Contacts of the helix formed by residues 444 - 452 (chain D) in PDB entry 1EJI
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 THR 444 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372D ARG* 3.5 3.0 + - - +
442D LYS* 3.2 6.3 + - - +
443D ALA* 1.3 77.7 - - - +
445D LEU* 1.3 60.3 + - - +
446D LYS* 2.7 21.7 + - - +
447D GLU* 2.5 52.7 + - - +
448D PHE* 3.0 8.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 445 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369D ASP* 5.8 0.9 - - - +
371D GLY* 5.8 9.0 - - - -
372D ARG* 3.6 35.3 - - + +
396D LEU* 4.2 19.7 - - - +
444D THR* 1.3 74.7 + - - +
446D LYS* 1.3 89.5 + - + +
448D PHE* 3.5 3.9 - - - +
449D LYS* 2.6 39.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 446 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444D THR* 2.7 13.2 + - - +
445D LEU* 1.3 101.4 - - + +
447D GLU* 1.3 63.9 + - - +
448D PHE 3.1 0.2 - - - -
449D LYS* 3.5 33.2 - - + +
450D GLU* 2.5 45.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 447 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439D MSE 3.7 6.3 - - + -
443D ALA* 3.6 21.9 - - + -
444D THR* 2.5 46.2 + - - +
446D LYS* 1.3 78.8 - - - +
448D PHE* 1.3 59.1 + - - +
450D GLU* 4.6 2.8 - - - +
451D LYS* 2.8 55.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 448 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372D ARG* 3.6 50.0 - - + +
375D LYS* 5.5 5.2 - - + -
376D VAL* 3.9 16.4 - - + -
432D THR* 3.5 31.2 - - + -
435D ILE* 3.3 39.9 - - + -
436D GLN* 3.8 13.2 - - + -
439D MSE 3.8 19.0 - - + +
444D THR 3.0 10.0 + - - +
445D LEU 3.5 8.3 - - - +
447D GLU* 1.3 74.0 - - - +
449D LYS* 1.3 72.5 + - - +
450D GLU 3.0 1.3 - - - -
451D LYS 4.7 0.2 - - - +
452D LEU* 2.7 38.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 449 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375D LYS* 4.8 34.8 - - + +
445D LEU* 2.6 24.6 + - + +
446D LYS* 3.5 43.5 - - + +
448D PHE* 1.3 79.5 - - - +
450D GLU* 1.3 65.6 + - + +
452D LEU* 3.6 10.8 - - - +
453D ALA* 3.9 6.6 + - - +
454D GLY 4.0 2.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 450 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446D LYS* 2.5 40.8 + - - +
447D GLU* 3.9 3.7 - - - +
448D PHE 2.9 1.2 + - - -
449D LYS* 1.3 75.9 - - + +
451D LYS* 1.3 68.5 + - + +
452D LEU 2.3 18.9 + - - -
454D GLY* 2.4 38.3 + - - -
455D ASP* 4.4 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 451 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435D ILE* 4.4 5.1 - - + +
438D HIS* 5.3 11.3 - - + +
439D MSE 4.1 26.2 - - + -
447D GLU* 2.8 56.3 + - - +
448D PHE 4.3 0.9 - - - +
450D GLU* 1.3 89.4 + - + +
452D LEU* 1.3 63.3 + - - +
455D ASP* 3.1 36.3 - - - +
456D GLU* 3.3 17.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 452 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375D LYS* 5.3 10.3 - - + +
376D VAL* 4.4 20.9 - - + +
379D ALA* 5.3 8.5 - - + -
431D LEU* 4.4 11.4 - - + -
435D ILE* 3.4 39.7 - - + +
448D PHE* 2.7 36.5 + - + +
449D LYS 3.6 7.0 - - - +
450D GLU 2.3 12.5 + - - -
451D LYS* 1.3 79.7 - - - +
453D ALA* 1.3 78.1 + - + +
454D GLY* 2.6 16.4 + - - -
455D ASP 3.5 2.8 + - - -
456D GLU* 4.2 13.7 - - - +
----------------------------------------------------------
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