Contacts of the helix formed by residues 358 - 380 (chain B) in PDB entry 4OL0
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 ASP 358 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356B THR* 3.6 20.0 - - + +
357B ASN* 1.3 77.4 + - - +
359B GLU* 1.3 73.2 + - - +
360B VAL* 3.4 25.6 + - - +
361B ILE* 3.2 25.0 - - + +
362B HIS* 2.8 34.2 + - - -
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Residues in contact with GLU 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358B ASP* 1.3 77.7 + - - +
360B VAL* 1.3 62.6 + - + +
362B HIS* 3.5 4.7 + - - +
363B GLY* 2.8 26.5 + - - -
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Residues in contact with VAL 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358B ASP* 3.4 23.3 + - - +
359B GLU* 1.3 79.4 - - + +
361B ILE* 1.3 62.5 + - + +
363B GLY* 3.2 3.0 + - - -
364B ILE* 2.7 46.3 + - + +
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Residues in contact with ILE 361 (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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311B VAL* 4.3 18.4 - - + +
312B CYS* 6.0 0.9 - - - +
314B PRO* 5.1 6.1 - - + -
352B HIS* 6.2 1.6 - - + +
353B LEU* 3.8 14.4 - - + -
356B THR* 4.2 13.9 - - + +
358B ASP* 3.2 36.3 + - + +
359B GLU 3.4 0.2 - - - -
360B VAL* 1.3 78.6 - - + +
362B HIS* 1.3 68.1 + - - +
364B ILE* 3.0 11.4 + - + +
365B PHE* 2.9 55.8 + - + -
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Residues in contact with HIS 362 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353B LEU* 3.2 32.9 + - + +
354B TYR* 5.4 0.4 - - - -
356B THR* 3.3 26.3 + - - -
357B ASN* 5.1 1.0 + - - -
358B ASP 2.8 27.8 + - - +
359B GLU* 3.8 5.2 - - - +
361B ILE* 1.3 76.4 - - - +
363B GLY* 1.3 54.2 + - - +
365B PHE* 4.6 1.8 - - - +
366B LYS* 2.8 39.9 + - - +
412B PHE* 5.8 2.7 - + - -
413B LEU* 3.7 33.7 - - + +
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Residues in contact with GLY 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359B GLU 2.8 16.6 + - - -
360B VAL* 3.4 5.4 - - - -
361B ILE 3.2 0.2 - - - -
362B HIS* 1.3 78.1 - - - +
364B ILE* 1.3 60.5 + - - +
366B LYS* 3.8 15.9 + - - +
367B ALA* 4.3 5.2 + - - +
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Residues in contact with ILE 364 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B PRO* 4.3 25.4 - - + +
321B LEU* 4.1 26.2 - - + -
360B VAL* 2.7 33.6 + - + +
361B ILE* 3.0 12.5 + - + +
363B GLY* 1.3 76.6 - - - +
365B PHE* 1.3 74.2 + - + +
367B ALA* 4.1 6.4 + - - +
368B TYR* 3.5 17.0 - - + -
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Residues in contact with PHE 365 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B ILE* 3.8 31.6 - - + -
311B VAL* 3.8 17.3 - - + -
314B PRO* 4.2 13.9 - - + -
321B LEU* 4.6 3.4 - - + -
324B LEU* 3.8 31.0 - - + -
349B LEU* 4.1 20.0 - - + -
353B LEU* 3.8 30.3 - - + -
361B ILE* 2.9 50.9 + - + +
362B HIS 4.3 1.3 - - - +
364B ILE* 1.3 76.0 - - + +
366B LYS* 1.3 66.0 + - - +
367B ALA 3.2 3.1 - - - -
368B TYR* 3.1 9.1 + + + +
369B ILE* 2.9 27.4 + - + +
413B LEU* 5.7 0.2 - - + -
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Residues in contact with LYS 366 (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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362B HIS 2.8 24.3 + - - +
363B GLY* 3.9 11.0 - - - +
364B ILE 3.4 0.4 - - - -
365B PHE* 1.3 72.4 - - - +
367B ALA* 1.3 57.5 + - - +
369B ILE* 3.3 11.3 + - - +
370B GLN* 2.8 47.4 + - - +
