Contacts of the helix formed by residues 337 - 360 (chain B) in PDB entry 4JYH
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 GLU 337 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B LEU* 4.6 2.7 - - + +
246B THR* 3.7 29.9 + - + +
249B ASP* 2.8 19.0 + - - +
336B GLU* 1.3 84.1 - - + +
338B PRO* 1.3 58.2 - - - +
339B THR* 3.2 4.0 - - - +
340B LYS* 3.0 67.9 + - + +
341B VAL* 3.2 10.6 + - - +
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Residues in contact with PRO 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330B GLY* 3.7 19.2 - - - +
332B ARG 5.9 0.2 - - - +
335B LEU* 3.6 31.0 - - + +
336B GLU 3.3 10.3 - - - +
337B GLU* 1.3 89.1 - - - +
339B THR* 1.3 65.8 + - + +
341B VAL* 3.4 4.8 - - + +
342B ASP* 2.9 32.7 + - - +
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Residues in contact with THR 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337B GLU* 4.9 1.4 - - - -
338B PRO* 1.3 84.2 - - + +
340B LYS* 1.3 64.1 + - - +
341B VAL 3.1 0.9 - - - -
342B ASP* 3.6 14.1 - - + +
343B LYS* 2.9 30.0 + - - +
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Residues in contact with LYS 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B GLY 3.8 18.1 + - - -
245B LEU* 4.1 17.3 - - + -
246B THR* 5.7 0.6 - - - +
337B GLU* 3.0 55.9 + - + +
339B THR* 1.3 81.5 + - - +
341B VAL* 1.3 59.2 + - - +
343B LYS* 3.6 6.7 + - - +
344B LEU* 3.3 27.5 + - + +
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Residues in contact with VAL 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B LEU* 4.2 20.6 - - + -
249B ASP* 4.9 1.6 - - + +
253B LEU* 4.2 8.5 - - + -
328B ILE* 3.5 17.9 - - + +
329B CYS 3.6 11.9 - - - +
330B GLY* 3.6 24.2 - - - +
335B LEU* 3.9 24.5 - - + -
337B GLU 3.2 14.8 + - - +
338B PRO 3.4 7.4 - - - +
339B THR 3.1 0.2 - - - -
340B LYS* 1.3 76.8 - - - +
342B ASP* 1.3 65.4 + - - +
344B LEU* 3.1 9.9 + - - +
345B GLN* 2.9 19.6 + - - +
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Residues in contact with ASP 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330B GLY* 3.8 22.3 + - - +
331B ASP* 5.4 3.1 - - - +
338B PRO* 2.9 25.1 + - - +
339B THR* 3.3 16.6 + - + +
341B VAL* 1.3 75.9 - - - +
343B LYS* 1.3 63.3 + - - +
345B GLN* 3.2 16.9 + - - +
346B GLU* 2.9 25.3 + - - +
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Residues in contact with LYS 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B THR 2.9 17.0 + - - +
340B LYS* 3.7 7.6 - - - +
342B ASP* 1.3 76.7 - - - +
344B LEU* 1.3 58.9 + - + +
346B GLU* 3.4 12.5 + - - +
347B PRO* 2.9 25.5 - - - +
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Residues in contact with LEU 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240B PRO* 3.5 21.8 - - + +
241B GLY* 3.7 34.1 - - - +
242B PHE* 4.1 2.0 - - - +
245B LEU* 3.8 30.7 - - + -
328B ILE* 3.8 14.1 - - + -
340B LYS* 3.3 10.7 + - + +
341B VAL* 3.1 9.5 + - - +
343B LYS* 1.3 80.7 - - + +
345B GLN* 1.3 61.7 + - - +
347B PRO* 3.1 18.0 - - - +
348B LEU* 3.7 10.8 - - - +
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Residues in contact with GLN 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B ILE* 3.4 31.0 + - + +
328B ILE* 2.9 35.1 + - - +
329B CYS* 3.6 18.3 - - - +
330B GLY 5.0 1.7 + - - -
341B VAL 2.9 9.6 + - - +
342B ASP* 3.6 19.8 - - - +
344B LEU* 1.3 76.4 - - - +
346B GLU* 1.3 67.8 + - - +
348B LEU* 2.9 19.3 + - - +
