Contacts of the helix formed by residues 382 - 395 (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 382 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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380D ALA* 3.3 2.1 - - - +
381D ASP* 1.3 79.2 - - + +
383D TRP* 1.3 89.3 + - - +
384D ARG* 3.4 26.7 - - - +
385D ASN* 3.2 29.7 + - - +
386D ARG* 3.2 23.2 + - - +
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Residues in contact with TRP 383 (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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336D GLN* 4.1 24.0 - - + -
337D ASN 4.0 13.2 - - - -
338D GLU* 4.0 27.0 + - - -
381D ASP 3.9 0.6 + - - -
382D ASN* 1.3 92.3 - - - +
384D ARG* 1.3 96.5 + - + +
386D ARG* 2.9 32.0 + - - +
387D GLU* 2.6 40.3 + - + +
424D SER* 3.4 28.7 - - - +
426D GLN* 3.3 44.9 - - + -
427D VAL* 3.6 1.4 - - + +
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Residues in contact with ARG 384 (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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334D THR* 3.1 24.7 + - - +
335D ARG* 3.7 2.2 - - - +
336D GLN* 2.9 82.0 + - - +
338D GLU* 3.4 43.0 + - - +
382D ASN* 3.9 21.3 - - - +
383D TRP* 1.3 103.2 - - + +
385D ASN* 1.3 60.2 + - - +
388D ALA* 3.1 17.2 + - - +
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Residues in contact with ASN 385 (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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334D THR* 4.0 16.9 - - - +
377D ASN* 2.8 40.0 - - - +
380D ALA* 3.9 17.6 - - + +
382D ASN* 3.2 34.7 + - - +
383D TRP 3.1 0.6 - - - -
384D ARG* 1.3 79.2 - - - +
386D ARG* 1.3 64.2 + - - +
388D ALA* 3.4 1.4 + - - +
389D ALA* 3.0 18.7 + - - +
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Residues in contact with ARG 386 (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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377D ASN 3.4 11.2 - - - +
378D ILE 3.4 24.5 - - - +
379D THR* 4.5 2.7 - - - +
380D ALA 3.0 32.9 + - - +
381D ASP 3.1 16.6 + - - -
382D ASN 3.2 10.8 + - - +
383D TRP* 2.9 34.6 + - - +
385D ASN* 1.3 77.7 - - - +
387D GLU* 1.3 62.6 + - - +
389D ALA* 3.4 9.7 + - - +
390D VAL* 3.3 17.4 + - - +
419D LEU* 4.3 8.8 - - + +
422D ASP* 2.9 42.7 + - - -
423D GLN* 5.2 3.0 - - - +
424D SER* 3.9 4.8 - - - +
427D VAL* 3.9 10.3 - - + +
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Residues in contact with GLU 387 (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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333D LEU 3.9 1.6 - - - +
336D GLN* 2.4 45.2 + - - +
383D TRP* 2.6 25.4 + - + +
386D ARG* 1.3 74.0 - - - +
388D ALA* 1.3 57.3 + - - +
389D ALA 3.2 0.3 + - - -
390D VAL* 3.3 9.9 - - - +
391D MET* 2.9 51.6 + - - +
426D GLN* 3.7 23.6 - - + +
427D VAL* 3.7 12.1 - - + +
430D THR* 2.9 28.5 + - - +
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Residues in contact with ALA 388 (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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333D LEU* 3.6 27.9 - - + +
334D THR* 3.6 19.1 - - + -
373D PHE* 3.7 10.3 - - + -
384D ARG 3.1 21.7 + - - +
385D ASN 3.8 3.4 - - - +
386D ARG 3.4 0.2 - - - -
387D GLU* 1.3 82.2 + - - +
389D ALA* 1.3 53.3 + - - +
391D MET* 3.5 6.1 - - - +
392D ALA* 2.8 35.0 + - - +
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Residues in contact with ALA 389 (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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373D PHE* 4.0 8.9 - - - -
374D VAL* 3.2 26.8 - - - +
