Contacts of the helix formed by residues 342 - 362 (chain B) in PDB entry 6CNB
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 PHE 342 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259B ALA 3.8 17.9 - - - -
260B CYS* 2.9 27.1 - - - +
261B GLY* 4.1 10.8 - - - +
297B THR* 5.3 1.6 - - - -
302B LEU* 5.0 12.1 - - + -
326B ALA* 4.9 10.1 - - + -
329B THR* 4.5 18.6 - - + -
330B THR* 3.7 29.4 - - + -
338B GLU 5.6 0.7 - - - -
340B LEU 4.1 10.1 - - - -
341B ASP* 1.3 81.8 - - - +
343B ARG* 1.3 66.2 + - - +
344B GLU 3.0 3.9 + - - -
345B LYS* 3.4 8.9 + - + +
346B ALA* 3.0 19.2 + - - +
230M SER* 4.7 0.2 - - - -
234M HIS* 3.9 26.5 - + - -
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Residues in contact with ARG 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B CYS 5.0 0.2 - - - -
261B GLY 5.7 3.1 - - - -
262B ILE* 4.1 14.3 - - - +
341B ASP* 3.6 11.7 + - - +
342B PHE* 1.3 77.1 - - - +
344B GLU* 1.3 63.5 + - - +
346B ALA* 3.4 7.1 - - + +
347B LEU* 2.9 39.5 + - + +
541B ILE* 3.7 30.3 + - + +
542B THR* 4.1 29.9 - - + +
544B ILE* 4.6 4.8 + - - +
546B SER* 2.6 34.9 + - - +
178M GLN* 4.7 18.5 - - - +
180M LYS* 3.9 27.9 - - - +
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Residues in contact with GLU 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337B VAL* 3.7 23.6 - - + -
339B ALA* 6.3 4.0 - - + -
341B ASP* 5.0 2.4 + - - +
342B PHE 3.0 2.4 + - - -
343B ARG* 1.3 79.6 - - - +
345B LYS* 1.3 53.4 + - - +
347B LEU* 3.6 1.6 - - - +
348B TYR* 2.7 36.0 + - + +
541B ILE* 3.3 32.5 - - - +
560B THR* 3.2 18.5 - - + +
561B LEU* 2.7 26.8 + - - +
562B ILE* 4.4 4.1 - - - +
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Residues in contact with LYS 345 (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 CYS* 5.3 2.7 - - - -
329B THR* 2.8 26.9 - - + +
330B THR* 3.0 32.0 + - - +
332B ILE* 4.8 6.2 - - + +
334B HIS* 3.1 36.6 + - - +
337B VAL* 3.2 29.4 - - + +
338B GLU* 4.0 8.5 - - - +
342B PHE* 3.4 8.6 + - + +
344B GLU* 1.3 77.6 - - - +
346B ALA* 1.3 64.0 + - - +
348B TYR* 4.0 5.8 - - + -
349B ILE* 2.9 45.8 + - + +
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Residues in contact with ALA 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B LEU* 3.6 12.1 - - + +
260B CYS* 3.1 45.5 + - + +
261B GLY 4.9 0.4 - - - -
262B ILE* 4.7 12.3 - - + +
342B PHE 3.0 8.9 + - - +
343B ARG* 3.4 13.7 - - + +
345B LYS* 1.3 80.8 - - - +
347B LEU* 1.3 59.5 + - - +
349B ILE* 3.3 1.2 + - - +
350B ALA* 2.9 23.2 + - - +
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Residues in contact with LEU 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B LEU* 4.1 31.2 - - + -
343B ARG* 2.9 37.7 + - + +
344B GLU 3.9 0.2 - - - +
346B ALA* 1.3 73.1 - - - +
348B TYR* 1.3 57.8 + - - +
350B ALA* 3.2 6.3 - - - +
351B MET* 2.9 33.1 + - + +
541B ILE* 3.6 31.9 - - + -
544B ILE* 5.9 3.1 - - + -
546B SER* 5.9 1.8 - - - -
548B SER* 5.1 7.2 - - - +
561B LEU* 3.6 36.3 - - + -
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Residues in contact with TYR 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B ASN* 5.0 5.5 + - - -
204B ARG* 5.1 1.4 - - - -
205B ILE* 3.8 26.5 + - + +
219B SER* 3.3 21.5 + - - -
334B HIS* 3.5 32.5 - + - -
336B THR* 5.3 7.0 - - + -
337B VAL* 5.0 13.0 - - + -
344B GLU* 2.7 25.7 + - - +
345B LYS* 3.5 10.8 - - + +
346B ALA 3.2 0.2 - - - -
347B LEU* 1.3 71.0 - - - +
349B ILE* 1.3 75.8 + - + +
351B MET* 3.1 8.0 + - + +
352B MET* 2.9 31.1 + - + +
