Contacts of the helix formed by residues 237 - 255 (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 ASP 237 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195D LYS* 2.7 52.0 + - + +
235D ALA* 3.3 2.7 - - + +
236D GLU* 1.3 78.5 - - - +
238D ILE* 1.3 65.5 + - - +
239D GLU 3.1 14.7 + - - -
240D VAL* 3.3 21.4 + - + +
241D GLN* 3.2 24.4 + - - +
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Residues in contact with ILE 238 (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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195D LYS* 5.5 1.8 - - - +
236D GLU 3.6 3.9 + - - +
237D ASP* 1.3 73.9 + - - +
239D GLU* 1.3 72.2 + - + +
241D GLN* 3.5 8.5 + - - +
242D ALA* 3.1 22.9 + - - +
279D ASN* 3.5 18.8 - - - +
281D LYS* 3.9 18.2 - - + -
282D VAL* 3.3 35.2 - - + -
285D MET* 3.5 20.4 - - + +
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Residues in contact with GLU 239 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195D LYS* 2.8 29.6 + - - +
199D LEU* 3.3 33.4 - - + +
237D ASP* 3.1 7.5 + - - +
238D ILE* 1.3 88.9 - - + +
240D VAL* 1.3 59.6 + - - +
242D ALA* 3.3 7.5 + - - +
243D ALA 3.0 23.2 + - - -
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Residues in contact with VAL 240 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195D LYS* 4.0 28.3 - - + +
198D ARG* 3.7 30.1 - - + +
199D LEU* 3.8 11.4 - - + +
202D LEU* 3.6 18.6 - - + +
232D ALA* 4.1 3.8 - - + +
235D ALA* 3.6 20.2 - - + -
237D ASP* 3.3 24.4 + - + +
239D GLU* 1.3 73.3 - - - +
241D GLN* 1.3 65.2 + - - +
243D ALA* 3.3 3.9 + - - +
244D ALA* 3.0 19.9 + - - +
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Residues in contact with GLN 241 (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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232D ALA 3.6 7.9 - - - -
233D THR* 2.7 27.5 + - - +
234D GLN* 4.0 4.4 + - - +
235D ALA 3.1 33.1 + - - +
236D GLU 4.7 2.3 - - - +
237D ASP 3.2 7.1 + - - +
238D ILE* 3.5 18.3 - - - +
240D VAL* 1.3 79.0 - - - +
242D ALA* 1.3 57.5 + - - +
244D ALA* 3.0 4.9 + - - +
245D PHE* 2.9 32.3 + - + -
274D THR* 4.6 5.3 - - - +
282D VAL* 3.3 37.7 - - - +
285D MET* 3.5 12.3 - - - -
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Residues in contact with ALA 242 (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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238D ILE 3.1 12.7 + - - +
239D GLU* 3.3 8.5 + - - +
241D GLN* 1.3 75.0 - - - +
243D ALA* 1.3 61.2 + - - +
245D PHE* 3.9 0.9 - - - +
246D GLY* 2.9 25.1 + - - -
281D LYS* 6.6 0.2 - - + -
285D MET* 3.3 26.7 - - + -
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Residues in contact with ALA 243 (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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199D LEU* 3.8 12.8 - - + -
202D LEU* 3.7 27.2 - - + +
203D ASN* 3.8 19.0 - - - +
206D ALA* 5.9 0.7 - - - +
239D GLU 3.0 13.0 + - - +
240D VAL 3.4 8.5 - - - +
242D ALA* 1.3 75.4 - - - +
244D ALA* 1.3 64.7 + - - +
246D GLY* 3.3 2.5 + - - -
247D CYS* 3.0 24.1 + - - +
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Residues in contact with ALA 244 (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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202D LEU* 4.2 8.2 - - - +
229D VAL* 3.7 13.0 - - - +
232D ALA* 3.4 21.1 - - + -
233D THR* 3.3 34.1 - - + +
240D VAL 3.0 7.3 + - - +
241D GLN 3.0 7.8 + - - +
243D ALA* 1.3 76.3 - - - +
245D PHE* 1.3 63.4 + - - +
247D CYS* 3.0 9.4 + - - +
248D LEU* 2.9 18.7 + - - +
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Residues in contact with PHE 245 (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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233D THR* 3.8 36.1 - - + +
234D GLN* 5.3 0.7 - - - -
241D GLN* 2.9 26.0 + - - +
242D ALA 4.1 3.4 - - - +
244D ALA* 1.3 71.7 - - - +
246D GLY* 1.3 66.5 + - - +
248D LEU* 3.2 13.6 + - + +
249D CYS* 2.9 31.5 + - - -
271D THR* 4.3 15.5 - - + -
274D THR* 3.9 13.7 - - + -
282D VAL* 5.0 1.1 - - + -
285D MET* 3.6 44.2 - - + +
286D THR* 3.6 32.3 - - + -
289D PHE* 3.9 23.6 - + + -
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Residues in contact with GLY 246 (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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142C LYS* 6.6 0.2 - - - -
206D ALA* 5.3 3.8 - - - -
242D ALA 2.9 16.4 + - - -
243D ALA* 3.6 4.7 - - - -
244D ALA 3.2 0.2 - - - -
245D PHE* 1.3 77.2 - - - +
247D CYS* 1.3 60.8 + - - +
249D CYS* 3.4 7.2 + - - +
250D LYS* 3.2 26.2 + - - +