349B LEU* 3.2 32.2 + - + +
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Residues in contact with GLU 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A HIS* 3.1 44.2 + - + +
342B ASP 2.9 14.1 + - - +
343B LYS* 3.4 14.0 - - - +
345B GLN* 1.3 75.6 - - - +
347B PRO* 1.3 70.5 - - + +
349B LEU* 3.1 26.3 + - + +
350B GLU* 3.3 7.4 + - - +
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Residues in contact with PRO 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B LEU* 4.7 6.1 - - + +
180B LEU* 3.8 21.8 - - + -
343B LYS 2.9 26.9 - - - +
344B LEU* 3.1 16.8 - - - +
346B GLU* 1.3 78.2 - - + +
348B LEU* 1.3 54.2 + - + +
349B LEU 3.0 2.2 + - - -
350B GLU* 3.0 7.3 + - + +
351B ALA* 2.6 39.4 + - - +
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Residues in contact with LEU 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B LEU* 4.0 21.8 - - + -
184B ILE* 4.1 26.5 - - + -
239B LEU* 5.4 3.8 - - + -
240B PRO* 6.0 1.3 - - + -
321B LEU* 4.1 11.7 - - + +
324B ALA* 3.6 36.1 - - + +
325B ILE* 3.7 18.7 - - + +
328B ILE* 4.1 17.3 - - + -
344B LEU* 3.7 16.6 - - + +
345B GLN* 2.9 11.9 + - - +
347B PRO* 1.3 77.0 - - + +
349B LEU* 1.3 56.1 + - - +
351B ALA* 3.7 5.2 - - - +
352B LEU* 3.2 25.6 + - - +
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Residues in contact with LEU 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A HIS* 5.6 9.2 - - + +
368A PRO* 4.3 24.9 - - + -
369A LYS* 5.8 0.7 - - - +
372A MET* 6.1 1.3 - - + -
325B ILE* 3.8 31.2 - - + -
345B GLN* 3.2 35.9 + - + +
346B GLU* 3.1 14.5 + - + +
347B PRO 3.0 0.2 - - - -
348B LEU* 1.3 76.2 - - - +
350B GLU* 1.3 61.5 - - - +
352B LEU* 3.2 4.0 + - - +
353B LYS* 2.9 28.3 + - - +
367B PHE* 3.9 8.9 - - + -
371B LEU* 4.0 24.5 - - + -
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Residues in contact with GLU 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A HIS* 3.6 31.5 + - + +
177B LEU* 4.1 16.6 - - + -
346B GLU 3.3 7.2 + - - +
347B PRO* 3.0 8.8 + - + +
349B LEU* 1.3 77.8 - - - +
351B ALA* 1.3 63.2 + - - +
353B LYS* 3.8 22.3 - - - +
354B ILE* 3.0 43.6 + - + +
357B ARG* 5.1 2.6 + - - -
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Residues in contact with ALA 351 (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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177B LEU* 3.4 24.0 - - + +
180B LEU* 4.7 7.6 - - + -
181B THR* 3.8 18.1 + - - +
321B LEU* 4.1 12.5 - - + +
347B PRO 2.6 22.9 + - - +
348B LEU* 3.7 9.4 - - - +
350B GLU* 1.3 74.5 - - - +
352B LEU* 1.3 57.3 + - - +
354B ILE* 3.8 1.6 - - - +
355B TYR* 3.0 30.8 + - - +
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Residues in contact with LEU 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B GLU* 4.4 19.3 - - + +
321B LEU* 3.8 30.2 - - + +
322B LEU* 4.7 9.4 - - + -
325B ILE* 3.6 22.9 - - + -
348B LEU 3.2 15.5 + - - +
349B LEU 3.5 3.4 - - - +
351B ALA* 1.3 77.5 - - - +
353B LYS* 1.3 65.4 + - - +
354B ILE 3.0 0.3 + - - -
355B TYR* 3.2 2.1 + - + +
356B ILE* 3.0 54.7 + - + +
367B PHE* 3.6 19.7 - - + -
370B ILE* 4.9 5.6 - - + -
371B LEU* 4.2 13.5 - - + -
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Residues in contact with LYS 353 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353A LYS* 4.4 23.6 - - - +
349B LEU 2.9 17.6 + - - +
350B GLU* 3.7 27.4 - - - +
352B LEU* 1.3 76.6 - - - +
354B ILE* 1.3 62.6 + - + +
356B ILE* 3.8 3.3 + - - +
