Contacts of the helix formed by residues 358 - 379 (chain A) in PDB entry 4KJW
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 ALA 358 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A LEU 5.6 0.2 - - - +
146A GLY* 4.3 4.7 - - - -
148A GLU* 3.1 26.0 + - - +
190A PHE* 4.1 10.3 - - + -
315A GLY* 4.6 5.9 - - - +
317A PHE* 4.1 22.0 - - + -
357A PHE* 1.3 74.6 - - - +
359A PRO* 1.3 65.6 - - + +
360A MET 3.0 5.2 - - - -
361A LEU* 2.8 36.5 + - - +
362A ALA* 3.6 2.8 + - - +
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Residues in contact with PRO 359 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A VAL* 4.0 25.6 - - + +
145A LEU* 4.0 27.1 - - - +
146A GLY 4.1 3.8 - - - +
315A GLY 4.2 13.5 - - - +
340A ARG* 4.0 4.9 + - - +
344A THR* 4.2 14.4 - - + +
355A GLY 4.0 8.5 - - - +
356A ILE* 3.4 18.2 - - - +
358A ALA* 1.3 93.0 - - + +
360A MET* 1.3 57.4 + - - +
361A LEU 3.2 0.2 - - - -
362A ALA* 3.6 4.9 + - - +
363A LEU* 3.3 29.7 + - - +
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Residues in contact with MET 360 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269A PHE* 3.9 20.0 - - + -
344A THR* 5.7 0.4 - - + -
356A ILE* 3.2 31.4 - - + +
357A PHE 3.3 6.5 + - - +
358A ALA 2.9 1.6 + - - -
359A PRO* 1.3 76.2 - - - +
361A LEU* 1.3 60.0 + - - +
363A LEU* 3.8 5.2 - - + -
364A GLY 3.1 18.9 + - - -
394A MET 3.7 5.9 - - - +
397A LEU* 3.7 49.6 - - + +
398A LEU* 3.7 16.4 - - + +
401A SER* 3.9 13.9 - - - -
402A ILE* 3.6 39.0 - - + -
444A LEU* 5.5 1.1 - - + -
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Residues in contact with LEU 361 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A PHE* 3.9 11.0 - - + -
317A PHE* 3.9 14.1 - - + -
320A ILE* 4.1 12.1 - - + -
357A PHE* 4.1 4.0 - - + +
358A ALA* 2.8 29.4 + - - +
360A MET* 1.3 76.2 - - - +
362A ALA* 1.3 60.6 + - - +
364A GLY* 3.4 0.5 + - - -
365A THR* 2.8 35.5 + - - -
394A MET* 3.6 28.9 - - + +
398A LEU* 3.7 26.0 - - + -
411A LEU* 4.1 10.1 - - + -
412A VAL* 4.5 4.7 - - + -
415A MET* 3.7 25.1 - - + -
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Residues in contact with ALA 362 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315A GLY 4.5 3.8 - - - +
316A GLY* 3.9 27.4 - - - +
317A PHE* 6.1 0.4 - - + -
319A LEU* 4.1 9.0 - - + -
320A ILE* 4.1 13.1 - - + +
340A ARG* 3.9 24.7 - - - +
358A ALA 3.6 2.6 + - - +
359A PRO 3.6 3.3 + - - +
361A LEU* 1.3 77.1 - - - +
363A LEU* 1.3 65.1 + - - +
365A THR* 3.8 0.7 - - - -
366A VAL* 3.1 30.1 + - - +
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Residues in contact with LEU 363 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262A PHE* 5.3 0.2 - - - -
265A PHE* 5.9 0.9 - - + -
269A PHE* 4.2 22.0 - - + -
337A PHE* 3.3 53.7 - - + +
340A ARG* 3.8 22.4 - - + +
341A VAL* 3.9 12.6 - - + +
344A THR* 4.2 15.9 - - + +
359A PRO 3.3 20.0 + - - +
360A MET* 4.1 2.7 - - - +
361A LEU 3.3 0.2 - - - -
362A ALA* 1.3 78.6 - - - +
364A GLY* 1.3 57.8 - - - +
366A VAL* 4.8 1.1 - - + -
367A LEU* 3.1 22.2 + - - +
397A LEU* 3.9 28.3 - - + -
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Residues in contact with GLY 364 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262A PHE* 3.5 18.7 - - - -
360A MET 3.1 17.9 + - - -
