Contacts of the helix formed by residues 355 - 376 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351B ARG 3.9 7.4 + - - +
352B GLN 4.0 13.5 + - - +
353B GLU 3.2 4.5 + - - -
354B VAL* 1.3 79.5 - - - +
356B ALA* 1.3 67.5 + - - +
357B VAL* 3.0 25.3 + - - +
358B VAL* 2.9 26.8 + - - +
359B LEU* 3.0 11.0 + - - +
454B TYR* 3.9 5.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 356 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355B ASN* 1.3 76.3 - - - +
357B VAL* 1.3 58.5 + - + +
359B LEU* 3.2 15.0 + - + +
360B LEU* 2.9 30.0 + - - +
454B TYR* 4.4 2.0 + - - -
484B PRO* 6.2 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 357 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355B ASN* 3.0 17.4 + - - +
356B ALA* 1.3 77.7 - - + +
358B VAL* 1.3 58.8 + - + +
360B LEU* 3.6 8.0 + - + +
361B TYR* 3.1 24.8 + - - +
516B PHE* 3.6 22.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 358 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353B GLU 3.4 20.6 - - - +
354B VAL* 3.8 13.9 - - + -
355B ASN* 2.9 24.3 + - - +
357B VAL* 1.3 77.2 - - + +
359B LEU* 1.3 66.0 + - - +
361B TYR* 3.2 7.9 + - + +
362B MET* 3.0 25.5 + - + +
394B HIS* 3.6 45.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 359 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B LEU* 3.6 31.6 - - + -
354B VAL* 3.9 13.2 - - + -
355B ASN 3.0 16.0 + - - +
356B ALA* 3.7 14.1 - - + +
358B VAL* 1.3 76.1 - - - +
360B LEU* 1.3 57.8 + - - +
362B MET* 3.3 8.5 + - + +
363B ALA* 2.9 29.5 + - - +
451B ILE* 3.8 34.3 - - + +
452B ALA* 4.7 6.3 - - - +
454B TYR* 3.6 31.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 360 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356B ALA 2.9 16.6 + - - +
357B VAL* 3.7 9.6 - - + +
359B LEU* 1.3 76.0 - - - +
361B TYR* 1.3 58.0 + - - +
363B ALA* 3.4 3.7 + - - +
364B THR* 2.4 37.7 + - - +
487B VAL* 5.8 4.0 - - + -
512B PHE* 3.5 31.0 - - + +
515B MET* 3.0 30.1 - - + +
516B PHE* 3.0 39.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 361 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357B VAL 3.1 9.4 + - - +
358B VAL* 3.2 13.0 + - + +
360B LEU* 1.3 77.5 - - - +
362B MET* 1.3 61.2 + - - +
364B THR* 3.8 3.4 - - - -
365B GLN* 3.2 59.2 + - + +
393B ASN 3.8 14.1 + - - -
394B HIS* 3.6 22.9 - - + -
395B LEU* 3.9 16.1 - - - +
516B PHE* 3.0 49.5 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 362 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342B LEU* 3.9 23.1 - - + -
345B TYR* 4.7 6.3 - - + -
346B LEU* 3.9 28.7 - - + -
354B VAL* 4.4 8.5 - - + -
358B VAL* 3.0 18.4 + - - +
359B LEU* 3.8 15.9 - - + +
361B TYR* 1.3 73.8 - - + +
363B ALA* 1.3 65.5 + - - +
365B GLN* 3.2 10.7 + - - +
366B ILE* 3.1 28.3 + - - +
390B VAL* 5.3 2.0 - - - -
394B HIS* 3.9 33.4 - - + +
396B VAL* 3.7 22.5 - - + +
451B ILE* 5.1 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 363 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359B LEU 2.9 16.9 + - - +
360B LEU* 3.9 5.2 - - - +
362B MET* 1.3 77.3 - - - +
364B THR* 1.3 62.7 + - - +
366B ILE* 3.3 5.4 + - - +
367B SER* 3.0 22.9 + - - -
444B PHE* 3.9 8.0 - - + -
448B LEU* 4.2 12.8 - - + -
451B ILE* 4.0 23.4 - - + +
512B PHE* 4.0 24.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 364 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360B LEU* 2.4 27.3 + - - +
361B TYR* 3.8 6.3 - - - -
363B ALA* 1.3 77.8 - - - +
365B GLN* 1.3 63.2 + - - +
367B SER* 2.9 20.7 + - - -
368B SER* 3.0 8.2 + - - -
509B HIS* 3.6 9.6 - - + +
512B PHE* 3.4 23.8 + - + +
513B GLU* 3.3 46.4 - - - +
516B PHE* 3.8 9.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 365 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316B ASN* 2.9 38.5 + - - +
361B TYR* 3.2 44.4 + - + +
362B MET* 3.2 12.5 + - - +
364B THR* 1.3 78.2 - - - +
366B ILE* 1.3 62.3 + - - +
368B SER* 3.1 7.9 + - - -
369B ALA 3.1 17.8 + - - -
394B HIS 2.8 24.2 + - - -
395B LEU* 3.4 11.1 - - - +
396B VAL* 2.9 29.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 366 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316B ASN* 5.5 0.7 - - - -
342B LEU* 3.8 22.2 - - + -
362B MET 3.1 15.1 + - - +
363B ALA 3.6 5.6 - - - +
