Contacts of the helix formed by residues 444 - 453 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372B ARG* 4.0 4.4 + - - -
397B ARG* 4.6 1.3 - - - +
442B LYS 4.6 4.0 - - - +
443B ALA* 1.3 79.5 - - - +
445B LEU* 1.3 60.1 + - - +
446B LYS* 3.1 10.9 + - - +
447B GLU* 2.7 47.0 + - + +
448B PHE* 3.1 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 445 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371B GLY* 4.2 10.3 - - - +
372B ARG* 3.7 42.4 - - + +
375B LYS* 6.0 1.6 - - + -
396B LEU 5.2 4.3 - - - +
397B ARG* 3.5 41.3 - - + +
444B THR* 1.3 71.9 - - - +
446B LYS* 1.3 69.3 + - + +
447B GLU 3.1 0.2 - - - -
448B PHE* 3.2 11.0 + - + +
449B LYS* 2.9 42.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 446 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444B THR* 3.1 8.0 + - - +
445B LEU* 1.3 85.6 - - + +
447B GLU* 1.3 59.5 + - + +
449B LYS* 3.3 30.3 - - + +
450B GLU* 2.9 30.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 447 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439B MSE 4.8 3.8 - - + +
440B ALA* 5.6 3.8 - - - +
442B LYS 4.1 3.6 - - - +
443B ALA* 4.0 13.6 - - + +
444B THR* 2.7 54.5 + - + +
446B LYS* 1.3 75.0 - - + +
448B PHE* 1.3 66.0 + - - +
450B GLU* 2.8 30.2 + - + +
451B LYS* 3.1 8.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 448 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372B ARG* 3.7 51.1 - - + +
375B LYS* 4.8 9.4 - - + -
376B VAL* 3.7 24.7 - - + -
432B THR* 3.9 5.2 - - + -
435B ILE* 3.2 34.1 - - + +
436B GLN* 3.9 20.0 - - + -
439B MSE 3.7 23.5 - - + +
444B THR 3.1 14.7 + - - +
445B LEU* 3.3 17.7 - - + +
447B GLU* 1.3 74.8 - - - +
449B LYS* 1.3 67.8 + - + +
450B GLU 3.0 1.2 + - - -
451B LYS* 3.4 3.5 + - - +
452B LEU* 3.1 28.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 449 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375B LYS* 4.4 36.7 - - + +
445B LEU* 2.9 33.3 + - - +
446B LYS* 3.3 37.0 - - + +
447B GLU 3.1 0.2 - - - -
448B PHE* 1.3 82.2 - - + +
450B GLU* 1.3 61.8 + - - +
452B LEU* 3.6 10.5 - - + +
453B ALA* 3.2 18.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 450 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446B LYS* 2.9 21.8 - - - +
447B GLU* 2.8 21.6 + - + +
449B LYS* 1.3 75.7 - - - +
451B LYS* 1.3 55.3 + - - +
452B LEU 2.7 4.2 + - - -
453B ALA* 2.5 38.4 + - - +
455B ASP* 3.5 10.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 451 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435B ILE* 4.3 19.5 - - + +
438B HIS* 2.8 41.5 + - - +
439B MSE 4.3 23.6 - - + +
447B GLU 3.1 6.1 + - - +
448B PHE 4.0 6.7 - - - +
450B GLU* 1.3 79.0 - - - +
452B LEU* 1.3 58.0 + - - +
453B ALA 3.7 0.6 - - - +
455B ASP* 3.4 23.9 - - - +
456B GLU* 4.5 24.1 + - + -
458B ILE* 3.3 19.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 452 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375B LYS* 4.4 23.3 - - + +
376B VAL* 4.5 28.0 - - + -
379B ALA* 4.2 24.2 - - + -
431B LEU* 5.5 1.6 - - + -
435B ILE* 5.5 3.6 - - + -
448B PHE* 3.1 22.9 + - + +
449B LYS* 3.6 10.8 - - + +
450B GLU 2.7 2.6 + - - -
451B LYS* 1.3 72.8 - - - +
453B ALA* 1.3 74.0 + - - +
458B ILE* 4.4 26.0 - - + +
459B GLN* 3.8 15.0 + - - +
462B VAL* 5.5 9.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 453 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449B LYS 3.2 10.3 + - - +
450B GLU* 2.5 23.7 + - - +
451B LYS 3.7 2.3 - - - +
452B LEU* 1.3 89.8 - - - +
454B GLY* 1.3 55.6 + - - +
455B ASP* 2.3 24.5 + - + +
456B GLU 4.1 0.7 + - - -
458B ILE* 4.6 0.3 - - - +
459B GLN* 3.9 9.7 - - - +
----------------------------------------------------------
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