Contacts of the helix formed by residues 418 - 429 (chain A) in PDB entry 1OMW
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 418 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A GLU* 2.6 37.9 + - - -
417A PHE* 1.3 75.1 - - - +
419A PRO* 1.3 69.6 - - - +
420A GLU* 3.2 14.2 + - - +
421A LEU* 2.9 17.0 + - - +
422A ARG* 2.8 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 419 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417A PHE 4.5 1.6 - - - +
418A SER* 1.3 87.0 - - - +
420A GLU* 1.3 80.5 + - - +
422A ARG* 3.8 16.7 - - + +
423A SER* 3.3 24.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 420 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A GLU* 5.2 0.7 - - - +
295A ARG* 6.0 0.7 - - - +
418A SER* 3.2 11.6 + - - +
419A PRO* 1.3 94.4 - - + +
421A LEU* 1.3 58.8 + - - +
422A ARG 3.6 0.2 + - - -
423A SER* 3.8 6.2 + - - -
424A LEU* 3.6 10.7 + - - +
451A PRO* 3.5 25.4 - - - +
452A PHE* 3.3 41.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 421 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A GLU* 3.6 24.0 - - + +
294A MET* 4.4 5.6 - - + -
385A LEU* 3.4 37.7 - - + -
417A PHE* 3.4 28.9 - - + -
418A SER* 2.9 15.9 + - - +
420A GLU* 1.3 77.9 - - - +
422A ARG* 1.3 63.0 + - - +
424A LEU* 3.6 3.0 + - + +
425A LEU* 3.2 42.6 + - + +
452A PHE* 3.4 36.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 422 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413A LEU* 3.6 41.3 - - + +
414A PRO 4.3 12.5 + - - -
415A ASP* 6.0 1.4 - - - +
417A PHE* 4.7 8.4 + - + -
418A SER 2.8 19.4 + - - +
419A PRO* 3.8 17.2 - - + +
420A GLU 3.2 0.6 - - - -
421A LEU* 1.3 80.4 - - - +
423A SER* 1.3 55.9 + - - +
426A GLU* 3.1 45.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 423 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419A PRO 3.3 11.7 + - - -
420A GLU* 3.8 8.7 + - - -
422A ARG* 1.3 77.6 - - - +
424A LEU* 1.3 60.7 + - - +
425A LEU 3.4 0.7 - - - -
426A GLU* 4.0 14.4 - - - +
427A GLY* 2.9 23.2 + - - -
437A LEU* 4.5 3.8 - - - +
450A SER* 4.7 0.4 + - - -
451A PRO* 4.3 19.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 424 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A MET* 4.7 1.6 - - + -
381A LEU* 4.6 11.4 - - + -
420A GLU 3.6 8.8 + - - +
421A LEU* 3.6 8.7 + - + +
423A SER* 1.3 78.4 + - - +
425A LEU* 1.3 67.6 + - + +
427A GLY* 3.6 0.2 - - - -
428A LEU* 2.8 56.4 + - + +
437A LEU* 4.1 11.4 - - + +
447A VAL* 4.4 5.4 - - + -
450A SER* 3.2 38.1 - - - +
452A PHE* 3.9 29.6 - - + -
453A PHE* 3.9 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 425 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A GLY* 3.9 28.9 - - - +
381A LEU* 4.9 6.1 - - + -
382A PHE* 4.6 17.0 - - + +
385A LEU* 4.6 2.9 - - + -
411A VAL* 6.2 0.7 - - - -
413A LEU* 4.0 11.2 - - + -
417A PHE* 3.5 35.0 - - + -
421A LEU* 3.2 36.1 + - + +
422A ARG 3.9 4.3 - - - +
424A LEU* 1.3 84.6 - - + +
426A GLU* 1.3 65.0 + - - +
428A LEU* 4.7 1.1 - - + -
429A LEU* 3.0 41.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 426 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413A LEU* 4.8 8.1 - - + +
422A ARG* 3.1 47.6 + - - +
423A SER* 4.0 14.3 - - - +
424A LEU 3.4 0.2 - - - -
425A LEU* 1.3 74.3 - - - +
427A GLY* 1.3 67.8 + - - +
429A LEU* 3.9 2.7 - - - -
430A GLN* 3.3 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 427 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A SER 2.9 20.1 + - - -
424A LEU 3.6 1.3 - - - -
425A LEU 3.3 0.2 - - - -
426A GLU* 1.3 79.9 - - - +
428A LEU* 1.3 58.9 + - - +
429A LEU 3.2 0.5 + - - -
430A GLN* 3.4 9.0 - - - +
435A ARG 5.7 0.7 - - - -
436A ARG* 3.3 12.4 - - - +
437A LEU* 3.2 33.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 428 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A TRP* 3.5 26.0 - - + +
375A PHE* 3.5 21.0 - - - -
377A LEU* 4.6 10.8 - - + -
378A GLY* 4.0 26.0 - - - +
381A LEU* 4.8 2.5 - - + -
424A LEU* 2.8 51.9 + - + +
425A LEU* 4.2 3.8 - - + +
427A GLY* 1.3 71.6 - - - +
429A LEU* 1.3 58.9 + - - +
430A GLN 3.5 0.4 - - - -
436A ARG* 3.6 15.0 + - - -
437A LEU* 3.8 29.6 - - + +
447A VAL* 4.1 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 429 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A PHE* 3.2 46.6 - - + +
378A GLY* 3.8 26.7 - - - +
379A CYS* 4.0 9.2 - - - -
382A PHE* 5.5 2.2 - - + -
390A PRO* 4.7 11.0 - - + -
391A PHE* 5.4 3.9 - - + -
410A ALA* 6.1 0.9 - - - -
411A VAL* 4.0 29.3 - - + +
413A LEU* 6.0 0.7 - - + -
425A LEU* 3.0 31.5 + - + +
426A GLU* 3.9 4.5 - - - +
427A GLY 3.2 0.4 - - - -
428A LEU* 1.3 86.8 - - + +
430A GLN* 1.3 63.2 + - - +
431A ARG* 3.4 7.3 + - - -
----------------------------------------------------------
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