364B THR 3.3 0.2 - - - -
365B GLN* 1.3 76.8 - - - +
367B SER* 1.3 61.7 + - - +
369B ALA* 3.2 3.1 + - - +
370B MET* 3.0 23.2 + - + +
383B LEU* 4.4 4.7 - - + -
388B CYS* 3.8 20.4 - - - -
396B VAL* 3.9 17.7 - - + -
398B VAL* 4.0 20.9 - - + -
444B PHE* 3.6 21.5 - - + -
447B LEU* 3.9 17.9 - - + -
451B ILE* 3.9 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 367 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363B ALA 3.0 13.6 + - - -
364B THR* 2.9 21.5 + - - -
366B ILE* 1.3 77.0 - - - +
368B SER* 1.3 56.4 + - - +
370B MET* 3.3 6.0 + - - +
371B GLU* 2.9 28.9 + - - +
444B PHE* 4.0 10.5 - - - -
505B PHE* 4.4 5.8 - - - +
508B ILE* 3.9 27.6 - - - -
509B HIS* 3.3 24.7 - - - +
512B PHE* 3.9 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 368 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B HIS* 3.3 24.4 + - - -
316B ASN* 4.5 2.6 + - - -
364B THR 3.0 12.9 + - - -
365B GLN* 3.1 12.8 + - - -
367B SER* 1.3 74.7 + - - +
369B ALA* 1.3 65.9 + - - +
371B GLU* 3.2 8.4 + - - +
372B TYR* 3.1 17.8 + - - +
509B HIS* 3.8 22.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 369 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B HIS* 3.6 14.4 - - - +
316B ASN* 3.8 26.9 - - + +
317B LEU* 4.0 15.5 - - + +
365B GLN 3.1 10.8 + - - +
366B ILE 3.2 8.5 + - - +
368B SER* 1.3 77.1 - - - +
370B MET* 1.3 62.8 + - + +
372B TYR* 3.1 5.4 + - - +
373B LEU* 3.1 25.1 + - - +
398B VAL* 4.1 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 370 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366B ILE* 3.0 25.2 + - + +
367B SER* 3.9 1.3 - - - +
368B SER 3.2 0.2 - - - -
369B ALA* 1.3 77.2 - - - +
371B GLU* 1.3 59.4 + - - +
373B LEU* 3.3 28.3 + - + +
374B GLU* 2.9 29.1 + - - +
380B HIS* 4.2 6.5 - - + -
383B LEU* 3.9 28.7 - - + -
398B VAL* 4.8 10.1 - - - -
437B ILE* 4.5 3.6 - - + -
440B ASP* 3.8 28.0 - - + +
444B PHE* 4.9 0.2 - - + -
505B PHE* 3.4 51.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 371 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367B SER 2.9 16.8 + - - +
368B SER* 3.2 8.3 + - - +
370B MET* 1.3 76.5 - - - +
372B TYR* 1.3 61.7 + - - +
374B GLU* 3.3 5.3 + - - +
375B LYS* 3.0 25.7 + - + +
505B PHE* 3.6 16.5 - - - +
506B ALA* 3.7 34.3 - - + +
509B HIS* 3.5 30.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 372 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311B GLU 4.0 8.3 + - - -
312B ILE* 4.6 14.4 - - + -
313B LYS* 3.3 44.8 + - - +
314B HIS* 3.6 36.1 - + + -
317B LEU* 4.2 9.2 - - + -
368B SER 3.1 6.1 + - - +
369B ALA 3.3 8.3 - - - +
370B MET 3.1 0.2 - - - -
371B GLU* 1.3 78.6 - - - +
373B LEU* 1.3 67.5 + - + +
375B LYS* 3.1 16.8 + - - +
376B LYS* 2.9 68.1 + - + +
378B PHE* 5.8 0.4 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 373 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B ILE* 4.0 10.3 - - + -
317B LEU* 3.9 27.1 - - + -
369B ALA 3.1 15.8 + - - +
370B MET* 3.3 36.5 + - + +
372B TYR* 1.3 80.9 - - + +
374B GLU* 1.3 62.5 + - - +
376B LYS* 3.6 2.1 - - - +
377B ASN 3.1 5.2 + - - -
378B PHE* 3.0 46.5 + - + +
380B HIS* 4.4 10.8 - - + +
403B LEU* 3.9 41.5 - - + -
437B ILE* 5.1 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 374 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370B MET 2.9 17.7 + - - +
371B GLU* 3.4 7.7 - - - +
373B LEU* 1.3 78.7 - - - +
375B LYS* 1.3 61.0 + - + +
377B ASN* 3.5 0.9 + - - +
408B THR* 2.5 42.8 + - + +
437B ILE* 3.7 29.4 - - + +
438B LYS* 5.2 0.2 + - - -
441B VAL* 5.0 0.5 - - - +
504B SER* 3.5 16.8 - - - -
505B PHE* 2.8 31.3 + - - +
506B ALA* 3.1 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 375 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371B GLU* 3.0 18.1 + - + +
372B TYR* 3.7 18.8 - - - +
374B GLU* 1.3 77.8 - - - +
376B LYS* 1.3 94.5 + - + +
377B ASN* 3.3 10.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 376 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372B TYR* 2.9 62.0 + - + +
373B LEU* 3.3 0.4 + - - -
375B LYS* 1.3 101.2 - - + +
377B ASN* 1.3 72.6 + - - +
378B PHE* 3.4 31.9 - - + -
----------------------------------------------------------
Back to top of page
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