559B GLY 3.1 27.6 + - - -
560B THR* 4.4 15.7 - - + -
561B LEU* 4.9 6.7 - - + +
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Residues in contact with ILE 349 (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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230B LYS* 5.7 0.7 - - - -
242B LEU* 5.4 5.2 - - + -
253B ILE* 4.1 25.6 - - + -
256B VAL* 4.8 6.7 - - + -
257B LEU* 5.2 6.1 - - + -
260B CYS* 3.9 22.2 - - - -
332B ILE* 4.7 15.9 - - + -
334B HIS* 4.8 8.5 - - + +
345B LYS* 2.9 42.7 + - + +
346B ALA* 3.7 3.4 - - - +
348B TYR* 1.3 82.7 - - + +
350B ALA* 1.3 62.3 + - - +
352B MET* 3.4 23.7 + - + +
353B THR* 2.9 28.4 + - - +
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Residues in contact with ALA 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B LEU* 4.3 12.0 - - + +
271B LEU* 3.6 30.7 - - + -
272B VAL* 3.6 21.4 - - + +
346B ALA 2.9 13.4 + - - +
347B LEU* 3.2 11.0 - - + +
348B TYR 3.1 0.2 - - - -
349B ILE* 1.3 75.6 - - - +
351B MET* 1.3 57.0 + - - +
353B THR* 2.6 29.1 + - - -
354B ARG* 2.9 9.8 + - - -
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Residues in contact with MET 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B ILE* 5.7 2.0 - - - -
271B LEU* 5.0 13.2 - - - +
272B VAL* 5.8 0.4 - - - -
347B LEU* 2.9 39.9 + - + +
348B TYR* 3.8 6.1 - - + +
350B ALA* 1.3 72.7 - - - +
352B MET* 1.3 62.4 + - - +
354B ARG* 3.5 28.5 + - - +
355B ARG* 3.7 13.8 - - + +
548B SER* 6.0 2.5 - - - -
549B LEU* 3.5 38.6 - - + -
553B TYR 6.0 0.4 - - - +
556B TYR* 3.1 27.6 - - + +
561B LEU* 3.7 15.9 - - + -
597B MET 6.0 0.9 - - - +
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Residues in contact with MET 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B ILE* 4.6 29.5 - - + +
217B GLN* 3.0 47.9 - - - +
218B ALA 5.2 0.7 - - - -
219B SER* 4.3 25.1 - - - -
230B LYS* 3.6 26.5 - - - +
242B LEU* 5.2 1.8 - - + -
334B HIS* 4.8 4.5 - - - +
348B TYR* 2.9 20.5 + - + +
349B ILE* 3.5 31.9 - - + +
351B MET* 1.3 74.4 - - - +
353B THR* 1.3 65.0 + - - +
355B ARG* 2.9 19.8 + - - +
356B VAL 3.7 1.6 + - - -
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Residues in contact with THR 353 (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 GLN* 4.0 7.9 + - - +
232B TYR* 4.8 2.1 - - + +
240B ILE* 4.7 8.3 - - + -
253B ILE* 3.8 39.8 - - + +
257B LEU* 6.0 1.4 - - + +
272B VAL* 4.3 11.0 - - + -
283B PHE* 4.5 17.0 - - + -
349B ILE* 2.9 15.2 + - - +
350B ALA* 2.6 16.1 + - - -
352B MET* 1.3 73.7 - - - +
354B ARG* 1.3 59.9 + - - +
356B VAL* 3.0 28.9 - - + +
357B VAL* 3.5 9.3 + - + +
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Residues in contact with ARG 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B VAL* 3.3 18.5 + - - +
273B CYS 2.3 34.2 + - - -
274B GLY* 3.9 3.4 - - - +
279B TYR* 4.6 15.1 - - - -
350B ALA 2.9 7.6 + - - +
351B MET* 3.5 23.6 - - - +
352B MET 3.0 0.2 - - - -
353B THR* 1.3 78.0 - - - +
355B ARG* 1.3 59.8 + - + +
357B VAL* 3.0 8.7 - - + +
358B MET* 2.9 60.9 + - + +
549B LEU* 3.2 47.7 - - - +
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Residues in contact with ARG 355 (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 ILE* 3.5 32.1 - - + +
207B VAL* 3.2 39.1 - - + +
351B MET* 3.7 15.9 - - + +
352B MET* 2.9 7.3 + - - +
354B ARG* 1.3 79.1 - - + +
356B VAL* 1.3 61.5 + - - +
358B MET* 3.4 20.0 - - - +
359B ALA* 3.1 20.3 + - - +
365B MET 5.4 2.8 + - - +
366B ILE* 5.1 5.2 - - - +
