Contacts of the helix formed by residues 362 - 379 (chain B) in PDB entry 4OIV
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 SER 362 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A GLU* 4.8 3.3 + - - -
360B GLY 3.6 2.6 + - - -
361B ILE* 1.3 78.6 - - - +
363B ASP* 1.3 62.0 + - - +
364B GLU* 3.0 23.0 + - - +
365B TYR* 2.9 37.5 + - - -
366B ILE* 3.3 10.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 363 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357B ARG* 4.8 12.2 + - - +
361B ILE 3.8 1.6 + - - +
362B SER* 1.3 70.3 + - - +
364B GLU* 1.3 66.7 + - - +
365B TYR 3.0 1.0 + - - -
366B ILE* 3.0 28.3 + - - +
367B THR* 3.1 29.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 364 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362B SER* 3.0 18.4 + - - +
363B ASP* 1.3 75.5 - - - +
365B TYR* 1.4 80.7 + - + +
368B PRO* 3.2 23.0 - - - +
448B ASN* 3.4 24.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 365 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A GLU* 5.5 1.6 - - - -
361B ILE* 4.2 11.7 - - + -
362B SER* 2.9 30.7 + - - +
364B GLU* 1.4 102.4 + - + +
366B ILE* 1.3 62.9 + - - +
367B THR 3.6 0.4 - - - -
368B PRO* 4.0 3.8 - - - +
369B MET* 3.0 29.8 + - - +
448B ASN* 3.7 42.0 + - + -
450B HIS* 5.2 2.4 - - - +
451B HIS* 3.4 55.0 + + + +
501B XX9 3.9 6.8 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
356B ILE* 3.6 35.4 - - + +
357B ARG* 3.8 32.1 - - + +
361B ILE* 3.5 36.8 - - + +
362B SER 3.6 7.4 - - - +
363B ASP* 3.0 17.5 + - - +
365B TYR* 1.3 79.1 - - - +
367B THR* 1.3 67.5 + - - +
369B MET* 3.1 2.8 + - - +
370B PHE* 2.9 46.3 + - + -
501B XX9 4.2 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 367 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357B ARG* 5.4 5.7 + - - +
363B ASP* 3.1 25.2 + - - +
366B ILE* 1.3 79.8 - - - +
368B PRO* 1.4 73.8 - - + +
369B MET 3.1 0.5 + - - -
370B PHE* 3.3 3.9 + - - +
371B SER* 3.0 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 368 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364B GLU* 3.2 27.1 - - - +
365B TYR* 4.0 5.6 - - - +
366B ILE 3.9 0.9 - - - -
367B THR* 1.4 93.7 - - + +
369B MET* 1.3 58.2 + - + +
371B SER* 3.3 8.5 + - - +
372B PHE* 3.0 28.2 + - - +
447B PHE* 3.6 32.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 369 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333B PHE* 4.0 38.1 - - + +
336B SER* 3.6 9.0 - - - +
365B TYR* 3.0 22.4 - - + +
366B ILE 3.1 7.0 + - - +
368B PRO* 1.3 78.3 - - + +
370B PHE* 1.3 57.8 + - + +
372B PHE* 3.1 8.6 + - + +
373B TYR* 2.9 66.7 + - + +
447B PHE* 3.9 24.9 - - + -
501B XX9 3.8 31.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 370 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340B PHE* 3.6 44.4 - + + -
353B GLU* 3.7 35.9 - - + -
356B ILE* 4.0 18.4 - - + -
357B ARG* 3.9 15.7 - - - +
366B ILE* 2.9 40.2 + - + +
367B THR* 4.2 2.9 - - - +
369B MET* 1.3 74.7 - - + +
371B SER* 1.3 63.5 + - - +
373B TYR* 3.2 24.6 + + + +
374B LYS* 3.1 41.2 + - - +
501B XX9 4.7 3.8 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 371 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367B THR* 3.0 20.7 + - - +