361A LEU 3.9 0.4 - - - -
363A LEU* 1.3 75.8 - - - +
365A THR* 1.3 58.8 + - - +
367A LEU 3.3 0.3 + - - -
368A GLY* 2.8 25.6 + - - -
393A GLY 3.1 29.1 - - - +
394A MET 4.4 0.2 - - - -
397A LEU* 4.7 1.3 - - - +
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Residues in contact with THR 365 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320A ILE* 3.8 39.9 - - + +
323A ALA* 4.0 12.3 - - + -
324A THR* 4.0 9.0 - - - +
361A LEU 2.8 24.1 + - - -
362A ALA 3.8 4.5 - - - -
364A GLY* 1.3 75.1 - - - +
366A VAL* 1.3 54.9 + - + +
368A GLY 3.3 0.5 + - - -
369A THR* 2.7 36.9 + - - -
390A ALA* 3.6 18.7 - - + +
393A GLY 3.9 1.0 + - - -
394A MET* 3.3 24.4 - - - +
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Residues in contact with VAL 366 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319A LEU* 3.8 22.9 - - + -
323A ALA* 4.8 4.9 - - + -
333A LEU* 3.2 47.5 - - + +
336A ILE* 3.9 16.2 - - + -
337A PHE* 3.9 18.2 - - + +
340A ARG* 5.7 0.2 - - - -
362A ALA 3.1 18.2 + - - +
363A LEU* 3.9 3.4 - - - +
365A THR* 1.3 78.7 - - - +
367A LEU* 1.3 64.7 + - - +
369A THR* 3.3 6.5 + - - -
370A ALA* 3.0 23.2 + - + +
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Residues in contact with LEU 367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258A LEU* 4.5 3.9 - - + +
261A ILE* 5.0 16.8 - - + -
262A PHE* 3.5 41.5 - - + -
265A PHE* 4.7 11.4 - - + -
337A PHE* 3.5 36.8 - - + -
363A LEU 3.1 19.4 + - - +
364A GLY 3.3 0.2 + - - -
366A VAL* 1.3 76.9 - - - +
368A GLY* 1.3 61.4 + - - +
370A ALA* 3.4 11.3 - - + +
371A PHE* 3.2 20.6 + - - +
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Residues in contact with GLY 368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258A LEU* 4.3 13.2 - - - -
262A PHE* 4.5 0.4 - - - -
364A GLY 2.8 16.4 + - - -
365A THR 3.8 0.9 - - - -
366A VAL 3.2 0.2 - - - -
367A LEU* 1.3 76.0 - - - +
369A THR* 1.3 59.2 + - - +
371A PHE* 3.0 4.9 + - - +
372A GLY 2.8 24.3 + - - -
389A PHE* 3.2 29.7 - - - +
390A ALA* 4.1 0.2 - - - -
393A GLY* 4.6 2.7 - - - -
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Residues in contact with THR 369 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323A ALA* 3.1 35.7 + - - +
326A GLY* 5.1 0.7 - - - -
328A PHE* 6.0 0.2 - - + -
333A LEU* 3.7 20.4 - - + -
365A THR 2.7 21.2 + - - -
366A VAL* 3.6 6.5 - - - -
368A GLY* 1.3 73.5 - - - +
370A ALA* 1.3 57.5 + - - +
372A GLY* 3.0 2.4 + - - -
373A MET* 2.8 44.4 + - + +
386A ALA* 3.9 21.2 - - + +
390A ALA* 3.1 15.2 - - - +
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Residues in contact with ALA 370 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330A MET* 3.5 30.2 - - + +
333A LEU* 3.8 10.2 - - + +
334A VAL* 5.9 0.7 - - + -
366A VAL* 3.0 18.6 + - + +
367A LEU* 3.4 15.3 - - + +
368A GLY 3.2 0.2 - - - -
369A THR* 1.3 78.5 - - - +
371A PHE* 1.3 60.6 + - - +
373A MET* 3.4 10.0 + - - +
374A VAL* 3.4 18.6 + - - +
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Residues in contact with PHE 371 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254A LEU* 3.2 40.4 - - + -
257A ILE* 4.0 16.2 - - + -
258A LEU* 3.6 27.4 - - + -
261A ILE* 3.7 31.9 - - + -
367A LEU 3.2 5.1 + - - +
368A GLY 3.0 8.3 + - - +
