Contacts of the helix formed by residues 444 - 454 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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372A ARG* 4.2 6.3 - - - +
397A ARG* 5.3 15.0 - - - +
439A MSE 5.8 0.2 - - - +
442A LYS 4.9 4.9 - - - +
443A ALA* 1.3 76.3 - - - +
445A LEU* 1.3 71.9 + - - +
446A LYS* 4.0 12.1 + - - +
447A GLU* 2.4 38.3 + - - +
448A PHE* 3.2 7.7 + - - +
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Residues in contact with LEU 445 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371A GLY* 4.7 13.5 - - - +
372A ARG* 3.1 43.5 - - + +
396A LEU 3.4 25.4 - - - +
397A ARG* 3.8 25.6 - - + +
444A THR* 1.3 76.8 - - - +
446A LYS* 1.3 64.7 + - + +
448A PHE* 2.7 37.6 + - + +
449A LYS* 3.0 15.4 + - + +
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Residues in contact with LYS 446 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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444A THR* 3.1 9.3 + - - +
445A LEU* 1.3 82.5 - - + +
447A GLU* 1.3 73.3 + - - +
449A LYS* 3.4 40.2 - - - +
450A GLU* 3.5 15.6 - - - +
80B GLN* 4.4 21.2 - - - +
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Residues in contact with GLU 447 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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439A MSE 4.4 12.3 - - + +
443A ALA* 3.6 21.8 - - + -
444A THR* 2.4 49.0 + - - +
446A LYS* 1.3 87.5 - - - +
448A PHE* 1.3 57.6 + - - +
449A LYS 2.9 2.2 - - - -
450A GLU* 2.5 48.0 + - + +
451A LYS 4.1 1.0 + - - -
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Residues in contact with PHE 448 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372A ARG* 3.4 50.0 - - + +
375A LYS* 4.4 13.9 - - + -
376A VAL* 3.4 25.8 - - + -
435A ILE* 3.0 38.8 - - + +
436A GLN* 3.5 22.4 - - - -
439A MSE 4.8 13.4 - - - +
444A THR 3.2 4.4 + - - +
445A LEU* 2.7 29.7 + - + +
447A GLU* 1.3 73.7 - - - +
449A LYS* 1.3 59.4 + - + -
450A GLU 3.0 1.2 + - - -
451A LYS* 3.9 2.9 + - - +
452A LEU* 3.2 30.2 + - + +
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Residues in contact with LYS 449 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375A LYS* 5.5 16.8 - - + +
445A LEU* 3.0 13.4 + - + +
446A LYS* 3.4 44.5 - - - +
447A GLU 2.9 0.4 + - - -
448A PHE* 1.3 78.6 - - + +
450A GLU* 1.3 62.2 + - - +
452A LEU* 4.1 9.4 - - - -
453A ALA* 2.6 43.8 + - + +
79B GLY 5.7 3.0 + - - -
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Residues in contact with GLU 450 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446A LYS 3.5 14.7 - - - +
447A GLU* 2.5 39.7 + - + +
448A PHE 2.9 0.2 - - - -
449A LYS* 1.3 74.7 - - - +
451A LYS* 1.3 59.8 + - + +
452A LEU 2.5 15.7 + - - -
453A ALA* 3.0 1.8 + - - +
454A GLY* 2.8 28.1 + - - +
455A ASP 4.8 0.7 - - - -
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Residues in contact with LYS 451 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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435A ILE* 4.5 10.3 - - + -
438A HIS* 2.4 48.7 + - - +
439A MSE 3.6 35.0 - - + -
447A GLU 4.1 0.6 + - - -
448A PHE 3.9 2.9 + - - +
450A GLU* 1.3 80.4 - - + +
452A LEU* 1.3 57.9 + - - +
455A ASP* 3.0 38.5 - - + +
457A LYS* 4.9 10.8 - - - +
458A ILE* 3.2 47.3 - - + +
459A GLN 4.9 0.2 + - - -
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Residues in contact with LEU 452 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375A LYS* 3.5 50.5 - - + +
376A VAL* 4.5 8.5 - - + +
379A ALA* 3.9 23.6 - - + -
435A ILE* 5.8 1.5 - - + +
448A PHE* 3.2 33.0 + - + +
449A LYS* 3.7 5.6 - - - +
450A GLU 2.5 6.1 + - - -
451A LYS* 1.3 74.6 - - - +
453A ALA* 1.3 73.2 + - - +
454A GLY 3.4 4.3 - - - +
458A ILE* 4.9 7.1 - - + +
459A GLN* 3.2 23.9 + - - +
462A VAL* 5.7 5.6 - - + -
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Residues in contact with ALA 453 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449A LYS* 2.6 27.3 + - + +
450A GLU* 5.0 1.1 - - - +
452A LEU* 1.3 80.0 - - - +
454A GLY* 1.3 67.5 + - - +
459A GLN* 3.2 19.8 + - - +
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Residues in contact with GLY 454 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450A GLU* 2.8 14.3 + - - +
451A LYS 4.1 0.2 - - - +
452A LEU 3.4 4.0 - - - +
453A ALA* 1.3 87.5 - - - +
455A ASP* 1.3 79.5 + - - +
456A GLU 3.5 0.3 + - - -
459A GLN* 3.7 5.2 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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