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Residues in contact with CYS 247 (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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202D LEU* 3.2 32.8 - - + -
205D LEU* 4.0 20.0 - - - -
206D ALA* 3.6 21.9 - - - +
209D LEU* 4.1 2.0 - - - +
229D VAL* 4.0 14.4 - - + -
243D ALA 3.0 9.6 + - - +
244D ALA* 3.0 12.2 + - - +
246D GLY* 1.3 75.4 - - - +
248D LEU* 1.3 52.3 + - - +
250D LYS* 3.1 7.5 + - - +
251D ILE* 2.8 44.3 + - + +
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Residues in contact with LEU 248 (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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226D MET* 4.0 16.4 - - + -
229D VAL* 3.7 24.7 - - + -
230D CYS* 5.0 1.8 - - - -
233D THR* 3.7 20.4 - - + -
244D ALA 2.9 9.5 + - - +
245D PHE* 3.5 21.3 - - + +
247D CYS* 1.3 74.8 - - - +
249D CYS* 1.3 56.4 + - - +
251D ILE* 3.4 5.4 + - + +
252D MET* 2.8 31.7 + - - +
259D MET* 5.8 2.1 - - - +
267D LEU* 3.4 46.7 - - + -
289D PHE* 3.8 22.5 - - + -
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Residues in contact with CYS 249 (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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245D PHE* 2.9 22.8 + - - +
246D GLY* 3.6 7.2 - - - +
248D LEU* 1.3 75.9 - - - +
250D LYS* 1.3 62.7 + - + +
252D MET* 3.1 5.6 + - - +
253D SER* 2.8 29.4 + - - +
285D MET 5.4 0.4 - - - -
288D GLU* 4.2 7.2 - - - -
289D PHE* 3.7 28.7 - - - -
292D THR* 3.4 30.2 - - + +
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Residues in contact with LYS 250 (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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164D GLU* 6.2 1.0 - - - +
206D ALA* 3.2 38.0 + - + +
207D ASP* 4.8 5.1 + - - +
209D LEU* 3.4 21.7 - - + +
210D ILE* 5.1 11.8 - - - +
211D PHE* 6.3 0.8 - - - -
246D GLY 3.2 12.0 + - - +
247D CYS* 3.1 6.7 + - - +
249D CYS* 1.3 77.9 - - + +
251D ILE* 1.3 58.0 + - - +
253D SER* 3.1 7.1 + - - -
254D LYS* 2.8 45.9 + - - +
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Residues in contact with ILE 251 (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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205D LEU* 5.4 0.2 - - + -
209D LEU* 3.5 31.0 - - + -
216D MET* 3.9 16.6 - - + -
225D LEU* 4.2 9.2 - - + -
226D MET* 3.3 36.1 - - + -
229D VAL* 4.5 2.9 - - + -
247D CYS* 2.8 37.4 + - + +
248D LEU* 3.8 6.3 - - + +
250D LYS* 1.3 72.2 - - - +
252D MET* 1.3 55.9 + - - +
255D TYR* 2.6 38.9 + - + -
259D MET* 3.6 32.8 - - + -
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Residues in contact with MET 252 (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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248D LEU 2.8 22.4 + - - +
249D CYS* 3.5 6.3 - - - +
251D ILE* 1.3 74.1 - - - +
253D SER* 1.3 60.8 + - - +
256D TYR* 3.4 54.8 + - + +
259D MET* 3.8 32.1 - - + -
263D MET* 4.0 14.4 - - + -
267D LEU* 5.7 0.2 - - + -
289D PHE* 3.8 22.2 - - + -
292D THR* 4.3 12.6 - - + +
293D ILE* 3.7 39.7 - - + -
296D GLU* 4.5 4.6 - - + +
317D PHE* 4.4 2.0 - - + -
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Residues in contact with SER 253 (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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309B GLN 4.6 2.4 - - - +
311B PRO* 3.8 10.9 - - - +
249D CYS 2.8 15.3 + - - -
250D LYS* 3.4 9.3 - - - -
252D MET* 1.3 78.0 - - - +
254D LYS* 1.3 75.6 + - - +
292D THR* 3.4 15.9 - - - +
296D GLU* 3.5 32.9 - - - +
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Residues in contact with LYS 254 (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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309B GLN* 4.9 14.0 + - - +
311B PRO* 3.9 19.6 - - - +
313B GLN* 6.0 0.3 + - - -
209D LEU* 4.8 8.3 - - + -
210D ILE* 3.6 37.0 - - + -
250D LYS* 2.8 35.6 + - - +
253D SER* 1.3 89.8 + - - +
255D TYR* 1.3 93.1 + - + +
256D TYR 3.7 1.1 - - - -
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Residues in contact with TYR 255 (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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311B PRO 5.9 0.2 - - - -
313B GLN* 5.0 10.3 - - - -
209D LEU* 2.9 34.3 + - + -
210D ILE* 4.2 4.2 - - - +
213D LYS* 3.2 29.8 - - + +
216D MET* 3.4 50.0 - - + -
217D GLU* 5.4 2.2 - - + -
251D ILE* 2.6 29.7 + - + +
254D LYS* 1.3 105.8 - - + +
256D TYR* 1.3 65.0 + - - +
257D THR* 3.1 8.5 - - + +
258D PHE* 2.9 37.3 + + + -
259D MET* 3.5 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
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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