Contacts of the helix formed by residues 241 - 263 (chain B) in PDB entry 3CRL
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 VAL 241 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B MET* 3.3 23.4 - - + +
167B MET* 3.8 16.4 - - + -
190B SER* 3.6 36.8 - - - +
191B ILE* 3.8 2.5 - - + -
240B TYR* 1.3 85.0 - - + +
242B PRO* 1.4 66.7 - - - +
243B SER* 3.3 24.0 - - - +
244B HIS* 3.0 36.7 + - + +
245B LEU 3.2 8.1 + - - -
340B PHE* 4.6 2.9 - - + -
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Residues in contact with PRO 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B HIS* 3.6 26.7 - - + +
190B SER 3.4 12.6 - - - +
192B ASP* 3.8 15.3 - - + +
195B CYS* 4.3 12.1 - - - -
200B VAL* 3.8 20.3 - - + +
240B TYR* 3.3 12.5 - - + +
241B VAL* 1.4 81.6 - - - +
243B SER* 1.3 51.2 + - - +
245B LEU* 3.3 9.8 + - + +
246B TYR* 2.6 36.4 + - - +
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Residues in contact with SER 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B SER* 5.4 2.3 - - - -
241B VAL* 3.0 14.9 + - - +
242B PRO* 1.3 79.1 - - - +
244B HIS* 1.3 64.7 + - - +
246B TYR* 3.4 9.2 - - - +
247B HIS* 2.8 35.2 + - - +
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Residues in contact with HIS 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B ILE* 3.8 18.5 + - + +
166B ARG* 6.5 0.7 - - + -
167B MET* 4.4 13.7 - - + -
190B SER* 5.8 0.2 - - - -
240B TYR* 3.9 11.9 - - + +
241B VAL* 3.0 32.4 + - + +
243B SER* 1.3 85.9 + - - +
245B LEU* 1.3 63.2 + - - +
247B HIS* 3.2 5.7 + - - +
248B MET* 3.1 33.0 + - + +
336B TYR* 3.7 41.0 - + + +
339B TYR* 4.0 24.1 - + - -
340B PHE* 4.4 8.7 - + - -
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Residues in contact with LEU 245 (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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195B CYS* 4.2 14.6 - - - -
197B VAL* 4.5 20.4 - - + +
200B VAL* 3.8 31.6 - - + -
238B MET* 5.2 2.7 - - - -
240B TYR* 3.9 14.1 - - + -
241B VAL 3.2 3.2 + - - +
242B PRO 3.4 8.5 - - - +
244B HIS* 1.3 79.1 - - - +
246B TYR* 1.3 62.1 + - - +
248B MET* 3.2 17.0 + - + +
249B LEU* 3.1 32.2 + - + +
286B ILE* 3.8 25.8 - - + -
358B ILE* 5.0 3.8 - - + -
360B LEU* 3.8 19.3 - - + -
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Residues in contact with TYR 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200B VAL* 3.7 13.3 - - + +
203B ASP* 4.1 15.5 - - + -
204B ALA* 3.7 31.2 - - + -
207B MET* 3.2 33.9 - - + +
242B PRO 2.6 21.2 + - - +
243B SER* 3.4 10.5 - - - +
245B LEU* 1.3 73.2 - - - +
247B HIS* 1.3 67.5 - - + +
249B LEU* 3.3 0.5 + - - +
250B PHE* 2.8 59.0 + + + +
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Residues in contact with HIS 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B SER 2.8 20.3 + - - +
244B HIS* 3.5 7.0 - - - +
246B TYR* 1.3 77.7 - - + +
248B MET* 1.3 63.2 + - - +
250B PHE* 3.8 4.2 - + - +
251B GLU* 3.1 45.4 + - + +
329B GLY* 5.0 1.6 + - - -
332B ILE* 3.6 19.1 - - + +
333B SER* 3.8 13.2 + - - -
336B TYR* 3.7 40.6 + + + -
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Residues in contact with MET 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240B TYR* 3.6 26.9 - - + +
244B HIS* 3.1 22.8 + - + +
245B LEU* 3.2 26.2 + - + +
247B HIS* 1.3 76.3 - - - +
249B LEU* 1.3 58.0 + - - +
251B GLU* 3.3 2.3 + - - +
252B LEU* 3.0 32.9 + - - +
333B SER* 3.5 29.5 + - - +
336B TYR* 3.9 8.5 - - + -
337B ALA* 3.5 37.5 - - - +
344B LEU* 4.9 1.6 - - + -
358B ILE* 3.7 26.0 - - + -
360B LEU* 4.4 4.0 - - + -
