Contacts of the helix formed by residues 355 - 376 (chain A) in PDB entry 1OPL
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 ASN 355 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A SER* 5.3 10.3 - - - -
351A ARG 3.9 7.0 - - - +
352A GLN* 4.0 13.7 + - - +
353A GLU 3.2 4.2 + - - -
354A VAL* 1.3 78.4 - - - +
356A ALA* 1.3 66.4 + - - +
357A VAL* 3.0 26.4 + - - +
358A VAL* 2.9 27.2 + - - +
359A LEU* 3.0 11.1 + - - +
454A TYR* 3.9 6.1 - - - -
522A SER* 5.2 3.8 + - - -
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Residues in contact with ALA 356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A ASN* 1.3 76.6 - - - +
357A VAL* 1.3 57.8 + - + +
359A LEU* 3.2 6.7 + - - +
360A LEU* 2.9 29.1 + - - +
454A TYR* 4.4 2.4 + - - -
521A ILE* 3.7 22.8 - - + +
522A SER* 5.2 2.5 - - - +
525A VAL* 3.8 30.3 - - + -
538A MYR 3.9 18.9 - - + +
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Residues in contact with VAL 357 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A ASN* 4.0 8.3 - - - +
157A GLU* 3.8 25.4 - - + +
158A TYR* 3.7 31.9 - - + +
161A SER* 5.7 2.7 - - - -
355A ASN* 3.0 17.2 + - - +
356A ALA* 1.3 76.5 - - - +
358A VAL* 1.3 57.3 + - + +
360A LEU* 3.6 7.0 + - + +
361A TYR* 3.1 24.9 + - - +
521A ILE* 3.3 26.0 - - + -
522A SER* 3.7 16.8 - - - +
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Residues in contact with VAL 358 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A TYR* 4.0 22.0 - - + -
161A SER* 5.1 5.4 - - - +
353A GLU 3.4 20.6 - - - +
354A VAL* 3.8 13.9 - - + -
355A ASN* 2.9 24.2 + - - +
357A VAL* 1.3 77.4 - - + +
359A LEU* 1.3 64.4 + - - +
361A TYR* 3.2 6.6 + - + +
362A MET* 3.0 26.4 + - + +
394A HIS* 3.6 42.0 - - + +
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Residues in contact with LEU 359 (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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346A LEU* 3.6 31.4 - - + -
354A VAL* 3.9 13.5 - - + -
355A ASN 3.0 16.3 + - - +
356A ALA* 3.2 6.3 + - - +
358A VAL* 1.3 76.0 - - - +
360A LEU* 1.3 57.8 + - - +
362A MET* 3.3 9.4 + - + +
363A ALA* 2.9 29.5 + - - +
451A ILE* 3.8 33.8 - - + +
452A ALA* 4.7 0.9 - - - -
454A TYR* 3.6 31.6 - - + +
538A MYR 3.9 33.5 - - + +
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Residues in contact with LEU 360 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A ASN* 3.1 47.8 - - + +
356A ALA 2.9 16.4 + - - +
357A VAL* 3.7 6.7 - - + +
359A LEU* 1.3 77.3 - - - +
361A TYR* 1.3 63.3 + - - +
363A ALA 3.4 0.5 + - - -
364A THR* 2.8 35.7 + - - +
512A PHE* 3.6 31.2 - - + +
515A MET* 5.4 0.7 - - - -
516A PHE* 3.9 26.0 - - + -
521A ILE* 4.1 13.5 - - + -
538A MYR 3.5 17.6 - - + +
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Residues in contact with TYR 361 (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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154A ASN* 5.5 4.7 - - - +
155A ALA* 4.2 32.8 - - + -
158A TYR* 3.9 32.8 - + + -
159A LEU* 5.4 4.9 - - + +
240A ASN* 4.6 5.0 + - - -
357A VAL 3.1 15.5 + - - +
358A VAL* 3.4 10.5 - - - +
360A LEU* 1.3 78.4 - - - +
362A MET* 1.3 60.5 + - - +
364A THR* 3.5 6.7 + - - -
365A GLN* 3.2 59.1 + - + +
393A ASN 3.8 13.8 + - - -
394A HIS* 3.6 21.5 - - + -
395A LEU* 3.9 17.2 - - - +
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Residues in contact with MET 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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342A LEU* 3.9 24.2 - - + -
345A TYR* 4.7 5.6 - - + -
346A LEU* 3.9 27.8 - - + -
