Contacts of the helix formed by residues 397 - 418 (chain B) in PDB entry 2JLF
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 397 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B PHE* 6.0 1.8 - - + -
283B ILE* 4.3 2.2 - - + -
287B ALA* 3.8 19.3 - - + -
291B ARG* 4.4 2.9 - - - +
357B PHE* 3.8 23.1 - - + -
395B GLN* 2.7 13.7 + - - +
396B GLY* 1.3 76.6 - - - +
398B THR* 1.3 67.0 + - - +
399B ASP* 3.1 4.0 - - - -
400B LEU* 2.8 22.4 + - + +
401B MET* 3.0 18.7 + - + +
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Residues in contact with THR 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B ARG* 6.0 0.9 - - - +
329B ASP* 5.5 1.0 + - - -
391B LEU* 3.6 20.2 - - - +
392B SER 3.6 20.3 + - - -
393B SER* 3.2 25.1 + - - +
394B GLY 4.6 0.2 - - - -
395B GLN* 2.9 25.9 + - - +
396B GLY 5.0 0.2 - - - -
397B ALA* 1.3 77.0 - - - +
399B ASP* 1.3 64.6 + - + +
401B MET* 3.3 8.3 + - - +
402B GLY* 3.3 16.8 + - - -
452B SER* 5.1 0.2 + - - -
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Residues in contact with ASP 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B ARG* 2.9 48.6 + - - +
295B TYR* 4.0 11.6 + - - -
397B ALA 3.9 0.3 - - - +
398B THR* 1.3 81.9 - - + +
400B LEU* 1.3 84.4 + - - +
402B GLY 3.3 0.3 + - - -
403B THR* 3.0 19.8 + - - -
451B LYS* 4.8 12.7 - - + -
452B SER* 3.2 15.6 + - - +
629B GLN 6.1 0.9 - - - +
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Residues in contact with LEU 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B MET* 4.7 8.7 - - - +
135B PHE* 5.0 5.2 - - + -
287B ALA* 3.5 31.4 - - + +
290B VAL* 3.3 33.4 - - + -
291B ARG* 3.7 22.2 - - + +
294B ILE* 4.1 22.4 - - + -
295B TYR* 5.7 0.9 - - - +
397B ALA* 2.8 10.7 + - + +
399B ASP* 1.3 95.0 + - - +
401B MET* 1.3 66.9 + - + +
403B THR* 3.0 5.8 + - - +
404B LEU* 2.7 35.5 + - - +
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Residues in contact with MET 401 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B MET* 6.4 0.2 - - - -
135B PHE* 4.3 17.7 - - + -
332B TRP* 2.6 45.6 + - + -
340B ILE* 3.7 28.0 - - + -
357B PHE* 3.6 33.0 - - + -
361B LEU* 4.6 3.4 - - + -
391B LEU* 3.7 17.0 - - + -
395B GLN* 4.1 14.1 - - - +
397B ALA* 3.0 17.7 + - + +
398B THR 3.5 8.5 - - - +
400B LEU* 1.3 92.8 - - + +
402B GLY* 1.3 56.8 + - - +
404B LEU* 4.2 4.3 - - + +
405B LEU 3.4 10.9 + - - -
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Residues in contact with GLY 402 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B HIS* 3.8 24.9 - - - -
332B TRP* 4.2 0.2 - - - -
391B LEU* 4.0 0.6 - - - +
398B THR 3.3 9.6 + - - -
399B ASP 3.3 0.4 + - - -
400B LEU 3.1 0.8 - - - -
401B MET* 1.3 77.2 - - - +
403B THR* 1.3 59.8 + - - +
405B LEU* 3.8 0.3 - - - +
406B MET* 2.9 36.2 + - - +
452B SER* 3.3 17.5 - - - -
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Residues in contact with THR 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B MET* 4.4 7.2 - - + -
294B ILE* 5.2 7.1 - - + +
302B PHE* 3.3 41.7 - - + -
399B ASP 3.0 14.5 + - - -
400B LEU* 3.0 8.9 + - - +
402B GLY* 1.3 74.7 - - - +
404B LEU* 1.3 69.5 + - - +
407B SER* 2.8 31.5 + - - +
450B SER* 4.8 3.4 - - - +
451B LYS* 4.5 4.0 - - - +
452B SER* 3.3 22.5 + - - +
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Residues in contact with LEU 404 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B PHE* 4.2 13.2 - - + +
130B ALA* 3.5 41.7 - - + +
131B VAL* 3.6 9.2 - - + +
134B MET* 3.6 26.2 - - + +
135B PHE* 4.9 3.8 - - + -
