Contacts of the helix formed by residues 234 - 257 (chain B) in PDB entry 1PBW
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 HIS 234 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B PRO* 4.1 18.4 - - + +
232B ILE 3.6 2.6 + - - -
233B PRO* 1.3 70.8 - - + +
235B GLN* 1.3 61.3 + - - +
236B TYR 3.1 1.0 + - - -
237B TRP* 3.3 9.7 + - + +
238B LEU* 2.9 44.5 + - + +
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Residues in contact with GLN 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B LEU* 3.6 18.8 - - + +
119B ALA* 3.2 25.3 + - + +
122B PHE* 2.9 61.3 + - + +
123B ALA* 3.8 12.9 - - - +
124B PRO* 4.1 11.5 - - + +
233B PRO* 3.1 18.1 + - - +
234B HIS* 1.3 77.1 + - - +
236B TYR* 1.3 56.8 + - + +
238B LEU* 4.3 0.9 - - - -
239B THR* 2.6 36.9 + - - -
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Residues in contact with TYR 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B ASP* 2.7 39.6 + - - -
118B LEU* 3.8 25.8 + - + -
119B ALA* 4.5 2.7 - - + -
195B ASN* 3.2 22.1 + - + +
196B PRO 3.4 19.1 - - - -
197B VAL* 3.4 27.2 - - - +
199B PRO* 3.6 11.4 - - + -
227B ILE* 4.3 7.6 - - + -
232B ILE* 3.8 26.5 - - + -
233B PRO* 3.7 28.9 - - + -
234B HIS 3.1 1.6 - - - -
235B GLN* 1.3 78.3 - - + +
237B TRP* 1.3 60.7 + - - +
239B THR* 3.4 2.3 + - - -
240B LEU* 3.1 22.7 + - - +
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Residues in contact with TRP 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223B LEU* 5.0 2.9 - - + -
224B LYS* 4.0 34.8 - - + -
227B ILE* 3.3 34.7 + - + +
228B ARG* 3.7 56.0 - - + +
233B PRO 4.6 0.6 + - - -
234B HIS* 3.3 11.2 + - + +
236B TYR* 1.3 74.3 - - - +
238B LEU* 1.3 72.6 + - + +
240B LEU* 3.3 25.4 + - + +
241B GLN* 2.9 76.3 + - + +
244B LEU* 5.3 3.4 - - + -
293B LEU* 5.8 3.1 - - + -
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Residues in contact with LEU 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B PHE* 3.9 16.8 - - + -
124B PRO* 3.8 33.0 - - + -
126B ASP 4.2 4.0 - - - +
127B ILE* 3.8 28.1 - - + +
234B HIS* 2.9 28.7 + - + +
235B GLN 3.9 3.8 - - - +
237B TRP* 1.3 86.9 - - + +
239B THR* 1.3 61.6 + - - +
241B GLN* 3.3 8.3 + - + +
242B TYR* 3.2 22.3 + - - +
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Residues in contact with THR 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B LEU* 3.8 28.7 - - + +
122B PHE* 3.4 18.4 - - - -
128B ALA* 5.1 0.4 - - - -
129B PRO* 3.8 6.0 - - + +
132B LEU* 3.7 25.8 - - + -
189B TYR* 5.4 1.8 - - + +
197B VAL* 4.2 15.5 - - + -
235B GLN 2.6 23.4 + - - -
236B TYR 3.8 3.4 - - - -
238B LEU* 1.3 77.4 - - - +
240B LEU* 1.3 61.6 + - - +
242B TYR* 3.2 6.7 + - - +
243B LEU* 2.9 25.9 + - + +
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Residues in contact with LEU 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B VAL* 3.8 20.1 - - + +
198B ILE* 4.3 20.6 - - + -
223B LEU* 4.2 20.2 - - + -
227B ILE* 4.3 9.0 - - + -
236B TYR 3.1 16.8 + - - +
237B TRP* 3.6 31.2 - - + +
238B LEU 3.3 0.2 - - - -
239B THR* 1.3 75.8 - - - +
241B GLN* 1.3 57.1 + - - +
243B LEU* 3.3 5.1 + - + +
244B LEU* 2.9 54.3 + - + +
272B LEU* 4.4 17.5 - - + -
290B ILE* 4.9 3.6 - - + -
293B LEU* 5.3 2.2 - - + -
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Residues in contact with GLN 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237B TRP* 2.9 71.0 + - + +
238B LEU* 3.6 9.9 - - + +
240B LEU* 1.3 72.4 - - - +
242B TYR* 1.3 65.3 + - - +
244B LEU* 3.5 12.0 + - - +
