Contacts of the helix formed by residues 271 - 285 (chain B) in PDB entry 1BK6
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 THR 271 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269B MET 3.3 7.2 + - - -
270B ASP* 1.3 72.8 + - - +
272B GLU* 1.3 60.2 + - - +
274B LEU* 3.5 8.5 - - - +
275B VAL* 2.8 50.2 + - + +
310B HIS* 5.0 8.6 + - + +
312B SER* 5.0 11.0 - - - +
314B LEU* 5.4 5.6 - - + -
315B VAL* 4.8 9.2 - - + -
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Residues in contact with GLU 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B ARG* 3.7 34.1 + - + +
270B ASP* 3.4 4.9 + - - +
271B THR* 1.3 79.4 - - - +
273B THR* 1.3 65.6 + - - +
275B VAL* 3.4 5.7 + - - +
276B ASP* 3.2 30.9 + - - +
129E LYS* 4.4 14.6 + - - +
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Residues in contact with THR 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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229B PRO 4.7 1.2 + - - -
232B ILE* 4.4 7.4 - - + +
233B ARG* 3.4 25.4 + - - +
236B THR* 3.6 30.2 - - + +
265B LEU* 4.5 16.8 - - + +
268B SER* 4.0 17.3 - - - +
270B ASP* 2.7 37.5 + - - +
272B GLU* 1.3 73.1 - - - +
274B LEU* 1.3 64.8 + - - +
276B ASP* 3.2 3.6 + - - -
277B ALA* 3.0 19.9 + - - +
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Residues in contact with LEU 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B LEU 4.5 9.4 - - - +
266B ILE* 4.6 13.9 - - - +
268B SER* 4.2 18.1 - - - +
269B MET 5.9 0.7 - - - +
270B ASP 2.9 18.6 + - - +
271B THR* 3.5 9.0 - - - +
273B THR* 1.3 78.6 - - - +
275B VAL* 1.3 63.8 + - - +
277B ALA* 3.2 3.0 + - - +
278B CYS* 3.2 38.0 + - - -
303B ARG* 6.1 0.9 - - - +
307B LEU* 4.2 18.2 - - + -
310B HIS* 4.0 18.6 - - + +
315B VAL* 3.8 26.7 - - + -
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Residues in contact with VAL 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B THR* 2.8 40.1 + - + +
272B GLU* 3.7 6.7 - - - +
274B LEU* 1.3 77.2 - - - +
276B ASP* 1.3 67.9 + - - +
278B CYS* 3.3 5.8 + - - +
279B TRP* 3.3 36.4 + - + +
314B LEU* 3.8 43.1 - - + +
315B VAL* 4.0 10.3 - - + -
318B PRO* 4.2 0.6 - - - +
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Residues in contact with ASP 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B ARG* 5.1 2.1 - - - +
236B THR* 4.0 20.8 - - + +
237B TRP* 3.7 31.4 - - - +
240B SER* 3.8 14.9 + - - -
272B GLU* 3.2 18.2 + - - +
273B THR 3.2 5.1 + - - +
275B VAL* 1.3 80.7 - - - +
277B ALA* 1.3 64.6 + - - +
279B TRP* 3.9 11.7 - - - -
280B ALA* 3.1 22.2 + - - +
127E LYS* 4.1 17.2 + - - -
129E LYS* 4.4 5.0 + - - -
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Residues in contact with ALA 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B THR* 3.8 9.1 - - + +
262B LEU* 4.7 5.9 - - + +
265B LEU* 3.9 32.8 - - + -
266B ILE* 4.2 12.3 - - + -
273B THR 3.0 13.1 + - - +
274B LEU 3.2 8.9 + - - +
276B ASP* 1.3 75.6 - - - +
278B CYS* 1.3 64.4 + - - +
280B ALA* 3.3 6.7 + - - +
281B ILE* 3.0 29.4 + - - +
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Residues in contact with CYS 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B ILE* 4.1 7.0 - - - -
274B LEU* 3.2 33.7 + - - -
275B VAL* 3.3 8.0 + - - +
277B ALA* 1.3 79.9 - - - +
279B TRP* 1.3 58.0 + - - +
281B ILE* 3.2 10.9 + - - +
282B SER* 2.9 28.6 + - - -
304B LEU* 5.1 4.9 - - + +
307B LEU* 3.9 18.8 - - - -
315B VAL* 4.6 12.3 - - - -
318B PRO* 3.7 22.2 - - + +
319B ALA* 4.3 11.2 - - - +
322B ALA* 4.9 0.9 - - - +