368B PRO* 3.3 12.6 + - - +
370B PHE* 1.3 74.8 - - - +
372B PHE* 1.4 61.7 + - - +
374B LYS* 3.2 16.3 + - - +
375B SER* 3.1 23.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 372 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333B PHE 4.6 5.8 - - - -
334B LEU* 4.2 11.0 - - + -
337B ALA* 4.2 11.4 - - + -
368B PRO 3.0 15.2 + - - +
369B MET* 3.1 11.0 + - + +
371B SER* 1.4 76.7 - - - +
373B TYR* 1.3 76.0 + + - +
375B SER* 3.0 8.7 + - - -
376B ILE* 3.0 52.8 + - + +
440B ARG* 3.7 35.2 - - + +
443B GLU* 4.1 9.9 - - + -
444B LEU* 3.6 48.5 - - + -
447B PHE* 3.8 12.3 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 373 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333B PHE 4.3 0.4 - - - -
336B SER* 2.6 32.6 + - - -
337B ALA* 3.5 26.9 - - + -
340B PHE* 3.3 36.3 - + + -
341B ASN* 2.8 37.4 + - - +
369B MET* 2.9 35.7 + - + +
370B PHE* 3.2 43.0 + + + +
372B PHE* 1.3 78.6 - + - +
374B LYS* 1.3 56.7 + - + +
376B ILE* 3.3 3.6 + - - +
377B GLY* 2.9 14.9 + - - -
501B XX9 3.2 22.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 374 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357B ARG* 5.6 2.6 - - - +
370B PHE* 3.1 34.8 + - - +
371B SER* 3.2 14.3 + - - +
373B TYR* 1.3 75.0 - - + +
375B SER* 1.3 57.8 + - - +
377B GLY* 3.1 3.4 + - - -
378B GLU* 3.0 39.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 375 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371B SER 3.1 13.3 + - - -
372B PHE* 3.0 13.7 + - - -
374B LYS* 1.3 76.2 - - - +
376B ILE* 1.3 60.5 + - - +
378B GLU* 3.6 15.4 + - - +
379B LEU* 3.4 26.3 + - - +
440B ARG* 2.8 37.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 376 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334B LEU* 4.8 7.0 - - + -
337B ALA* 4.4 5.4 - - + -
341B ASN* 3.4 11.7 - - + +
372B PHE* 3.0 50.3 + - + +
373B TYR* 3.6 8.1 - - - +
375B SER* 1.3 75.4 + - - +
377B GLY* 1.3 65.3 + - - +
378B GLU 3.2 0.2 - - - -
379B LEU* 3.2 19.1 + - + +
380B LYS 3.9 2.6 + - - -
381B MET* 4.3 21.1 + - + +
386B TYR* 3.2 31.2 - - + +
440B ARG* 3.4 31.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 377 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B ASN* 3.9 16.2 - - - -
373B TYR 2.9 14.0 + - - -
374B LYS* 3.1 4.4 + - - -
376B ILE* 1.3 77.1 - - - +
378B GLU* 1.3 60.6 + - - +
380B LYS* 3.3 23.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 378 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374B LYS* 3.0 23.3 + - + +
375B SER* 3.7 17.1 - - - +
376B ILE 3.2 0.2 - - - -
377B GLY* 1.3 77.3 - - - +
379B LEU* 1.3 63.9 + - + +
380B LYS* 3.2 11.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 379 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375B SER 3.4 11.0 - - - +
376B ILE* 3.2 10.3 + - + +
377B GLY 3.2 1.0 - - - -
378B GLU* 1.3 79.1 - - + +
380B LYS* 1.3 69.9 - - - +
381B MET* 3.3 12.3 + - + -
427B GLN* 4.4 2.8 + - - +
433B HIS* 3.3 26.1 - - + +
436B GLU* 4.1 33.2 - - + +
437B LEU* 3.9 20.2 - - + -
440B ARG* 3.5 38.1 - - + +
----------------------------------------------------------
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