Contacts of the helix formed by residues 444 - 454 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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372C ARG* 3.3 3.7 + - - +
397C ARG* 5.3 0.2 - - - +
442C LYS 3.9 3.9 + - - -
443C ALA* 1.3 85.7 + - - +
445C LEU* 1.3 57.9 + - - +
446C LYS* 3.2 20.2 - - + -
447C GLU* 2.9 51.8 + - + +
448C PHE 3.1 4.5 + - - -
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Residues in contact with LEU 445 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369C ASP* 4.5 3.4 - - - +
371C GLY* 3.6 33.2 - - - +
372C ARG* 3.5 32.8 - - + +
386C LYS* 6.2 1.1 - - - +
396C LEU 5.9 2.9 - - - +
398C PRO* 6.5 0.2 - - + -
444C THR* 1.3 68.2 - - - +
446C LYS* 1.3 63.1 + - - +
447C GLU 2.9 5.8 + - - -
448C PHE* 3.9 12.8 - - + -
449C LYS* 2.9 65.4 + - + +
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Residues in contact with LYS 446 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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444C THR* 3.2 17.2 - - + +
445C LEU* 1.3 77.8 - - - +
447C GLU* 1.3 63.6 + - + +
449C LYS* 3.8 14.6 + - - +
450C GLU* 3.5 19.6 + - + +
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Residues in contact with GLU 447 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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439C MSE 3.4 18.4 - - + +
443C ALA 4.0 7.4 - - - +
444C THR* 2.9 31.0 + - + +
445C LEU 2.9 0.8 - - - -
446C LYS* 1.3 86.9 - - + +
448C PHE* 1.3 62.9 + - - +
449C LYS 3.4 0.2 - - - -
450C GLU* 3.0 29.6 - - - +
451C LYS 3.1 6.2 + - - -
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Residues in contact with PHE 448 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372C ARG* 3.6 57.0 - - + +
375C LYS* 5.1 0.9 - - + -
376C VAL* 3.6 32.1 - - + -
432C THR* 3.6 24.7 - - + -
435C ILE* 3.4 36.7 - - + +
436C GLN* 4.0 5.6 - - + -
439C MSE 4.0 17.6 - - - +
444C THR 3.1 4.9 + - - -
445C LEU* 2.9 16.7 + - + +
447C GLU* 1.3 76.7 - - - +
449C LYS* 1.3 64.3 + - + +
450C GLU 2.9 0.9 + - - -
451C LYS* 3.2 2.1 + - - +
452C LEU* 2.9 39.1 + - + +
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Residues in contact with LYS 449 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375C LYS* 3.7 39.7 - - + -
445C LEU* 2.9 46.7 + - + -
446C LYS* 3.8 16.7 + - - +
448C PHE* 1.3 74.2 - - + +
450C GLU* 1.3 63.9 + - - +
452C LEU* 3.6 18.6 - - + +
453C ALA* 3.7 7.6 + - - +
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Residues in contact with GLU 450 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446C LYS* 3.5 18.5 + - + +
447C GLU* 3.0 25.4 + - - +
448C PHE 2.9 0.2 + - - -
449C LYS* 1.3 75.7 - - - +
451C LYS* 1.3 71.5 + - - +
453C ALA* 3.1 16.1 + - - +
454C GLY* 3.6 10.4 + - - +
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Residues in contact with LYS 451 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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435C ILE* 4.1 9.0 - - + +
438C HIS 4.9 5.9 + - - -
439C MSE 3.5 44.4 - - + +
447C GLU 3.1 2.0 + - - -
448C PHE 3.8 1.3 - - - +
450C GLU* 1.3 85.2 + - - +
452C LEU* 1.3 66.5 + - - +
453C ALA 2.9 1.9 + - - -
454C GLY 3.2 23.2 + - - +
455C ASP* 3.7 21.6 + - + +
458C ILE* 3.7 19.5 - - + -
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Residues in contact with LEU 452 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375C LYS* 3.8 35.2 - - + +
376C VAL* 4.3 37.7 - - + +
379C ALA* 5.2 9.2 - - + -
431C LEU* 5.2 2.0 - - + -
435C ILE* 4.4 11.6 - - + +
448C PHE* 2.9 27.2 + - + +
449C LYS* 3.6 10.3 - - - +
450C GLU 3.1 0.2 - - - -
451C LYS* 1.3 77.1 - - - +
453C ALA* 1.3 64.6 + - - +
458C ILE* 3.5 32.9 - - + +
459C GLN* 4.9 5.0 + - - +
462C VAL* 6.0 5.2 - - + -
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Residues in contact with ALA 453 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449C LYS 3.7 6.4 + - - +
450C GLU* 3.1 11.6 + - - +
451C LYS 2.9 2.8 + - - -
452C LEU* 1.3 81.9 - - - +
454C GLY* 1.3 60.7 + - - +
455C ASP 3.6 2.9 + - - -
459C GLN* 3.9 32.8 - - - +
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Residues in contact with GLY 454 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450C GLU* 3.6 8.8 + - - +
451C LYS* 3.2 12.8 + - - +
453C ALA* 1.3 78.0 - - - +
455C ASP* 1.3 65.8 + - - +
456C GLU* 4.4 4.9 - - - -
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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