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Residues in contact with TRP 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491A GLN* 3.8 48.0 - - + +
240B SER* 4.0 10.8 - - - +
275B VAL* 3.3 36.9 + - + +
276B ASP* 3.9 14.1 - - - +
277B ALA 3.4 0.2 - - - -
278B CYS* 1.3 77.2 - - - +
280B ALA* 1.3 62.7 + - - +
282B SER* 2.7 37.2 + - - -
283B TYR* 3.0 45.9 + + + +
314B LEU 4.7 0.6 + - - -
317B THR* 3.7 30.7 - - + -
318B PRO* 3.5 23.6 - - + +
321B ARG* 4.3 21.5 - - + -
127E LYS* 6.1 2.0 - - - -
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Residues in contact with ALA 280 (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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236B THR* 5.6 1.1 - - + +
239B LEU* 5.0 4.0 - - + +
240B SER* 4.1 18.1 + - - +
243B CYS* 4.2 10.4 - - - +
262B LEU* 4.3 19.1 - - + -
276B ASP 3.1 15.0 + - - +
277B ALA* 3.5 11.2 - - - +
278B CYS 3.2 0.2 - - - -
279B TRP* 1.3 76.6 - - - +
281B ILE* 1.3 61.9 + - - +
283B TYR* 3.0 24.0 + - - +
284B LEU* 3.1 17.0 + - - +
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Residues in contact with ILE 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B LEU* 5.5 0.9 - - + -
262B LEU* 3.7 29.4 - - + -
266B ILE* 3.7 35.4 - - + -
277B ALA 3.0 12.7 + - - +
278B CYS* 3.2 7.8 + - - +
280B ALA* 1.3 76.0 - - - +
282B SER* 1.3 57.3 + - - +
284B LEU* 3.3 7.2 + - - +
285B SER* 2.7 40.0 + - - +
295B VAL* 4.4 9.6 - - + -
300B ILE* 3.7 39.9 - - + -
304B LEU* 4.3 15.5 - - + -
322B ALA* 4.4 1.8 - - + -
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Residues in contact with SER 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B CYS 2.9 13.1 + - - -
279B TRP* 2.7 39.7 + - - -
281B ILE* 1.3 76.5 - - - +
283B TYR* 1.3 65.7 + - - +
285B SER* 3.5 1.1 + - - -
286B ASP* 3.4 8.7 + - - +
318B PRO 3.7 17.3 - - - -
321B ARG* 4.1 12.0 - - - +
322B ALA* 3.7 21.5 - - - +
325B ASN* 3.3 19.6 + - - -
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Residues in contact with TYR 283 (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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240B SER* 3.7 23.5 + - - -
243B CYS 3.7 19.6 - - - +
244B ARG* 3.3 70.4 + - + -
245B GLY 5.3 1.1 - - - +
249B GLN* 4.2 3.1 - - - +
279B TRP* 3.0 58.3 + + + +
280B ALA* 3.0 9.9 + - - +
282B SER* 1.3 78.5 - - - +
284B LEU* 1.3 59.4 + - - +
285B SER 3.1 2.0 - - - -
286B ASP* 2.6 38.9 - - - +
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Residues in contact with LEU 284 (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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243B CYS* 3.8 20.4 - - + +
250B PRO* 5.4 1.8 - - + -
252B TRP* 3.6 20.1 - - + -
255B VAL* 3.8 48.5 - - + +
256B SER* 5.0 1.3 - - - -
258B ALA* 5.3 0.2 - - + -
259B LEU* 3.5 33.2 - - + +
262B LEU* 3.9 19.3 - - + -
280B ALA 3.1 14.3 + - - +
281B ILE* 3.3 7.4 + - - +
283B TYR* 1.3 77.4 - - - +
285B SER* 1.3 59.7 + - - +
286B ASP* 3.4 0.4 - - - -
287B GLY* 4.1 2.0 + - - -
291B ALA* 3.5 25.3 - - - +
295B VAL* 5.1 3.1 - - + -
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Residues in contact with SER 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B ILE* 2.7 26.6 + - - +
282B SER* 3.7 9.1 - - - -
283B TYR 3.1 0.4 - - - -
284B LEU* 1.3 77.2 - - - +
286B ASP* 1.3 55.9 + - - +
287B GLY 2.7 18.5 + - - +
291B ALA* 5.2 1.6 - - - -
292B ILE* 4.3 14.0 - - - +
295B VAL* 3.7 21.7 - - - +
322B ALA* 4.3 9.6 + - - +
325B ASN* 3.6 27.1 - - - +
326B ILE* 4.8 6.2 - - - +
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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