Contacts of the helix formed by residues 252 - 267 (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 TRP 252 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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250B PRO* 3.0 8.9 + - + +
251B ASP* 1.3 72.9 + - - +
253B SER* 1.3 56.8 + - - +
254B VAL 3.0 0.2 - - - -
255B VAL* 3.8 14.4 - - + -
256B SER* 2.7 66.0 + - - -
259B LEU* 4.7 4.7 - - + -
284B LEU* 3.6 42.0 - - + -
288B PRO* 6.2 2.7 - - + -
290B GLU* 4.5 9.5 + - + +
291B ALA* 3.5 41.5 - - + +
294B ALA* 3.8 17.9 - - + -
295B VAL* 5.7 0.7 - - + -
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Residues in contact with SER 253 (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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251B ASP* 2.5 23.8 + - - -
252B TRP* 1.3 81.5 - - - +
254B VAL* 1.3 62.0 + - - +
256B SER* 3.6 10.9 + - - -
257B GLN* 3.4 17.7 - - - +
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Residues in contact with VAL 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B LEU* 3.9 29.8 - - + +
213B GLN* 4.8 9.0 - - - +
217B MET* 3.9 31.5 - - + +
251B ASP* 3.0 32.4 + - + +
253B SER* 1.3 79.8 - - - +
255B VAL* 1.3 67.6 + - - +
256B SER 3.2 1.1 - - - -
257B GLN* 3.1 30.5 + - - +
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Residues in contact with VAL 255 (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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212B LEU* 4.1 18.8 - - + -
217B MET* 4.3 11.2 - - + -
242B LEU 4.1 12.3 - - - +
243B CYS* 4.2 12.7 - - - -
250B PRO* 4.0 29.4 - - + -
251B ASP 3.2 15.9 - - - +
252B TRP* 3.8 14.6 - - + -
254B VAL* 1.3 77.8 - - - +
256B SER* 1.3 64.9 + - - +
258B ALA* 3.0 20.8 + - - +
284B LEU* 3.8 30.4 - - + +
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Residues in contact with SER 256 (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 TRP* 2.7 61.9 + - - -
253B SER* 3.6 12.1 + - - -
255B VAL* 1.3 78.5 - - - +
257B GLN* 1.3 65.2 + - - +
258B ALA 3.1 1.4 + - - -
259B LEU* 3.2 28.3 + - - +
260B PRO* 4.4 1.0 - - - +
284B LEU* 5.0 0.7 - - - -
294B ALA* 5.7 0.4 - - - -
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Residues in contact with GLN 257 (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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217B MET* 4.9 7.6 - - + +
221B LEU* 4.0 21.1 - - + +
253B SER 3.4 21.8 - - - +
254B VAL* 3.1 22.8 + - - +
255B VAL 3.0 0.4 - - - -
256B SER* 1.3 79.5 + - - +
258B ALA* 1.3 55.7 + - - +
259B LEU 3.3 0.2 - - - -
260B PRO* 3.2 17.5 - - - +
261B THR* 5.1 1.0 + - - -
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Residues in contact with ALA 258 (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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217B MET* 4.5 6.9 - - + -
221B LEU* 4.2 15.7 - - + -
239B LEU* 4.1 22.9 - - + -
243B CYS* 5.4 2.9 - - - -
254B VAL 4.5 0.4 + - - -
255B VAL 3.0 14.4 + - - +
257B GLN* 1.3 77.6 - - - +
259B LEU* 1.3 64.4 + - - +
260B PRO 3.3 0.7 - - - -
261B THR* 3.1 5.8 + - - -
262B LEU* 3.0 41.4 + - + +
284B LEU* 5.3 0.9 - - + -
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Residues in contact with LEU 259 (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 TRP* 4.7 7.2 - - + -
255B VAL 4.4 0.2 + - - -
256B SER* 3.3 18.1 - - - +
258B ALA* 1.3 76.8 - - - +
260B PRO* 1.3 72.3 - - + +
262B LEU* 3.2 10.4 + - + +
263B ALA* 2.8 24.3 + - - +
281B ILE* 5.5 2.2 - - + -
284B LEU* 3.5 28.5 - - + +
294B ALA* 3.5 42.8 - - + +
295B VAL* 4.2 17.3 - - + +
298B VAL* 4.2 12.2 - - + +
300B ILE* 4.5 14.2 - - + +
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Residues in contact with PRO 260 (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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256B SER 4.4 0.9 - - - +