357B ARG* 3.2 51.4 + - - +
364B PRO 5.5 4.2 + - - -
367B PHE* 3.4 49.4 - - + +
368B PRO* 6.0 0.6 - - - +
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Residues in contact with ILE 354 (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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174B THR* 3.8 34.8 - - + +
177B LEU* 3.6 32.1 - - + -
178B ASP* 5.0 1.8 - - - +
350B GLU* 3.0 32.8 + - + +
351B ALA 3.8 3.1 - - - +
353B LYS* 1.3 75.7 - - + +
355B TYR* 1.3 63.2 + - - +
356B ILE 3.1 1.8 - - - -
357B ARG* 2.8 34.1 + - + +
358B LYS* 2.9 27.0 + - + +
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Residues in contact with TYR 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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181B THR* 4.0 13.2 - - + +
315B ASP* 2.5 32.0 + - - -
317B THR* 3.3 33.1 + - + -
318B GLU* 3.7 17.3 - - + -
321B LEU* 4.5 9.0 - - + -
351B ALA 3.0 16.0 + - - +
352B LEU 3.9 3.1 - - - +
354B ILE* 1.3 82.0 - - - +
356B ILE* 1.3 56.8 + - + +
358B LYS* 3.8 9.3 - - + +
359B ARG* 2.8 61.3 + - + +
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Residues in contact with ILE 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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318B GLU* 3.9 18.4 - - + +
352B LEU* 3.0 44.2 + - + +
353B LYS 4.0 3.8 - - - +
355B TYR* 1.3 75.5 - - - +
357B ARG* 1.3 60.2 + - - +
359B ARG* 4.5 0.4 - - - +
360B ARG* 2.9 48.2 + - + +
363B LYS 5.6 0.7 - - - +
366B MET* 3.8 20.4 - - + +
367B PHE* 3.9 25.8 - - + +
370B ILE* 3.7 23.8 - - + -
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Residues in contact with ARG 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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350B GLU* 5.1 2.6 + - - -
353B LYS* 3.2 52.6 + - - +
354B ILE* 2.8 18.9 + - + +
356B ILE* 1.3 80.3 - - - +
358B LYS* 1.3 58.5 + - + +
360B ARG 2.6 23.5 - - - +
361B PRO* 4.0 4.0 - - - +
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Residues in contact with LYS 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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170B SER 5.5 1.6 - - - +
171B TYR* 4.7 20.4 - - + -
172B GLU 5.0 10.0 + - - -
174B THR* 4.2 12.4 + - - -
178B ASP* 3.6 26.1 + - - -
354B ILE* 2.9 24.9 + - + +
355B TYR* 3.9 11.0 - - + +
357B ARG* 1.3 76.2 - - + +
359B ARG* 1.3 64.0 + - - +
360B ARG* 3.1 4.4 + - - -
361B PRO* 4.6 4.7 - - - +
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Residues in contact with ARG 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B GLU* 2.8 25.0 + - - +
314B MET 4.1 0.6 + - - -
315B ASP* 3.5 26.8 + - - +
318B GLU* 3.1 22.3 + - - +
355B TYR* 2.8 46.6 + - + +
356B ILE 4.2 2.2 - - - +
358B LYS* 1.3 73.2 - - - +
360B ARG* 1.3 102.8 + - + +
361B PRO* 4.2 4.2 - - - +
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Residues in contact with ARG 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B LEU 2.7 28.9 + - - -
313B GLU* 4.7 1.0 - - - +
318B GLU* 3.1 28.5 + - - -
356B ILE* 2.9 34.8 + - + +
357B ARG* 2.6 26.5 - - - +
358B LYS 3.1 0.9 - - - -
359B ARG* 1.3 114.1 - - - +
361B PRO* 1.3 64.4 - - + +
362B SER* 3.4 3.0 + - - +
363B LYS* 4.4 20.8 - - - +
364B PRO* 6.1 0.2 - - - +
366B MET* 4.1 26.5 - - - +
370B ILE* 4.2 9.5 - - - +
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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