367B ASP* 2.7 39.7 + - - +
596B GLN* 3.6 35.8 + - - +
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Residues in contact with VAL 356 (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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207B VAL* 4.6 3.4 - - + -
214B GLY 5.8 0.4 - - - +
215B ILE* 3.7 27.6 - - + +
217B GLN* 3.1 48.2 - - + +
232B TYR* 4.3 15.9 - - + -
233B VAL* 5.8 0.2 - - - -
240B ILE* 5.4 4.9 - - + -
352B MET 3.7 0.6 + - - -
353B THR* 3.0 26.9 - - + +
355B ARG* 1.3 74.7 - - - +
357B VAL* 1.3 59.2 + - + +
359B ALA* 2.8 23.7 + - - +
360B MET* 2.8 14.5 + - - +
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Residues in contact with VAL 357 (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 ILE* 6.2 3.8 - - + -
272B VAL* 4.6 9.2 - - + +
273B CYS* 5.3 3.1 - - - -
279B TYR* 4.0 20.3 - - + +
282B ILE* 3.7 33.0 - - + -
283B PHE* 4.6 22.9 - - + +
353B THR* 3.6 11.7 - - + +
354B ARG* 3.0 22.0 - - + +
356B VAL* 1.3 81.2 - - + +
358B MET* 1.3 62.2 + - + +
360B MET* 3.3 8.4 + - - +
361B TYR* 3.0 21.7 + - - +
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Residues in contact with MET 358 (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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279B TYR* 3.5 34.1 + - + +
354B ARG* 2.9 56.1 + - + +
355B ARG* 3.4 21.8 - - - +
357B VAL* 1.3 77.3 - - + +
359B ALA* 1.3 59.8 + - - +
361B TYR* 3.3 16.8 - - - +
362B ASN* 3.4 12.1 - - - +
365B MET* 4.8 27.6 - - + +
595B HIS 5.7 2.7 - - - +
596B GLN* 5.5 14.6 - - + -
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Residues in contact with ALA 359 (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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207B VAL* 4.4 0.4 - - + -
209B ALA* 5.6 0.7 - - + -
215B ILE* 3.5 31.0 - - + +
355B ARG 3.1 10.8 + - - +
356B VAL 2.8 9.8 + - - +
358B MET* 1.3 73.5 - - - +
360B MET* 1.3 63.7 + - - +
361B TYR 3.1 1.8 - - - -
362B ASN 2.7 27.4 - - - +
363B PRO* 3.7 5.2 - - + +
364B LYS 5.1 0.2 - - - -
365B MET 5.2 1.3 + - - -
366B ILE* 3.5 30.1 - - + -
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Residues in contact with MET 360 (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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214B GLY* 4.9 5.8 - - - +
215B ILE* 4.3 17.4 - - + +
234B ILE* 3.7 40.4 - - + -
238B GLY* 4.8 11.7 - - - +
240B ILE* 4.7 7.0 - - + -
282B ILE* 3.7 30.3 - - + +
356B VAL 2.8 13.3 + - - +
357B VAL* 3.3 13.0 + - - +
359B ALA* 1.3 76.3 - - - +
361B TYR* 1.3 65.0 + - - +
362B ASN* 4.6 0.2 - - - -
363B PRO* 5.4 1.7 - - - +
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Residues in contact with TYR 361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B SER* 3.2 39.0 + - - -
279B TYR* 4.3 24.7 - + + -
282B ILE* 4.3 17.6 - - + +
357B VAL 3.0 12.0 + - - +
358B MET 3.3 11.0 - - - +
360B MET* 1.3 81.9 - - - +
362B ASN* 1.3 91.3 + - + +
363B PRO* 4.5 1.9 - - - +
365B MET* 5.2 3.8 - - + -
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Residues in contact with ASN 362 (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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279B TYR* 5.7 0.2 + - - -
358B MET 3.4 8.8 - - - +
359B ALA* 2.7 24.2 + - - +
361B TYR* 1.3 94.7 - - + +
363B PRO* 1.3 77.5 + - + +
364B LYS* 3.7 2.8 - - - +
365B MET* 2.7 43.6 - - - +
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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