D LEU* 3.1 7.4 + - - +
356D GLN* 3.1 31.5 + - - +
391D MET* 5.1 7.2 - - - -
395D SER* 4.1 8.9 + - - -
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Residues in contact with ALA 353 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140C ARG* 3.6 35.0 - - + +
345D TRP* 4.8 5.4 - - + -
349D MET 3.0 12.9 + - - +
350D SER* 3.6 8.5 - - - +
352D GLY* 1.3 75.0 - - - +
354D CYS* 1.3 61.7 + - - +
356D GLN* 3.3 14.5 + - - +
357D LEU* 3.2 28.8 + - - +
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Residues in contact with CYS 354 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287D VAL* 3.5 25.8 - - + -
290D TRP* 4.0 13.5 - - - -
291D SER* 3.2 33.4 + - - +
294D CYS* 4.7 0.4 - - - -
329D LEU* 3.6 22.0 - - + -
350D SER 2.9 16.9 + - - +
351D ALA 3.6 4.7 - - - +
352D GLY 3.2 0.2 - - - -
353D ALA* 1.3 75.7 - - - +
355D LEU* 1.3 57.3 + - - +
357D LEU* 3.3 6.1 + - - +
358D PHE* 2.9 34.6 + - - -
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Residues in contact with LEU 355 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326D VAL* 4.2 25.6 - - + -
329D LEU* 4.5 13.5 - - + -
330D LEU* 3.6 26.0 - - + -
333D LEU* 4.4 7.6 - - + -
351D ALA 2.9 17.2 + - - +
352D GLY* 3.1 6.9 + - - +
354D CYS* 1.3 74.3 - - - +
356D GLN* 1.3 53.2 + - - +
358D PHE* 2.9 9.5 + - + +
359D ALA* 2.8 34.0 + - - +
366D ILE* 4.3 9.9 - - + -
370D VAL* 4.3 14.1 - - + -
392D ALA* 4.0 27.1 - - - +
395D SER* 4.2 9.0 - - - -
396D ILE* 4.7 4.3 - - + -
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Residues in contact with GLN 356 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352D GLY* 3.1 17.3 + - - +
353D ALA* 3.6 11.9 - - - +
355D LEU* 1.3 75.3 - - - +
357D LEU* 1.3 58.6 + - + +
359D ALA* 3.2 3.3 + - - +
360D GLN* 2.8 44.7 + - - +
391D MET* 6.0 0.6 - - - -
395D SER* 3.4 43.6 + - - +
398D ASP* 4.2 0.8 - - + +
433D TRP* 4.1 17.8 - - - -
437D ARG* 4.0 19.3 + - - +
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Residues in contact with LEU 357 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140C ARG* 4.0 17.7 - - - +
291D SER* 3.6 43.5 - - - +
294D CYS* 3.7 14.1 - - + -
295D GLU* 4.0 14.4 - - + -
298D ILE* 3.8 13.9 - - + +
353D ALA 3.2 12.7 + - - +
354D CYS 3.4 7.2 - - - +
355D LEU 3.2 0.2 - - - -
356D GLN* 1.3 75.9 - - + +
358D PHE* 1.3 59.1 + - - +
360D GLN* 3.3 18.5 + - - +
361D ASN* 2.8 33.3 + - - +
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Residues in contact with PHE 358 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290D TRP* 3.9 15.9 - + + -
294D CYS* 3.7 18.2 - - - -
318D ALA* 3.4 37.0 - - + -
322D ILE* 4.4 3.8 - - + -
325D VAL* 3.5 32.8 - - + -
326D VAL* 3.9 22.4 - - + -
329D LEU* 3.9 13.7 - - + -
354D CYS* 2.9 27.7 + - - +
355D LEU* 2.9 13.5 + - + +
357D LEU* 1.3 76.2 - - - +
359D ALA* 1.3 57.0 + - - +
361D ASN* 4.5 0.9 - - - -
362D CYS* 2.8 50.8 + - - +
366D ILE* 3.8 15.5 - - + -
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Residues in contact with ALA 359 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355D LEU 2.8 15.1 + - - +
356D GLN 3.4 8.3 - - - +
358D PHE* 1.3 72.9 - - - +
360D GLN* 1.3 56.6 + - - +
363D GLY* 2.7 34.0 + - - -
366D ILE* 3.9 23.3 - - + +
395D SER 3.7 13.2 - - - +
396D ILE* 3.9 14.1 - - + -
398D ASP 3.6 13.2 - - - +
399D GLY* 3.5 5.3 - - - -
400D PRO* 4.4 2.5 - - + -
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Residues in contact with GLN 360 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134C LYS* 2.7 26.9 + - - +
298D ILE* 3.7 18.7 - - + +
356D GLN* 2.8 29.1 + - - +
357D LEU* 3.3 25.8 + - - +
359D ALA* 1.3 73.4 - - - +
361D ASN* 1.3 59.0 + - - +
363D GLY* 4.5 1.6 + - - -
398D ASP* 2.7 44.2 + - - +
399D GLY* 3.8 11.2 - - - +
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Residues in contact with ASN 361 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294D CYS* 3.7 15.0 - - + +
297D GLU* 2.8 54.8 + - - +
298D ILE* 3.7 13.8 + - + +
301D ALA* 6.0 0.7 - - - +
318D ALA* 3.4 18.8 - - - +
357D LEU 2.8 21.5 + - - +
358D PHE 3.9 2.5 - - - +
360D GLN* 1.3 75.7 - - - +
362D CYS* 1.3 62.1 + - - +
363D GLY 3.6 0.2 - - - -
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Residues in contact with CYS 362 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318D ALA* 4.0 7.2 - - - -
319D LEU* 3.9 35.9 - - + -
322D ILE* 4.1 16.6 - - + -
358D PHE* 2.8 37.7 + - - +
361D ASN* 1.3 80.2 - - - +
363D GLY* 1.3 66.9 + - - +
364D ASN 3.3 0.3 + - - -
365D HIS* 3.2 27.5 + - + -
366D ILE* 4.6 4.7 - - + +
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Residues in contact with GLY 363 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359D ALA 2.7 21.9 + - - -
360D GLN 4.4 1.9 + - - -
361D ASN 3.6 1.8 - - - -
362D CYS* 1.3 70.8 - - - +
364D ASN* 1.3 64.3 + - - -
365D HIS 3.0 2.1 + - - -
366D ILE* 3.0 24.8 + - - +
399D GLY 3.5 20.0 - - - -
400D PRO* 3.8 6.7 - - - -
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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
------------------------------------------------------------
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