245B LYS* 3.2 22.7 + - - +
297B GLU* 4.0 20.7 + - - +
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Residues in contact with TYR 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B ILE* 3.9 29.8 - - + +
128B ALA* 3.5 20.0 - - + -
132B LEU* 3.9 17.3 - - + -
133B ILE* 3.4 44.8 + - + +
136B VAL* 3.8 39.0 - - + +
137B GLU* 4.3 6.2 + - - +
238B LEU 3.2 10.9 + - - +
239B THR* 3.2 8.3 + - - +
241B GLN* 1.3 77.2 - - - +
243B LEU* 1.3 66.1 + - + +
245B LYS* 3.1 37.1 - - + +
246B HIS* 3.2 7.4 + - - +
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Residues in contact with LEU 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B LEU* 3.8 22.0 - - + -
136B VAL* 4.9 4.3 - - + -
186B PHE* 3.6 37.5 - - + -
190B LEU* 3.9 16.6 - - + -
197B VAL* 4.1 12.1 - - + -
239B THR* 2.9 25.7 + - + +
240B LEU* 3.7 6.5 - - + +
242B TYR* 1.3 77.2 - - + +
244B LEU* 1.3 56.3 + - - +
246B HIS* 3.1 7.0 + - + +
247B PHE* 2.9 45.1 + - + -
272B LEU* 3.8 28.0 - - + -
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Residues in contact with LEU 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237B TRP* 5.3 2.2 - - + -
240B LEU* 2.9 42.7 + - + +
241B GLN* 3.8 23.3 - - - +
242B TYR 3.3 0.2 - - - -
243B LEU* 1.3 76.7 - - - +
245B LYS* 1.3 55.6 + - - +
247B PHE* 3.8 8.7 - - + +
248B PHE* 2.9 29.3 + - - +
272B LEU* 6.1 0.2 - - + -
290B ILE* 4.4 12.1 - - + -
293B LEU* 3.9 36.6 - - + -
294B ILE* 3.8 27.4 - - + +
297B GLU* 4.0 23.0 - - + +
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Residues in contact with LYS 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B ILE* 5.3 7.2 - - + +
241B GLN 3.2 13.3 + - - +
242B TYR* 3.1 34.3 - - + +
244B LEU* 1.3 74.8 - - - +
246B HIS* 1.3 60.6 + - - +
248B PHE* 3.7 8.8 - - + +
249B LYS* 3.0 43.6 + - - +
297B GLU* 4.9 4.9 - - - +
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Residues in contact with HIS 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B VAL* 3.6 22.9 - - + +
139B ILE* 4.2 10.9 - - + +
140B GLU* 2.7 47.4 + - + +
150B TYR* 2.7 30.9 + - - -
186B PHE* 3.9 25.2 - + - -
242B TYR 3.2 7.0 + - - +
243B LEU* 3.1 9.1 + - + +
245B LYS* 1.3 79.8 - - - +
247B PHE* 1.3 75.5 + + - +
249B LYS* 3.1 4.4 + - - +
250B LEU* 3.0 36.8 + - + +
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Residues in contact with PHE 247 (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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186B PHE* 4.1 9.9 - + - -
190B LEU* 5.5 0.2 - - + -
240B LEU* 6.4 0.2 - - + -
243B LEU* 2.9 39.6 + - + +
244B LEU* 3.8 7.4 - - + +
246B HIS* 1.3 98.0 - + - +
248B PHE* 1.3 55.8 + - - +
250B LEU* 3.3 4.4 + - + -
251B SER* 2.9 26.5 + - - -
264B LEU* 3.3 30.4 - - + +
268B PHE* 3.5 50.7 - + + -
272B LEU* 4.5 14.4 - - + -
290B ILE* 5.3 1.3 - - + -
294B ILE* 3.7 39.9 - - + -
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Residues in contact with PHE 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B LEU 2.9 19.2 + - - +
245B LYS* 3.7 7.6 - - + +
247B PHE* 1.3 72.3 - - - +
249B LYS* 1.3 69.9 + - + +
251B SER* 3.0 26.4 + - - -
252B GLN* 3.3 41.0 + - + +
294B ILE* 3.4 25.5 - - - +
295B SER* 4.2 7.2 - - - -
297B GLU* 3.8 16.4 - - + -
298B TRP* 3.7 40.2 - + + -
299B ASN* 4.7 4.9 - - + -
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Residues in contact with LYS 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B GLU* 3.1 35.5 + - - +
144B LEU* 4.4 18.5 - - + +
245B LYS* 3.0 39.1 + - - +
