Contacts of the helix formed by residues 266 - 277 (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 ALA 266 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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230B CYS* 5.3 7.0 - - + -
262B TYR* 3.0 10.3 + - + +
263B MET 3.5 2.4 + - - -
264B GLU 3.5 0.2 - - - -
265B GLN* 1.3 83.5 - - + +
267B LEU* 1.3 67.9 + - + +
268B TYR 3.2 2.2 - - - -
269B ALA* 3.0 13.0 + - - +
270B LEU* 2.9 36.0 + - + +
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Residues in contact with LEU 267 (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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226B MET* 5.2 2.5 - - - -
230B CYS* 3.6 24.2 - - - -
233B THR* 5.4 1.3 - - + -
248B LEU* 3.5 44.9 - - + -
259B MET* 5.1 10.5 - - - -
262B TYR* 2.9 35.7 + - + +
263B MET* 3.8 23.6 - - - -
266B ALA* 1.3 74.8 - - - +
268B TYR* 1.3 63.7 + - - +
270B LEU* 4.4 9.2 - - + +
271B THR* 2.9 40.7 + - + +
289B PHE* 4.4 8.1 - - + -
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Residues in contact with TYR 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B MET* 2.9 44.2 + - + +
264B GLU* 4.8 6.5 - - - +
267B LEU* 1.3 80.2 - - - +
269B ALA* 1.3 62.0 + - + +
271B THR* 3.3 8.9 + - - -
272B ILE* 3.2 37.4 - - + +
290B TRP* 4.9 2.4 - + - -
317B PHE* 6.0 3.1 - + - -
320B SER* 3.3 27.0 + - - -
321B SER* 3.1 30.7 - - - -
324B ASP* 2.8 29.9 + - - -
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Residues in contact with ALA 269 (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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265B GLN 6.2 0.2 - - - -
266B ALA* 3.0 11.2 + - - +
268B TYR* 1.3 83.1 - - + +
270B LEU* 1.3 65.7 + - + +
272B ILE* 3.7 5.7 + - - +
273B ALA* 3.4 20.6 + - - +
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Residues in contact with LEU 270 (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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230B CYS* 4.3 26.5 - - + +
233B THR* 4.2 9.0 - - - +
234B GLN* 4.0 33.1 + - + +
245B PHE* 5.9 1.1 - - + -
266B ALA* 2.9 30.4 + - + +
267B LEU* 3.9 8.5 - - + +
269B ALA* 1.3 78.2 - - + +
271B THR* 1.3 61.5 + - + +
273B ALA* 3.6 5.0 - - - +
274B THR* 3.1 32.8 + - - +
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Residues in contact with THR 271 (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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245B PHE* 4.2 18.8 - - + -
267B LEU* 2.9 31.6 + - + +
268B TYR 3.3 5.5 + - - -
270B LEU* 1.3 76.5 - - + +
272B ILE* 1.3 63.1 + - - +
273B ALA 3.3 0.2 - - - -
274B THR* 3.5 5.8 - - - -
275B MET* 3.1 26.0 + - - +
286B THR* 3.2 13.4 + - - -
289B PHE* 3.9 26.4 - - + -
290B TRP* 3.1 30.6 + - - -
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Residues in contact with ILE 272 (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* 3.2 31.8 + - + +
269B ALA* 4.0 6.3 - - - +
271B THR* 1.3 80.6 + - - +
273B ALA* 1.3 64.8 + - - +
275B MET* 3.4 12.2 + - + +
276B LYS* 3.3 35.3 + - - +
290B TRP* 5.0 1.3 - - + -
324B ASP* 3.5 28.3 - - + +
325B VAL* 3.4 36.3 - - + +
328B ASN* 4.0 12.8 + - - +
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Residues in contact with ALA 273 (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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234B GLN* 6.1 0.7 - - - +
269B ALA 3.4 11.6 + - - +
270B LEU* 3.6 11.9 - - + +
271B THR 3.3 0.2 - - - -
272B ILE* 1.3 80.5 - - - +
274B THR* 1.3 59.4 + - + +
276B LYS* 3.1 31.5 + - - +
277B SER* 3.5 4.3 + - - -
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Residues in contact with THR 274 (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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233B THR 5.1 3.4 - - - +
234B GLN* 4.0 24.7 - - - +
241B GLN* 5.2 3.1 - - - +
245B PHE* 3.7 12.4 - - + -
270B LEU 3.1 17.6 + - - +
271B THR* 3.5 5.0 + - - -
273B ALA* 1.3 79.2 - - + +
275B MET* 1.3 64.5 + - - +
276B LYS 3.1 0.2 - - - -
277B SER* 3.2 22.9 + - - +
282B VAL* 3.6 15.1 - - + +
283B ALA* 3.6 5.9 - - - -
286B THR* 3.0 34.7 - - - +
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Residues in contact with MET 275 (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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271B THR 3.1 21.7 + - - +
272B ILE* 3.5 8.5 - - + +
273B ALA 3.2 0.4 - - - -
274B THR* 1.3 77.3 + - - +
276B LYS* 1.3 60.8 + - - +
283B ALA* 3.8 7.2 - - - +
286B THR* 3.7 18.6 + - - +
287B VAL* 4.6 7.4 - - + -
290B TRP* 3.4 37.5 - - + +
325B VAL* 3.7 30.3 - - + +
328B ASN* 3.7 28.8 - - + +
329B LEU* 4.2 13.2 - - + -
332B LEU* 3.7 35.7 - - + +
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Residues in contact with LYS 276 (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* 3.3 32.6 + - - +
273B ALA* 3.1 12.7 + - - +
275B MET* 1.3 78.1 - - - +
277B SER* 1.3 68.6 + - - +
278B PRO* 3.4 2.7 - - - +
328B ASN* 3.7 32.3 - - - +
331B ASN* 6.3 0.4 - - - +
332B LEU* 5.7 0.4 - - - -
335B ARG* 3.4 10.3 + - - +
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Residues in contact with SER 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B ALA 3.5 4.9 + - - -
274B THR* 3.2 20.6 + - - -
276B LYS* 1.3 80.9 - - - +
278B PRO* 1.3 71.7 - - - +
279B ASN* 3.1 24.4 + - - +
282B VAL* 3.5 25.3 - - - +
283B ALA* 4.2 2.6 - - - +
335B ARG* 3.0 16.5 + - - -
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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