370A ALA* 1.3 75.5 - - - +
372A GLY* 1.3 62.2 + - - +
374A VAL* 3.2 12.0 + - + +
375A ALA* 2.9 31.7 + - + +
389A PHE* 3.7 29.4 - + - -
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Residues in contact with GLY 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368A GLY 2.8 10.9 + - - -
369A THR 3.0 4.2 + - - -
371A PHE* 1.3 76.4 - - - +
373A MET* 1.3 57.2 + - - +
375A ALA* 3.5 2.9 - - - +
376A VAL* 2.8 35.2 + - - +
386A ALA* 3.6 12.1 - - - -
389A PHE* 3.7 31.4 - - - -
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Residues in contact with MET 373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326A GLY* 4.5 15.5 - - - +
328A PHE 3.1 28.0 - - - +
329A SER* 5.2 0.2 - - - -
330A MET* 4.2 29.4 - - - +
333A LEU* 3.6 24.9 - - + -
369A THR* 2.8 27.5 + - + +
370A ALA 3.5 8.1 - - - +
371A PHE 3.1 0.4 - - - -
372A GLY* 1.3 77.2 - - - +
374A VAL* 1.3 62.6 + - - +
376A VAL* 3.4 13.6 + - - +
377A GLU* 3.4 14.7 + - - +
386A ALA* 4.3 9.2 - - + -
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Residues in contact with VAL 374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330A MET* 4.7 12.6 - - - -
370A ALA 3.4 16.8 - - - +
371A PHE* 3.2 10.0 + - + +
373A MET* 1.3 74.6 - - - +
375A ALA* 1.3 61.3 + - - +
377A GLU* 3.4 13.4 - - - +
378A LEU* 3.1 44.8 + - + +
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Residues in contact with ALA 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254A LEU* 4.3 8.5 - - + -
371A PHE* 2.9 27.6 + - + +
372A GLY* 3.5 10.3 - - - +
373A MET 3.2 0.2 - - - -
374A VAL* 1.3 76.6 - - - +
376A VAL* 1.3 64.5 + - - +
378A LEU* 5.7 0.2 - - - -
379A PHE* 3.2 29.3 + - + -
384A LEU* 3.2 27.2 - - + +
389A PHE* 4.3 10.8 - - + -
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Residues in contact with VAL 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372A GLY 2.8 20.3 + - - +
373A MET* 3.7 7.6 - - - +
374A VAL 3.3 0.2 - - - -
375A ALA* 1.3 78.4 - - - +
377A GLU* 1.3 64.6 + - + +
379A PHE 3.5 15.9 - - - +
380A PRO* 3.7 6.8 - - - +
384A LEU* 3.7 36.1 + - + +
385A GLU* 4.3 0.2 - - - -
386A ALA* 3.9 21.8 - - + +
57C THR* 5.4 9.0 - - + +
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Residues in contact with GLU 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373A MET 3.4 10.0 + - - +
374A VAL* 3.4 20.4 - - - +
376A VAL* 1.3 81.6 - - + +
378A LEU* 1.3 83.4 + - + +
379A PHE 3.5 0.2 + - - -
380A PRO* 3.8 9.6 - - - +
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Residues in contact with LEU 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A VAL* 3.1 37.2 + - + +
377A GLU* 1.3 96.4 - - + +
379A PHE* 1.3 96.6 + - + +
380A PRO* 3.7 5.2 - - - +
381A GLN* 4.4 2.1 + - - +
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Residues in contact with PHE 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253A TRP* 4.0 24.5 - + - -
254A LEU* 3.8 23.1 - - + -
375A ALA* 3.2 24.9 + - - +
376A VAL 3.5 8.6 - - - +
378A LEU* 1.3 111.1 - - + +
380A PRO* 1.3 61.9 - - - +
381A GLN* 3.1 25.6 + - - -
382A TYR* 3.4 43.7 + + + +
383A HIS 4.2 2.1 + - - -
384A LEU* 4.2 4.3 + - - +
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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