336B LEU* 4.0 15.7 - - + -
340B ILE* 3.5 32.3 - - + -
400B LEU 2.7 22.5 + - - +
401B MET* 4.2 6.1 - - + +
403B THR* 1.3 75.7 - - - +
405B LEU* 1.3 65.5 + - - +
407B SER* 4.3 1.2 - - - -
408B ILE* 3.6 16.6 + - - +
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Residues in contact with LEU 405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B PHE* 3.6 19.4 - - + -
328B HIS* 4.1 2.9 - - - +
332B TRP* 3.4 30.3 - - + +
333B PRO* 4.0 17.7 - - + -
335B TRP* 5.1 1.1 - - + -
336B LEU* 3.3 29.8 - - + +
401B MET 3.4 5.2 + - - +
402B GLY 3.8 1.3 - - - +
403B THR 3.1 0.4 - - - -
404B LEU* 1.3 84.1 - - - +
406B MET* 1.3 88.6 + - + +
408B ILE 3.4 0.5 + - - -
409B THR* 2.8 33.6 + - - +
485B TYR* 5.1 4.3 - - + -
486B MET* 3.8 22.9 - - + -
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Residues in contact with MET 406 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B VAL* 3.4 17.3 - - + -
328B HIS* 3.5 27.4 - - + +
402B GLY 2.9 21.1 + - - +
403B THR* 4.8 0.2 - - - -
405B LEU* 1.3 93.8 - - + +
407B SER* 1.3 62.6 + - - +
409B THR* 3.2 8.6 + - - -
410B TYR* 3.0 67.2 + - + +
452B SER* 3.7 21.8 - - - +
453B ASP* 4.6 0.4 - - - +
486B MET* 3.8 15.9 - - - -
488B ILE* 3.9 11.0 - - + -
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Residues in contact with SER 407 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B PHE* 3.7 14.6 - - - -
403B THR* 2.8 25.9 + - - +
404B LEU 4.3 0.7 - - - -
406B MET* 1.3 73.0 - - - +
408B ILE* 1.3 57.9 + - - +
410B TYR* 3.1 6.6 + - - +
411B LEU* 2.9 25.4 + - - +
440B TRP* 3.0 33.6 + - - -
448B GLN* 2.6 31.8 + - - -
450B SER* 4.7 2.0 + - - -
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Residues in contact with ILE 408 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B LEU* 3.5 46.0 - - + +
127B PHE* 3.5 35.9 - - + +
130B ALA* 3.7 15.0 - - + -
404B LEU 3.6 13.7 + - - +
405B LEU 3.4 1.2 + - - +
407B SER* 1.3 76.0 - - - +
409B THR* 1.3 58.2 + - - +
411B LEU* 3.2 7.3 + - + +
412B VAL* 2.7 44.9 + - + +
436B LEU* 3.7 26.0 - - + -
440B TRP* 4.3 7.2 - - + +
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Residues in contact with THR 409 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B PHE* 4.3 3.6 - - - -
405B LEU* 2.8 39.7 + - - +
406B MET* 3.2 25.7 - - + -
407B SER 3.2 0.2 - - - -
408B ILE* 1.3 76.5 - - - +
410B TYR* 1.3 58.9 + - - +
412B VAL* 3.6 7.1 + - - +
413B MET* 3.0 25.3 + - + +
483B SER* 3.3 30.1 + - - +
485B TYR* 4.1 19.9 - - + +
486B MET* 4.6 6.3 - - + -
488B ILE* 4.6 4.5 - - + -
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Residues in contact with TYR 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323B THR* 3.1 32.0 + - + -
325B VAL* 3.4 3.8 - - - +
406B MET* 3.0 53.3 + - + +
407B SER* 3.1 4.2 + - - +
409B THR* 1.3 73.5 - - - +
411B LEU* 1.3 69.4 + - - +
413B MET* 2.7 40.1 + - + +
414B GLN* 2.9 16.4 + - - +
439B TYR* 5.1 0.2 - - - +
448B GLN* 4.1 16.6 - - - +
450B SER* 4.7 1.3 - - - -
452B SER 4.0 9.9 - - - -
453B ASP 3.3 21.0 + - - -
455B ALA* 3.5 22.3 - - + +
457B LEU* 4.0 24.0 - - + -
488B ILE* 4.2 6.1 - - + -
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Residues in contact with LEU 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B LEU* 3.5 31.2 - - + -
407B SER 2.9 11.3 + - - +
408B ILE* 3.6 12.3 - - + +
410B TYR* 1.3 74.4 - - - +
412B VAL* 1.3 64.2 + - - +
414B GLN* 2.8 14.2 + - - +
415B LEU* 3.0 25.7 + - + +
435B PHE* 4.0 19.5 - - + -
436B LEU* 4.0 27.4 - - + -
439B TYR* 3.6 39.6 + - + -
