Contacts of the helix formed by residues 418 - 427 (chain L) in PDB entry 6QX2
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 L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379L HIS* 2.6 36.6 + - - -
412L GLN* 3.9 3.4 - - - +
416L LYS 4.4 0.2 + - - -
417L LEU* 1.3 75.0 - - - +
419L GLU* 1.3 58.2 + - - +
420L LYS* 3.5 5.2 + - - +
421L GLN* 3.0 25.8 + - - +
422L ALA* 3.0 27.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 419 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408L MET* 3.4 25.3 - - + +
412L GLN* 3.7 24.3 - - - +
418L SER* 1.3 71.5 - - - +
420L LYS* 1.3 58.4 + - + +
422L ALA 3.3 0.3 + - - -
423L GLN* 3.0 44.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 420 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376L ASP* 6.1 4.7 - - - +
379L HIS* 4.6 9.9 - - + +
380L ILE* 3.4 24.9 - - + +
418L SER* 3.3 8.3 + - - +
419L GLU* 1.3 80.7 - - + +
421L GLN* 1.3 55.5 + - - +
423L GLN* 3.6 6.8 + - - +
424L ALA* 3.2 20.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 421 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379L HIS* 2.8 58.7 + - + +
380L ILE* 4.3 6.7 - - - +
382L GLU* 3.9 9.5 + - - +
383L GLY* 3.5 27.6 - - - +
386L ILE* 5.4 2.8 - - - +
416L LYS 4.8 1.2 - - - +
417L LEU* 3.6 17.0 - - + +
418L SER* 3.0 35.2 + - - +
420L LYS* 1.3 74.5 - - - +
422L ALA* 1.3 60.4 + - - +
424L ALA* 3.3 5.0 + - - +
425L ILE* 3.1 33.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 422 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408L MET* 3.7 35.7 - - + +
411L LEU* 4.3 13.9 - - + +
412L GLN* 4.1 6.5 - - + -
417L LEU* 4.6 4.9 - - + +
418L SER 3.0 16.4 + - - +
419L GLU 3.7 2.0 - - - +
421L GLN* 1.3 73.4 - - - +
423L GLN* 1.3 66.2 + - - +
425L ILE* 3.3 11.0 + - - +
426L LEU* 3.1 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 423 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431J ARG* 3.2 25.7 + - - +
408L MET* 3.2 29.7 - - + +
419L GLU* 3.0 30.7 + - - +
420L LYS* 3.7 7.9 - - - +
422L ALA* 1.3 75.9 - - - +
424L ALA* 1.3 56.3 + - - +
426L LEU* 3.2 6.8 + - - +
427L ASP* 3.0 39.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 424 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380L ILE* 3.7 32.5 - - + +
384L LEU* 4.1 11.2 - - + +
420L LYS 3.2 12.9 + - - +
421L GLN* 3.4 9.9 - - - +
422L ALA 3.3 0.2 - - - -
423L GLN* 1.3 80.0 - - - +
425L ILE* 1.3 56.0 + - - +
427L ASP* 3.4 7.9 + - - +
428L MET* 3.0 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 425 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430J LEU* 3.4 16.4 - - + +
383L GLY 3.5 24.7 - - - +
384L LEU* 4.2 11.0 - - + -
387L ALA* 3.7 22.4 - - + -
394L ILE* 3.9 29.2 - - + -
398L ILE* 4.7 1.6 - - + -
411L LEU* 4.5 10.3 - - + -
417L LEU* 3.5 30.1 - - + -
421L GLN 3.1 21.9 + - - +
422L ALA* 3.3 5.6 + - - +
423L GLN 3.3 0.2 - - - -
424L ALA* 1.3 73.2 - - - +
426L LEU* 1.3 65.0 + - - +
427L ASP 3.2 0.2 - - - -
428L MET* 3.3 21.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 426 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429J ARG* 4.1 0.7 - - - +
430J LEU* 3.7 7.5 + - - -
431J ARG* 3.1 67.0 + - + +
434J THR* 5.5 0.4 - - + -
398L ILE* 4.0 32.1 - - + -
404L ASP* 4.0 12.1 - - + +
407L ALA* 4.2 11.2 - - + -
408L MET* 3.6 44.4 - - + +
411L LEU* 4.1 5.4 - - + -
422L ALA 3.1 10.4 + - - +
423L GLN* 3.6 11.7 - - - +
425L ILE* 1.3 76.3 - - - +
427L ASP* 1.3 59.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 427 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429J ARG* 2.2 46.0 + - - +
431J ARG* 3.0 28.8 + - - -
423L GLN* 3.0 24.8 + - - +
424L ALA* 3.6 8.4 - - - +
425L ILE 3.2 0.2 - - - -
426L LEU* 1.3 73.8 - - - +
428L MET* 1.3 65.5 + - - +
429L ARG* 3.5 4.0 + - - +
----------------------------------------------------------
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