Contacts of the helix formed by residues 316 - 333 (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 316 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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297B GLU* 3.4 6.3 + - - -
313B GLN* 5.9 0.6 + - - -
314B SER* 2.9 35.2 + - - -
315B TYR* 1.3 81.1 + - - +
317B PHE* 1.3 66.0 + - - +
318B ALA 3.2 2.7 - - - -
319B LEU* 3.9 30.6 - - + +
320B SER* 2.9 26.9 + - - +
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Residues in contact with PHE 317 (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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252B MET* 4.4 5.8 - - - -
256B TYR* 3.6 29.6 - + - -
259B MET* 3.9 10.3 - - + -
260B LYS* 3.6 23.8 - - + -
263B MET* 3.5 45.3 - - + -
264B GLU* 6.0 0.7 - - + -
268B TYR* 6.0 3.4 - + - -
290B TRP* 3.9 8.1 - - + -
293B ILE* 3.8 19.5 - - + -
297B GLU* 2.6 24.3 + - - +
315B TYR* 3.6 32.1 - + + -
316B ASN* 1.3 74.4 - - - +
318B ALA* 1.3 58.9 + - - +
320B SER* 3.4 4.5 + - - -
321B SER* 2.5 32.8 + - - -
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Residues in contact with ALA 318 (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* 4.0 5.4 - - - -
293B ILE* 4.2 3.3 - - + +
294B CYS* 4.0 9.9 - - - -
297B GLU* 3.4 4.4 + - - +
316B ASN 3.2 0.4 - - - -
317B PHE* 1.3 79.0 - - - +
319B LEU* 1.3 54.4 + - - +
321B SER* 2.7 24.1 + - - -
322B ILE* 3.2 13.2 + - - +
358B PHE* 3.5 30.3 - - + -
361B ASN* 3.4 28.7 - - - +
362B CYS* 3.8 6.3 - - - -
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Residues in contact with LEU 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B GLU* 4.8 0.4 + - - -
316B ASN* 3.4 31.3 + - + +
318B ALA* 1.3 77.9 - - - +
320B SER* 1.3 62.0 + - - +
321B SER 3.1 1.2 + - - -
322B ILE* 3.4 20.8 + - + +
361B ASN* 5.3 0.2 - - - +
362B CYS* 3.7 21.1 - - + -
365B HIS* 3.9 43.3 - - + +
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Residues in contact with SER 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B TYR* 3.3 16.4 + - - -
315B TYR 4.5 4.2 + - - -
316B ASN* 2.9 24.0 + - - +
317B PHE* 3.7 7.0 - - - -
319B LEU* 1.3 75.0 - - - +
321B SER* 1.3 58.6 + - - +
322B ILE 3.5 0.8 + - - -
323B LYS* 5.1 3.1 + - - +
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Residues in contact with SER 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B TYR* 3.1 27.6 - - - -
290B TRP* 3.1 28.1 - - - -
317B PHE* 2.5 22.2 + - - -
318B ALA 2.7 11.6 + - - -
320B SER* 1.3 71.2 - - - +
322B ILE* 1.3 56.7 + - - +
323B LYS 3.1 3.1 - - - -
324B ASP* 3.1 4.8 + - - -
325B VAL* 2.7 45.7 + - - +
358B PHE* 5.1 0.2 - - - -
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Residues in contact with ILE 322 (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 3.2 9.6 + - - +
319B LEU* 3.4 22.8 + - + +
320B SER 3.5 0.6 - - - -
321B SER* 1.3 78.3 - - - +
323B LYS* 1.3 67.8 + - - +
326B VAL* 3.3 22.7 + - + -
327B PRO* 3.2 19.9 - - - +
358B PHE* 3.9 14.6 - - + -
362B CYS* 3.7 29.4 - - + -
365B HIS* 3.8 28.3 - - + +
366B ILE* 4.6 3.1 - - + +
369B PRO* 3.8 24.5 - - + +
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Residues in contact with LYS 323 (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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320B SER 5.1 3.1 + - - +
321B SER 3.1 1.2 - - - -
322B ILE* 1.3 88.8 - - - +
324B ASP* 1.3 64.4 + - - +
327B PRO* 3.4 17.9 - - - +
368B GLU* 5.8 6.7 - - - -
369B PRO* 5.9 9.0 - - + -
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Residues in contact with ASP 324 (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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268B TYR* 2.8 32.7 + - - +
272B ILE* 3.5 29.2 - - + +
321B SER* 3.1 5.1 + - - +
323B LYS* 1.3 83.1 - - - +
325B VAL* 1.3 60.1 + - - +
326B VAL 3.6 0.2 - - - -
327B PRO* 3.6 8.7 - - - +
328B ASN* 2.8 28.2 + - - +
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Residues in contact with VAL 325 (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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272B ILE* 3.4 24.0 - - + -