354A VAL* 4.4 9.0 - - + -
358A VAL* 3.0 16.8 + - + +
359A LEU* 3.8 16.2 - - + +
361A TYR* 1.3 75.1 - - + +
363A ALA* 1.3 65.0 + - - +
365A GLN* 3.2 9.3 + - - +
366A ILE* 3.1 28.3 + - - +
390A VAL* 5.3 1.6 - - - -
394A HIS* 3.9 34.8 - - + +
396A VAL* 3.7 22.7 - - + +
451A ILE* 5.1 7.0 - - + -
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Residues in contact with ALA 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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359A LEU 2.9 17.0 + - - +
360A LEU 3.9 3.6 - - - +
362A MET* 1.3 76.9 - - - +
364A THR* 1.3 63.1 + - - +
366A ILE* 3.3 6.0 + - - +
367A SER* 3.0 23.4 + - - -
444A PHE* 3.9 7.3 - - + -
448A LEU* 4.2 5.4 - - + -
451A ILE* 4.0 22.1 - - + +
512A PHE* 4.0 16.8 - - + -
538A MYR 3.9 18.4 - - + -
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Residues in contact with THR 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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152A SER* 5.8 0.4 - - - +
154A ASN* 5.2 2.5 + - - +
360A LEU* 2.8 26.9 + - - +
361A TYR* 3.8 8.5 - - - -
363A ALA* 1.3 77.8 - - - +
365A GLN* 1.3 61.8 - - + +
367A SER* 2.9 21.4 + - - +
368A SER* 3.0 8.2 + - - -
509A HIS* 3.6 25.3 - - + +
512A PHE* 3.6 25.0 - - + +
513A GLU* 4.1 22.3 + - - +
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Residues in contact with GLN 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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316A ASN* 3.1 38.7 + - - +
361A TYR* 3.2 46.3 + - + +
362A MET* 3.2 11.1 + - - +
364A THR* 1.3 78.0 - - - +
366A ILE* 1.3 62.0 + - - +
368A SER* 3.1 7.4 + - - -
369A ALA 3.1 17.5 + - - -
394A HIS 2.8 24.5 + - - -
395A LEU* 3.4 12.5 - - - +
396A VAL* 2.9 28.9 + - + +
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Residues in contact with ILE 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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316A ASN* 5.4 0.2 - - - -
342A LEU* 3.8 21.8 - - + -
362A MET 3.1 16.2 + - - +
363A ALA* 3.6 6.5 - - - +
365A GLN* 1.3 77.0 - - - +
367A SER* 1.3 61.5 + - - +
369A ALA* 3.2 3.5 + - - +
370A MET* 3.0 22.6 + - + +
383A LEU* 4.4 5.2 - - + -
388A CYS* 3.8 20.2 - - - -
396A VAL* 3.9 17.7 - - + -
398A VAL* 4.0 21.8 - - + -
444A PHE* 3.6 20.6 - - + -
447A LEU* 3.9 17.7 - - + -
451A ILE* 3.9 15.9 - - + -
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Residues in contact with SER 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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363A ALA 3.0 14.1 + - - -
364A THR 2.9 18.2 + - - -
366A ILE* 1.3 77.1 - - - +
368A SER* 1.3 56.0 + - - +
370A MET* 3.3 6.1 + - - +
371A GLU* 2.9 29.1 + - - +
444A PHE* 4.0 10.5 - - - -
505A PHE* 4.4 5.2 - - - +
508A ILE* 3.9 27.6 - - - -
509A HIS* 3.3 24.5 - - - +
512A PHE* 3.7 6.6 - - - -
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Residues in contact with SER 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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314A HIS* 3.1 28.2 + - - -
316A ASN* 4.1 5.0 + - - -
364A THR 3.0 12.9 + - - -
365A GLN* 3.1 11.2 + - - -
367A SER* 1.3 75.3 + - - +
369A ALA* 1.3 66.7 + - - +
371A GLU* 3.2 9.5 + - - +
372A TYR* 3.1 17.8 + - - +
509A HIS* 3.8 22.2 + - - -
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Residues in contact with ALA 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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314A HIS* 3.6 12.7 - - - -
316A ASN* 3.4 33.7 - - + +
317A LEU* 3.9 12.0 - - + +