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Residues in contact with LEU 249 (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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200B VAL* 4.4 4.5 - - + -
201B VAL* 3.7 37.0 - - + +
204B ALA* 3.8 12.3 - - + -
245B LEU* 3.1 39.6 + - + +
248B MET* 1.3 73.6 - - - +
250B PHE* 1.3 57.9 + - - +
252B LEU* 3.9 7.1 - - + +
253B PHE* 2.7 52.1 + - + -
275B ILE* 4.7 7.2 - - + -
286B ILE* 3.9 22.9 - - + -
288B MET* 5.4 3.6 - - + -
358B ILE* 3.8 22.4 - - + -
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Residues in contact with PHE 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B ALA* 3.6 23.1 - - + +
207B MET* 3.5 29.4 - - + -
208B ALA* 3.7 14.4 - - + -
211B LEU* 3.7 25.4 - - + -
246B TYR* 2.8 53.0 + + + +
247B HIS* 3.8 4.9 - + - +
249B LEU* 1.3 71.2 - - - +
251B GLU* 1.3 74.2 + - - +
253B PHE* 3.7 1.8 - - - +
254B LYS* 3.1 44.7 + - + +
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Residues in contact with GLU 251 (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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247B HIS* 3.1 36.5 + - + +
248B MET 3.5 0.9 - - - +
250B PHE* 1.3 84.0 - - + +
252B LEU* 1.3 66.3 + - + +
254B LYS* 3.1 42.6 + - - +
255B ASN* 3.2 19.5 + - - +
329B GLY* 3.2 28.8 - - - +
333B SER* 3.4 25.4 - - - +
1001B ANP 3.3 13.2 + - - -
2001B MG 3.7 4.0 - - - -
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Residues in contact with LEU 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B MET 3.0 17.9 + - - +
249B LEU* 3.9 7.0 - - + +
251B GLU* 1.3 74.5 - - + +
253B PHE* 1.3 64.7 + - - +
255B ASN* 3.0 11.9 + - + +
256B ALA 3.0 14.0 + - - -
288B MET* 3.0 32.0 - - + +
330B LEU* 4.1 21.8 - - + -
333B SER* 5.6 1.1 - - - -
344B LEU* 4.0 22.0 - - + -
346B LEU* 5.2 1.8 - - + -
356B ALA* 3.8 31.6 - - + -
358B ILE* 3.6 37.2 - - + -
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Residues in contact with PHE 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B VAL* 3.4 27.4 - - + -
204B ALA* 3.9 3.8 - - + -
205B TYR* 3.6 33.2 - + + -
208B ALA* 3.7 17.5 - - + -
222B LEU* 3.7 33.0 - - + -
249B LEU* 2.7 40.5 + - + +
250B PHE 3.7 1.3 - - - +
252B LEU* 1.3 72.8 - - - +
254B LYS* 1.3 57.2 + - - +
256B ALA* 3.3 2.3 + - - +
257B MET* 2.9 36.1 + - + +
273B ILE* 3.9 28.0 - - + +
275B ILE* 3.9 15.3 - - + -
288B MET* 3.5 13.9 - - - -
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Residues in contact with LYS 254 (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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208B ALA* 3.9 17.9 - - + -
211B LEU* 4.1 22.3 - - + +
250B PHE* 3.1 36.7 + - + +
251B GLU* 3.1 41.3 + - - +
253B PHE* 1.3 75.0 - - - +
255B ASN* 1.3 60.0 + - - +
257B MET* 3.4 0.8 + - - -
258B ARG* 3.0 30.8 + - - +
323B LEU* 3.6 51.0 + - + +
1001B ANP 3.9 9.3 + - - -
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Residues in contact with ASN 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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251B GLU* 3.2 13.4 + - - +
252B LEU* 3.0 13.0 + - + +
254B LYS* 1.3 77.3 - - - +
256B ALA* 1.3 57.7 + - - +
258B ARG* 3.9 6.2 + - - +
259B ALA* 3.2 28.4 + - - +
288B MET* 5.6 0.2 - - + -
330B LEU* 3.6 23.8 - - - +
1001B ANP 2.7 58.7 + - - +
2001B MG 2.3 25.3 - - - -
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Residues in contact with ALA 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 LEU 3.0 5.6 + - - +
253B PHE 3.7 0.7 - - - +
255B ASN* 1.3 73.6 - - - +
257B MET* 1.3 60.8 + - - +