413B LEU* 3.7 19.7 - - - +
414B ILE* 3.6 29.8 - - + +
415B GLY 5.4 1.4 - - - +
418B GLU* 6.4 0.4 - - - +
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Residues in contact with ALA 367 (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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363B GLY 4.3 4.3 + - - +
364B ILE 4.1 9.5 + - - +
365B PHE 3.2 0.6 - - - -
366B LYS* 1.3 77.9 - - - +
368B TYR* 1.3 63.7 + - + +
370B GLN* 3.1 16.2 + - - +
371B ARG* 2.9 37.0 + - + +
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Residues in contact with TYR 368 (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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321B LEU* 3.5 40.6 - - + +
324B LEU* 3.8 35.7 - - + -
325B GLU* 3.3 15.6 + - - -
328B LEU* 3.5 21.2 - - + +
346B TRP* 4.6 11.7 - - + -
364B ILE* 3.5 22.4 - - + -
365B PHE* 3.1 10.9 + + + +
367B ALA* 1.3 81.9 - - + +
369B ILE* 1.3 58.3 + - + +
371B ARG* 3.2 32.3 + - - +
372B LEU* 2.9 29.7 + - - +
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Residues in contact with ILE 369 (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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346B TRP* 4.8 15.3 - - + -
349B LEU* 5.2 3.1 - - + -
350B GLY* 5.9 0.2 - - - -
353B LEU* 4.0 14.6 - - + -
365B PHE* 2.9 23.2 + - + +
366B LYS* 3.5 8.7 - - - +
368B TYR* 1.3 77.0 - - - +
370B GLN* 1.3 56.6 - - - +
372B LEU* 3.2 8.8 + - - +
373B LEU* 2.9 34.2 + - + +
410B LEU* 4.3 27.1 - - + +
413B LEU* 3.4 41.1 - - + -
414B ILE* 3.9 21.8 - - + -
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Residues in contact with GLN 370 (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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366B LYS* 2.8 37.4 + - - +
367B ALA* 3.1 15.1 + - - +
369B ILE* 1.3 73.1 - - - +
371B ARG* 1.3 58.0 + - + +
373B LEU* 3.2 4.4 + - - +
374B HIS* 2.8 29.2 + - - +
414B ILE* 3.3 44.1 - - + +
422B GLN* 4.6 15.3 + - - +
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Residues in contact with ARG 371 (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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325B GLU* 2.9 41.0 + - - -
328B LEU* 3.3 29.5 - - + +
367B ALA* 2.9 19.2 + - + +
368B TYR* 3.2 30.7 - - - +
370B GLN* 1.3 76.2 - - + +
372B LEU* 1.3 63.5 + - - +
374B HIS* 3.1 9.5 + - - +
375B ALA* 2.9 23.9 + - - +
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Residues in contact with LEU 372 (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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328B LEU* 3.9 13.8 - - + +
331B ALA* 4.6 11.4 - - + -
339B VAL* 5.3 2.2 - - + -
343B PHE* 5.6 0.7 - - + -
346B TRP* 3.5 55.0 - - + +
368B TYR 2.9 15.5 + - - +
369B ILE* 3.3 10.3 - - - +
371B ARG* 1.3 74.6 - - - +
373B LEU* 1.3 58.1 + - + +
375B ALA* 3.1 6.9 + - - +
376B LEU* 2.8 57.1 + - + +
406B LEU* 4.7 1.1 - - + -
410B LEU* 3.5 30.1 - - + -
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Residues in contact with LEU 373 (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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369B ILE* 2.9 25.9 + - + +
370B GLN* 3.2 5.6 + - - +
372B LEU* 1.3 73.3 - - - +
374B HIS* 1.3 52.8 + - - +
376B LEU* 3.7 8.6 - - + +
377B ALA* 2.7 36.2 + - - +
407B VAL* 3.7 34.9 - - + +
410B LEU* 4.3 19.5 - - + -
411B ILE* 4.1 25.1 - - + +
414B ILE* 3.4 27.1 - - + -
419B CYS* 4.5 14.4 - - - -
443B ILE* 5.0 1.6 - - - +
447B ILE* 5.9 0.4 - - + -