446B ILE* 4.0 11.4 - - + -
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Residues in contact with VAL 412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B ARG* 3.5 9.6 - - - +
123B ASP* 3.5 36.3 - - + +
126B LEU* 4.0 10.5 - - + -
408B ILE* 2.7 42.0 + - + +
409B THR* 3.6 7.6 - - - +
411B LEU* 1.3 72.4 - - - +
413B MET* 1.3 58.0 + - - +
414B GLN 3.0 0.3 + - - -
415B LEU* 3.1 8.9 + - - +
416B ASP* 2.8 46.1 + - - +
484B PRO* 5.3 4.0 - - + -
485B TYR* 4.5 12.1 - - + -
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Residues in contact with MET 413 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323B THR* 5.3 1.8 - - + -
409B THR 3.0 11.0 + - - +
410B TYR* 2.7 49.5 + - + +
412B VAL* 1.3 72.2 - - - +
414B GLN* 1.3 58.6 + - + -
416B ASP* 3.8 7.9 - - - -
417B HIS* 3.2 28.4 + - + +
457B LEU* 4.6 7.9 - - + -
471B LEU* 4.2 21.6 - - + +
475B LEU* 5.3 4.9 - - - -
482B PRO* 3.8 44.9 - - + +
483B SER* 4.6 6.1 - - - +
488B ILE* 3.8 27.4 - - + -
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Residues in contact with GLN 414 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410B TYR 2.9 10.1 + - - +
411B LEU* 2.8 11.1 + - - +
413B MET* 1.3 75.8 - - - +
415B LEU* 1.3 59.8 + - - +
416B ASP 3.1 1.1 - - - -
418B THR* 2.5 44.5 + - - +
419B ALA* 3.0 2.2 + - - -
439B TYR* 2.6 37.1 + - - -
446B ILE* 3.9 16.0 - - + +
447B ARG 3.2 22.6 + - - +
457B LEU* 3.8 16.3 - - + +
458B GLY 3.7 10.3 + - - -
459B TRP* 3.5 35.7 - - + -
471B LEU* 5.2 1.6 - - + -
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Residues in contact with LEU 415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B ARG* 3.4 37.0 + - - +
126B LEU* 3.9 28.3 - - + -
411B LEU* 3.0 23.7 + - + +
412B VAL* 3.6 4.7 - - - +
414B GLN* 1.3 76.0 - - - +
416B ASP* 1.3 63.4 + - - +
418B THR 3.9 0.2 + - - -
419B ALA 3.4 20.4 + - - +
420B PRO* 3.5 15.9 - - - +
422B LEU* 3.9 37.9 - - + -
423B ASN* 4.1 6.0 + - - +
426B ILE* 4.1 9.4 - - + -
435B PHE* 4.2 4.7 - - + -
446B ILE* 4.1 9.9 - - + -
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Residues in contact with ASP 416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B ARG* 2.8 26.4 + - - -
123B ASP* 5.2 0.5 - - - +
412B VAL* 2.8 32.7 + - - +
413B MET* 3.7 7.7 - - - +
414B GLN 3.1 0.2 - - - -
415B LEU* 1.3 79.1 - - - +
417B HIS* 1.3 77.7 + - + +
420B PRO* 5.4 3.9 - - - +
482B PRO 4.8 6.2 - - - +
484B PRO* 4.9 8.8 - - - +
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Residues in contact with HIS 417 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413B MET* 3.2 22.2 + - + +
416B ASP* 1.3 92.1 + - + +
418B THR* 1.3 68.7 + - + +
420B PRO* 5.6 1.8 - - - -
467B GLY* 3.5 14.2 - - - +
470B ARG* 5.0 3.2 - - + +
471B LEU* 4.1 29.1 - - + +
474B MET* 3.7 33.1 - - + +
480B VAL* 6.1 0.7 - - + -
482B PRO* 3.2 28.9 + - + +
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Residues in contact with THR 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414B GLN* 2.5 25.9 + - - +
416B ASP 3.7 0.6 - - - -
417B HIS* 1.3 90.5 - - + +
419B ALA* 1.3 60.4 + - - +
420B PRO* 3.6 10.4 - - - +
421B HIS* 4.2 1.7 + - - -
446B ILE* 3.9 2.3 - - - +
459B TRP* 3.2 29.9 + - + +
463B ARG 4.7 0.3 - - - -
464B ALA* 3.0 29.4 - - - +
467B GLY* 3.3 8.8 - - - +
468B GLY* 3.2 35.0 - - - +
471B LEU* 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) + - + + + + + -
------------------------------------------------------------
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