259B ALA* 3.5 1.6 + - - +
260B THR* 2.8 35.1 + - - -
273B ILE* 3.5 19.5 - - + -
288B MET* 3.5 28.3 - - + -
290B ASP* 3.6 27.3 - - + +
1001B ANP 3.9 2.5 - - - +
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Residues in contact with MET 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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205B TYR* 3.5 39.5 - - + +
208B ALA* 3.5 20.4 - - + +
209B LYS* 3.5 38.4 - - + +
212B CYS* 3.7 20.2 - - - -
219B SER* 4.6 0.4 - - - +
220B PRO* 3.9 20.2 - - + +
253B PHE* 2.9 18.6 + - + +
254B LYS 3.8 3.6 - - - +
256B ALA* 1.3 75.4 - - - +
258B ARG* 1.3 65.4 + - - +
260B THR* 3.3 1.2 + - - -
261B VAL* 3.1 30.0 + - - +
273B ILE* 3.8 15.3 - - + -
323B LEU* 4.0 3.6 - - + -
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Residues in contact with ARG 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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216B TYR* 3.5 32.5 + - + +
254B LYS 3.0 16.7 + - - +
255B ASN* 3.9 7.6 + - - +
257B MET* 1.3 75.9 - - - +
259B ALA* 1.3 59.0 + - - +
261B VAL* 3.9 1.2 - - - +
262B GLU* 2.9 64.5 + - - +
323B LEU* 4.3 5.5 - - + +
324B ALA* 3.4 34.0 - - - +
1001B ANP 3.5 48.4 + - - -
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Residues in contact with ALA 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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255B ASN 3.2 15.9 + - - +
256B ALA* 3.7 5.2 - - - +
258B ARG* 1.3 81.5 - - - +
260B THR* 1.3 53.7 + - - +
262B GLU* 4.0 4.1 - - - +
263B SER* 2.7 38.0 + - - -
290B ASP* 4.6 0.7 - - - +
292B GLY* 3.4 12.7 - - - +
1001B ANP 3.4 33.9 - - + +
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Residues in contact with THR 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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220B PRO* 4.0 20.2 - - + +
256B ALA 2.8 22.8 + - - -
257B MET 3.9 3.1 - - - -
259B ALA* 1.3 74.4 - - - +
261B VAL* 1.3 62.3 + - - +
263B SER* 3.9 3.8 - - - -
264B HIS* 2.7 32.6 + - + +
270B LEU* 4.2 7.4 - - + +
271B PRO* 3.8 44.7 + - + +
273B ILE* 4.7 1.9 - - - +
290B ASP* 4.1 15.6 - - - +
291B ARG 4.5 1.0 + - - -
292B GLY* 3.9 8.2 + - - -
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Residues in contact with VAL 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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212B CYS* 4.1 10.8 - - - -
216B TYR* 3.9 34.8 - - + +
218B ALA* 3.8 29.2 - - + +
220B PRO* 4.5 5.4 - - + -
257B MET 3.1 16.8 + - - +
258B ARG 4.0 2.0 - - - +
260B THR* 1.3 75.1 - - - +
262B GLU* 1.3 61.6 + - - +
264B HIS* 3.4 15.2 + - - +
265B GLU* 3.9 6.4 - - - +
270B LEU* 4.3 22.6 - - + +
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Residues in contact with GLU 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B TYR* 2.8 32.4 + - + +
258B ARG* 2.9 53.8 + - - +
259B ALA* 4.2 4.0 - - - +
261B VAL* 1.3 77.1 - - - +
263B SER* 1.3 58.1 + - - +
264B HIS 3.3 1.1 - - - -
265B GLU* 3.0 33.9 - - - +
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Residues in contact with SER 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B ALA 2.7 23.2 + - - -
261B VAL 3.3 0.2 - - - -
262B GLU* 1.3 75.6 - - - +
264B HIS* 1.3 77.5 + - - +
265B GLU* 3.5 3.6 + - - -
292B GLY* 3.1 27.9 + - - -
293B GLY* 4.4 6.3 - - - -
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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) + - + + + + + -
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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