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Residues in contact with HIS 374 (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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370B GLN 2.8 13.3 + - - +
371B ARG* 3.1 13.4 + - - +
373B LEU* 1.3 76.6 - - - +
375B ALA* 1.3 65.9 + - - +
377B ALA* 3.1 9.1 + - + +
378B ARG* 2.9 28.1 + - + +
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Residues in contact with ALA 375 (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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328B LEU* 6.0 0.2 - - + -
331B ALA* 3.6 37.7 - - + +
332B GLY* 4.9 3.1 - - - +
371B ARG 2.9 12.2 + - - +
372B LEU* 3.4 8.1 - - - +
374B HIS* 1.3 79.1 + - - +
376B LEU* 1.3 57.8 + - + +
378B ARG* 3.0 13.8 + - - +
379B HIS* 2.8 33.4 + - + -
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Residues in contact with LEU 376 (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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339B VAL* 3.9 17.7 - - + -
343B PHE* 3.6 28.9 - - + -
372B LEU* 2.8 41.7 + - + +
373B LEU* 3.9 7.4 - - + +
375B ALA* 1.3 73.1 - - + +
377B ALA* 1.3 62.3 + - - +
379B HIS* 3.2 19.0 + - + +
380B CYS* 3.2 19.9 + - - -
399B PHE* 5.3 0.7 - - + -
403B VAL* 3.9 17.9 - - + +
406B LEU* 3.9 26.2 - - + -
407B VAL* 3.9 21.8 - - + -
443B ILE* 4.4 1.6 - - - -
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Residues in contact with ALA 377 (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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373B LEU 2.7 19.9 + - - +
374B HIS* 3.3 9.9 - - + +
375B ALA 3.1 0.2 - - - -
376B LEU* 1.3 75.7 - - - +
378B ARG* 1.3 64.7 + - - +
379B HIS 3.3 0.3 + - - -
380B CYS* 3.4 13.2 + - - +
381B GLN* 4.3 1.1 + - - +
423B LEU* 4.9 16.2 - - + -
439B ALA* 4.0 13.4 - - - +
440B VAL* 6.4 2.7 - - + -
443B ILE* 3.5 23.8 - - + +
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Residues in contact with ARG 378 (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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331B ALA 4.2 1.0 + - - -
332B GLY* 3.0 33.3 + - - -
333B HIS 3.3 20.2 + - - -
334B PRO* 3.7 18.4 - - - +
374B HIS* 2.9 20.0 + - + +
375B ALA* 3.0 13.1 + - - +
377B ALA* 1.3 75.8 - - - +
379B HIS* 1.3 73.0 + - - +
381B GLN* 3.2 43.5 + - - +
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Residues in contact with HIS 379 (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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331B ALA 3.2 12.9 + - - -
333B HIS 2.9 30.0 + - - -
334B PRO 3.3 14.4 + - - -
335B GLN 3.1 18.4 - - - -
336B TYR* 4.0 10.7 - - - +
339B VAL* 3.1 25.4 - - + +
375B ALA 2.8 23.7 + - - -
376B LEU* 3.2 15.6 + - + +
378B ARG* 1.3 86.0 + - - +
380B CYS* 1.3 57.8 + - - +
381B GLN 3.0 7.7 + - - +
396B PHE* 3.5 19.8 - - - -
399B PHE* 3.8 21.5 - + + -
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Residues in contact with CYS 380 (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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376B LEU 3.2 17.3 + - - -
377B ALA 3.9 8.5 - - - +
378B ARG 3.3 1.2 - - - -
379B HIS* 1.3 74.8 - - - +
381B GLN* 1.3 61.2 + - - +
382B LEU 3.6 1.6 + - - -
396B PHE* 4.1 3.0 - - - -
399B PHE* 4.8 0.7 - - - -
400B ARG* 3.3 41.4 + - - +
403B VAL* 3.6 30.3 - - - -
438B GLU* 4.0 0.5 - - - +
439B ALA* 3.9 13.4 - - + +
442B PHE* 4.0 28.7 - - + -
443B ILE* 4.1 9.2 - - + -
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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