257B GLN* 3.2 20.0 - - - +
258B ALA 3.5 1.1 - - - -
259B LEU* 1.3 91.9 - - + +
261B THR* 1.3 62.3 + - - +
263B ALA* 3.3 15.3 - - + +
264B LYS* 3.5 12.5 + - - +
298B VAL* 4.0 16.8 - - + -
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Residues in contact with THR 261 (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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221B LEU* 3.4 26.3 + - + +
224B PHE* 3.7 45.3 - - + -
239B LEU* 5.4 0.4 - - + -
257B GLN 5.2 0.7 + - - -
258B ALA* 3.1 8.4 + - - -
260B PRO* 1.3 75.3 - - - +
262B LEU* 1.3 69.6 + - + +
264B LYS* 3.0 19.6 + - + +
265B LEU* 3.0 21.1 + - + +
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Residues in contact with LEU 262 (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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239B LEU* 3.3 34.5 - - + -
243B CYS* 5.4 0.9 - - - -
258B ALA* 3.0 27.8 + - + +
259B LEU* 3.4 12.3 - - + +
261B THR* 1.3 77.8 - - - +
263B ALA* 1.3 62.8 + - - +
265B LEU* 2.9 25.7 + - + +
266B ILE* 3.1 18.3 + - - +
277B ALA* 4.7 5.1 - - + +
280B ALA* 4.3 11.0 - - + -
281B ILE* 3.7 38.4 - - + +
284B LEU* 3.9 27.6 - - + -
300B ILE* 5.0 1.1 - - + -
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Residues in contact with ALA 263 (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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259B LEU 2.8 16.3 + - - +
260B PRO 3.3 13.5 - - - +
262B LEU* 1.3 72.0 - - - +
264B LYS* 1.3 58.3 + - + +
266B ILE* 3.0 29.3 - - - +
267B TYR* 3.4 14.2 - - - -
298B VAL* 4.0 26.5 - - + +
299B ARG 6.1 0.2 - - - -
300B ILE* 4.3 9.8 - - + +
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Residues in contact with LYS 264 (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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260B PRO 3.7 13.5 - - - +
261B THR* 3.0 10.1 + - + +
263B ALA* 1.3 75.0 - - + +
265B LEU* 1.3 66.6 + - + +
266B ILE 3.1 2.2 - - - -
267B TYR* 2.9 28.8 + - - +
268B SER* 4.2 0.3 + - - -
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Residues in contact with LEU 265 (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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224B PHE* 3.8 39.7 - - + -
232B ILE* 4.4 11.0 - - + -
236B THR* 3.9 22.7 - - + +
239B LEU* 4.7 1.3 - - + -
261B THR* 3.0 27.0 + - + +
262B LEU* 2.9 23.9 + - + +
264B LYS* 1.3 77.6 - - + +
266B ILE* 1.3 56.5 + - - +
267B TYR 3.1 5.3 + - - -
268B SER* 3.2 24.3 + - - -
273B THR* 4.5 8.4 - - + +
274B LEU* 4.5 4.9 - - - -
277B ALA* 3.9 17.3 - - + +
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Residues in contact with ILE 266 (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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262B LEU 3.1 6.8 + - - +
263B ALA* 3.0 27.1 - - - +
264B LYS 3.0 0.2 + - - -
265B LEU* 1.3 74.9 - - - +
267B TYR* 1.3 56.2 + - + +
268B SER 3.4 2.2 - - - -
274B LEU* 4.6 9.8 - - + +
277B ALA* 4.2 10.5 - - + -
278B CYS* 4.1 23.6 - - - -
281B ILE* 3.7 24.0 - - + -
300B ILE* 4.1 26.0 - - + -
303B ARG* 3.0 49.8 + - + -
304B LEU* 4.3 4.7 - - + -
307B LEU* 3.9 13.8 - - + +
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Residues in contact with TYR 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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263B ALA 3.4 24.5 - - - -
264B LYS* 2.9 14.2 + - - +
266B ILE* 1.3 78.5 - - + +
268B SER* 1.3 64.5 + - - +
269B MET* 3.9 5.9 + - - +
299B ARG 5.4 2.6 + - - -
303B ARG* 3.5 63.1 - - + +
306B GLU* 4.7 2.8 + - - -
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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