377D ASN* 3.9 4.0 - - + -
378D ILE* 3.7 32.3 - - + +
385D ASN 3.0 16.9 + - - +
386D ARG 3.5 6.5 - - - +
387D GLU 3.1 0.4 - - - -
388D ALA* 1.3 78.6 - - - +
390D VAL* 1.3 57.3 + - - +
392D ALA* 3.3 1.1 + - - -
393D PHE* 3.0 23.2 + - - +
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Residues in contact with VAL 390 (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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378D ILE* 4.1 8.1 - - + -
386D ARG 3.3 12.3 - - - +
387D GLU* 3.3 19.5 - - - +
389D ALA* 1.3 73.0 - - - +
391D MET* 1.3 64.6 + - - +
393D PHE* 3.4 3.5 + - - +
394D GLY* 3.0 19.6 + - - -
416D ILE* 4.2 25.6 - - + -
419D LEU* 3.5 26.2 - - + -
427D VAL* 4.3 2.7 - - + +
430D THR* 3.9 14.4 - - + -
431D THR* 3.9 25.8 - - - +
433D TRP* 4.3 0.5 - - - -
434D CYS* 3.6 14.1 - - + +
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Residues in contact with MET 391 (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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333D LEU* 4.0 25.8 - - + +
336D GLN* 6.3 0.7 - - + -
348D SER 5.9 2.0 - - - +
349D MET* 6.2 6.7 - - + -
352D GLY* 5.1 6.5 - - - -
356D GLN* 6.0 0.4 - - - -
387D GLU* 2.9 43.1 + - - +
388D ALA* 3.5 8.7 - - - +
390D VAL* 1.3 79.2 - - - +
392D ALA* 1.3 65.2 + - - +
394D GLY* 3.1 6.8 + - - -
395D SER* 3.1 23.6 + - - +
430D THR* 3.5 15.2 - - + +
433D TRP* 3.8 27.2 - - + -
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Residues in contact with ALA 392 (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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330D LEU* 3.9 26.9 - - + -
333D LEU* 3.9 8.7 - - + -
355D LEU* 4.0 6.9 - - - +
370D VAL* 3.9 5.5 - - + +
373D PHE* 4.1 5.2 - - + -
374D VAL* 3.9 11.9 - - + -
388D ALA 2.8 22.5 + - - +
389D ALA 3.3 6.3 + - - +
391D MET* 1.3 74.1 - - - +
393D PHE* 1.3 64.0 + - - +
395D SER* 3.2 13.7 + - - -
396D ILE* 3.6 13.3 + - - +
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Residues in contact with PHE 393 (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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370D VAL* 4.6 0.4 - - - -
371D LEU* 3.6 31.9 - - + -
374D VAL* 4.0 20.9 - - + -
389D ALA 3.0 16.1 + - - +
390D VAL* 3.8 6.7 - - + +
391D MET 3.2 0.4 - - - -
392D ALA* 1.3 77.6 - - - +
394D GLY* 1.3 62.4 + - - +
396D ILE* 3.1 25.9 + - + +
397D MET* 3.3 36.9 - - + +
408D TYR* 4.0 20.0 - - + -
409D VAL* 4.1 14.6 - - + -
412D ALA* 3.9 16.2 - - + -
416D ILE* 3.7 24.9 - - + -
434D CYS* 3.9 9.2 - - - -
438D ILE* 4.4 4.9 - - + -
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Residues in contact with GLY 394 (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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390D VAL 3.0 14.6 + - - -
391D MET 3.1 3.1 + - - -
393D PHE* 1.3 75.9 - - - +
395D SER* 1.3 60.6 + - - +
396D ILE 3.3 1.2 + - - -
397D MET* 3.4 11.7 + - - +
433D TRP* 4.0 17.3 - - - -
434D CYS* 3.9 13.4 - - - -
437D ARG* 3.3 33.4 + - - +
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Residues in contact with SER 395 (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* 4.1 8.5 + - - -
355D LEU* 4.2 16.6 - - - +
356D GLN* 3.4 55.7 + - - +
359D ALA* 3.7 5.0 - - - +
391D MET* 3.1 19.7 + - - +
392D ALA* 3.5 10.7 - - - -
393D PHE 3.1 1.2 - - - -
394D GLY* 1.3 77.4 - - - +
396D ILE* 1.3 58.2 + - - +
397D MET 3.5 1.0 + - - -
398D ASP 4.4 2.9 - - - +
433D TRP* 3.8 5.7 - - - -
437D ARG* 4.4 2.9 + - - -
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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