275B MET* 3.7 21.8 - - + -
290B TRP* 3.9 20.2 - - + +
321B SER* 2.7 37.3 + - - +
324B ASP* 1.3 71.5 - - - +
326B VAL* 1.3 65.9 + - - +
328B ASN* 3.1 9.1 + - - +
329B LEU* 2.9 26.7 + - + +
358B PHE* 3.8 30.5 - - + -
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Residues in contact with VAL 326 (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* 3.3 28.1 + - + +
325B VAL* 1.3 75.4 - - - +
327B PRO* 1.3 72.5 - - + +
329B LEU* 3.1 8.4 + - + +
330B LEU* 2.9 38.1 + - + +
355B LEU* 4.0 18.8 - - + -
358B PHE* 3.7 33.2 - - + -
366B ILE* 3.7 10.3 - - + -
369B PRO* 4.2 15.7 - - + -
370B VAL* 4.2 3.4 - - + -
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Residues in contact with PRO 327 (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 3.2 15.0 - - - +
323B LYS* 3.4 21.1 - - + +
324B ASP 3.6 6.3 - - - +
326B VAL* 1.3 93.8 - - + +
328B ASN* 1.3 57.9 + - - +
330B LEU* 3.4 14.1 + - + +
331B ASN* 3.0 26.7 + - - +
369B PRO* 4.9 11.2 - - + -
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Residues in contact with ASN 328 (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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272B ILE* 4.0 25.7 + - - +
275B MET* 3.7 21.8 - - + +
276B LYS* 3.7 29.1 - - + +
324B ASP* 2.8 24.3 + - - +
325B VAL* 3.1 9.2 + - - +
327B PRO* 1.3 76.6 - - - +
329B LEU* 1.3 61.9 - - - +
331B ASN* 3.5 9.3 + - - +
332B LEU* 3.1 30.1 + - - +
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Residues in contact with LEU 329 (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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275B MET* 4.2 5.8 - - + -
287B VAL* 3.9 37.7 - - + -
325B VAL* 2.9 33.2 + - + +
326B VAL* 3.1 12.8 + - - +
328B ASN* 1.3 75.6 - - - +
330B LEU* 1.3 65.1 + - - +
332B LEU* 3.0 14.9 + - - +
333B LEU* 3.2 15.8 + - - +
351B ALA* 3.7 22.7 - - + +
354B CYS* 3.8 24.0 - - + -
355B LEU* 4.6 16.8 - - + +
358B PHE* 4.0 13.5 - - + -
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Residues in contact with LEU 330 (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* 2.9 34.0 + - + +
327B PRO* 3.7 11.4 - - + +
329B LEU* 1.3 75.4 - - - +
331B ASN* 1.3 62.0 + - - +
333B LEU* 3.3 24.0 + - + +
334B THR* 4.1 2.4 + - - +
355B LEU* 3.7 29.2 - - + -
369B PRO* 3.7 15.5 - - + +
370B VAL* 4.3 6.5 - - + -
373B PHE* 3.6 55.3 - - + -
392B ALA* 3.8 21.3 - - + -
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Residues in contact with ASN 331 (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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276B LYS* 6.3 0.4 - - - +
327B PRO 3.0 13.9 + - - +
328B ASN* 3.5 13.9 + - - +
329B LEU 3.1 0.2 - - - -
330B LEU* 1.3 78.0 - - - +
332B LEU* 1.3 68.9 + - - +
334B THR* 2.7 31.0 + - - -
335B ARG* 4.5 12.7 + - - +
373B PHE* 4.7 3.5 - - - -
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Residues in contact with LEU 332 (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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275B MET* 3.7 29.8 - - + +
276B LYS* 5.7 0.2 - - - -
283B ALA* 4.2 8.1 - - + -
287B VAL* 3.5 32.3 - - + -
328B ASN 3.1 16.8 + - - +
329B LEU* 3.0 13.9 + - + +
331B ASN* 1.3 76.5 - - - +
333B LEU* 1.3 62.9 + - - +
334B THR 3.1 2.7 - - - -
335B ARG* 3.1 51.2 + - - +
347B VAL* 4.1 14.1 - - + -
348B SER* 3.2 15.8 + - - -
351B ALA* 3.8 8.7 - - + -
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Residues in contact with LEU 333 (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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329B LEU 3.2 10.2 + - - +
330B LEU* 3.4 36.8 - - + +
331B ASN 3.2 1.0 - - - -
332B LEU* 1.3 77.0 - - - +
334B THR* 1.3 55.9 + - - +
335B ARG 3.2 1.7 + - - -
336B GLN* 3.1 27.5 + - - +
348B SER* 3.5 15.2 - - - +
351B ALA* 3.8 4.5 - - + +
352B GLY* 3.5 35.9 - - - +
355B LEU* 4.3 7.2 - - + -
373B PHE* 5.2 0.7 - - + -
387B GLU* 4.1 1.7 - - - +
388B ALA* 3.7 32.4 - - + +
391B MET* 4.1 13.2 - - + -
392B ALA* 4.1 11.7 - - + +
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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