365A GLN 3.1 6.2 + - - +
366A ILE 3.2 7.6 + - - +
368A SER* 1.3 77.4 - - - +
370A MET* 1.3 63.1 + - - +
372A TYR* 3.1 6.2 + - - +
373A LEU* 3.1 24.6 + - - +
398A VAL* 3.8 15.5 - - + -
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Residues in contact with MET 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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366A ILE* 3.0 26.3 + - + +
367A SER* 3.9 1.1 - - - +
368A SER 3.2 0.2 - - - -
369A ALA* 1.3 74.1 - - - +
371A GLU* 1.3 60.2 + - - +
373A LEU* 3.3 27.5 + - + +
374A GLU* 2.9 29.3 + - - +
380A HIS* 4.2 5.8 - - + -
383A LEU* 3.9 28.9 - - + -
398A VAL* 4.6 11.4 - - - -
437A ILE* 4.5 3.8 - - + -
440A ASP* 3.8 27.8 - - + +
444A PHE* 4.9 0.2 - - + -
505A PHE* 3.4 50.6 - - + -
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Residues in contact with GLU 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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367A SER 2.9 15.7 + - - +
368A SER* 3.5 7.8 + - - +
370A MET* 1.3 76.0 - - - +
372A TYR* 1.3 63.4 + - - +
374A GLU* 3.3 5.7 + - - +
375A LYS* 3.0 26.2 + - + +
505A PHE* 3.6 16.5 - - - +
506A ALA* 3.7 34.1 - - + +
509A HIS* 3.5 31.5 + - - -
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Residues in contact with TYR 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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311A GLU 3.7 9.9 + - - -
312A ILE* 4.0 19.7 - - + -
313A LYS* 3.0 48.4 + - - +
314A HIS* 3.4 31.9 - + + -
317A LEU* 3.7 16.6 - - + -
368A SER 3.1 5.8 + - - +
369A ALA 3.3 8.1 - - - +
370A MET 3.1 0.2 - - - -
371A GLU* 1.3 78.9 - - - +
373A LEU* 1.3 66.2 + - + +
375A LYS* 3.1 16.4 + - - +
376A LYS* 2.9 67.3 + - + +
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Residues in contact with LEU 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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312A ILE* 4.1 10.3 - - + -
317A LEU* 3.7 28.9 - - + -
369A ALA 3.1 15.1 + - - +
370A MET* 3.3 36.5 + - + +
372A TYR* 1.3 79.4 - - + +
374A GLU* 1.3 63.6 + - - +
376A LYS* 3.3 2.1 + - - +
377A ASN 3.1 5.4 + - - -
378A PHE* 3.0 47.4 + - + +
380A HIS* 4.4 11.0 - - + +
403A LEU* 3.9 41.3 - - + -
437A ILE* 5.1 0.2 - - + -
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Residues in contact with GLU 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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370A MET 2.9 18.3 + - - +
371A GLU* 3.4 6.1 - - - +
373A LEU* 1.3 77.4 - - - +
375A LYS* 1.3 62.2 + - - +
377A ASN 3.5 0.7 + - - -
408A THR* 2.5 43.3 + - + +
437A ILE* 3.8 30.5 - - + +
438A LYS* 5.2 0.2 + - - -
441A VAL* 5.0 0.3 - - - +
504A SER* 3.5 16.6 - - - -
505A PHE* 2.8 30.7 + - - -
506A ALA* 3.1 29.5 + - - +
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Residues in contact with LYS 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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371A GLU* 3.0 18.5 + - + +
372A TYR* 3.1 19.4 + - - +
374A GLU* 1.3 78.2 - - + +
376A LYS* 1.3 92.2 + - + +
377A ASN* 3.3 10.7 + - - +
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Residues in contact with LYS 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 TYR* 2.9 62.0 + - + +
373A LEU* 3.3 1.3 + - - +
375A LYS* 1.3 101.1 - - + +
377A ASN* 1.3 73.8 + - - +
378A PHE* 3.4 31.5 - - + -
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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
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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