246B HIS* 3.1 5.5 + - - +
248B PHE* 1.3 78.4 - - + +
250B LEU* 1.3 61.3 + - - +
252B GLN* 3.2 32.2 + - - +
253B THR* 3.7 7.8 - - - +
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Residues in contact with LEU 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B ILE* 5.7 0.4 - - + -
140B GLU* 5.0 0.4 - - + -
144B LEU* 3.8 28.9 - - + -
149B LEU* 4.1 16.4 - - + -
150B TYR* 3.5 33.9 - - + -
246B HIS* 3.0 38.0 + - + +
247B PHE* 3.7 6.3 - - + +
249B LYS* 1.3 75.5 - - - +
251B SER* 1.3 57.2 + - - +
252B GLN 3.0 0.2 - - - -
253B THR* 2.9 20.4 + - - -
257B ASN* 3.0 32.3 + - - +
259B LEU* 4.2 11.0 - - + -
264B LEU* 4.3 15.0 - - + -
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Residues in contact with SER 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B PHE 2.9 18.9 + - - -
248B PHE* 3.0 26.0 + - - -
250B LEU* 1.3 71.5 - - - +
252B GLN* 1.3 54.8 + - - +
253B THR 3.2 0.9 - - - -
254B SER* 3.1 24.4 + - - -
259B LEU 3.0 21.5 + - - -
260B ASN* 4.3 1.0 - - - -
261B ALA* 4.0 20.0 - - - +
264B LEU* 4.1 3.6 - - - +
294B ILE* 4.5 6.2 - - - +
295B SER* 5.7 1.4 - - - -
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Residues in contact with GLN 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B PHE* 3.3 43.6 + - + +
249B LYS* 3.2 27.7 + - - +
250B LEU 3.0 0.2 + - - -
251B SER* 1.3 78.2 + - - +
253B THR* 1.3 59.1 + - - +
254B SER* 3.5 0.7 - - - -
298B TRP* 6.2 0.2 - - - -
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Residues in contact with THR 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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144B LEU* 3.3 39.7 + - + +
145B GLU* 3.8 19.8 + - - +
249B LYS 3.7 5.8 - - - +
250B LEU 2.9 15.0 + - - +
252B GLN* 1.3 74.7 - - - +
254B SER* 1.3 58.7 + - - +
255B SER* 3.2 5.8 - - - -
256B LYS* 2.9 24.9 + - - +
257B ASN* 3.0 25.9 + - - +
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Residues in contact with SER 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B SER 3.1 18.6 + - - -
252B GLN 3.5 1.0 - - - -
253B THR* 1.3 74.0 - - - +
255B SER* 1.3 62.4 + - - +
256B LYS 3.1 0.4 - - - -
257B ASN* 3.2 10.3 + - - -
258B LEU* 2.6 32.0 + - - +
259B LEU 3.3 26.5 - - - -
260B ASN* 4.1 9.5 - - - +
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Residues in contact with SER 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B THR* 3.2 3.5 + - - -
254B SER* 1.3 81.3 + - - +
256B LYS* 1.3 68.4 + - - +
258B LEU* 3.8 12.8 - - - +
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Residues in contact with LYS 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B GLU* 3.3 50.9 + - + +
147B SER* 3.4 17.3 - - - -
253B THR* 2.9 15.2 + - - +
255B SER* 1.3 89.8 + - - +
257B ASN* 1.3 62.6 + - - +
258B LEU* 3.4 3.5 + - - +
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Residues in contact with ASN 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B GLY 4.9 0.9 - - - +
144B LEU 2.8 28.2 + - - +
145B GLU 4.0 0.4 + - - -
146B CYS 3.3 24.0 - - - +
147B SER* 3.4 5.6 - - - +
151B ARG* 2.7 38.3 + - - -
250B LEU* 3.0 33.2 + - - +
253B THR* 3.0 15.9 + - - +
254B SER* 3.2 10.4 - - - -
256B LYS* 1.3 76.5 - - - +
258B LEU* 1.3 53.9 + - - +
259B LEU* 2.9 39.4 + - + +
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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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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