Contacts of the helix formed by residues 446 - 453 (chain A) in PDB entry 1IEQ
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 446 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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420A ALA 4.6 0.2 - - - -
421A ASP* 2.6 41.7 + - - +
422A ASN 4.2 0.2 - - - -
423A LEU* 3.7 29.8 - - + +
426A GLN* 3.1 11.2 - - - -
440A ARG* 3.9 15.0 - - - +
445A THR* 1.3 75.8 - - - +
447A ILE* 1.3 64.8 + - - +
448A LEU 3.5 1.6 + - - -
449A GLU* 2.6 33.0 + - - +
450A ALA* 3.0 21.0 + - - +
550A GLY* 4.5 1.6 - - - -
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Residues in contact with ILE 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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415A VAL* 5.0 3.6 - - + -
419A HIS 4.1 7.9 - - - +
420A ALA* 3.2 15.3 + - + +
426A GLN* 3.6 13.8 + - + +
446A THR* 1.3 75.7 - - - +
448A LEU* 1.3 58.1 + - - +
450A ALA* 3.2 7.1 + - - +
451A VAL* 2.9 45.0 + - + +
481A ILE* 4.5 17.3 - - + -
483A ALA* 3.8 24.2 - - + -
521A VAL* 4.0 22.2 - - + -
523A ILE* 4.5 12.1 - - + -
550A GLY 5.0 2.7 - - - +
553A VAL* 4.4 28.0 - - + -
554A THR* 5.0 2.7 - - + -
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Residues in contact with LEU 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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415A VAL* 3.9 35.9 - - + -
420A ALA 2.7 19.8 + - - +
421A ASP* 3.8 22.9 - - + +
446A THR* 3.3 4.7 - - - +
447A ILE* 1.3 72.9 - - - +
449A GLU* 1.3 66.1 + - + +
451A VAL* 3.0 6.1 + - - +
452A LYS* 3.0 50.3 + - + +
461A VAL* 4.3 5.8 - - + -
463A PHE* 3.5 38.8 - - + -
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Residues in contact with GLU 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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421A ASP* 4.2 5.8 - - - +
440A ARG* 2.8 30.9 + - - -
444A GLY 4.2 2.9 - - - +
445A THR* 3.1 20.5 - - + -
446A THR* 2.6 35.1 + - - +
448A LEU* 1.3 80.2 - - + +
450A ALA* 1.3 57.0 + - - +
452A LYS* 3.2 12.5 + - + +
453A ALA* 2.9 29.6 + - - +
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Residues in contact with ALA 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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445A THR* 3.5 6.0 - - + +
446A THR 3.0 17.9 + - - +
447A ILE 3.4 5.6 - - - +
449A GLU* 1.3 75.6 - - - +
451A VAL* 1.3 63.6 + - - +
453A ALA* 3.2 5.0 + - - +
454A ALA* 3.2 23.6 + - - +
550A GLY 3.7 3.8 - - - +
551A GLN* 3.6 31.1 - - + +
554A THR* 3.4 24.1 + - + +
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Residues in contact with VAL 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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413A ILE* 3.8 30.1 - - + -
415A VAL* 3.8 22.2 - - + -
447A ILE* 2.9 28.0 + - + +
448A LEU 3.0 6.5 + - - +
450A ALA* 1.3 76.1 - - - +
452A LYS* 1.3 62.5 + - - +
454A ALA* 3.0 11.1 + - - -
455A VAL* 3.2 15.9 + - + +
461A VAL* 4.2 5.8 - - + -
481A ILE* 4.1 18.6 - - + -
554A THR* 3.7 18.6 - - + -
558A PHE* 4.2 12.3 - - + -
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Residues in contact with LYS 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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448A LEU* 3.0 45.7 + - + +
449A GLU* 3.2 12.8 + - + +
451A VAL* 1.3 76.2 - - - +
453A ALA* 1.3 60.6 + - - +
454A ALA 3.2 0.7 + - - -
455A VAL* 3.9 18.4 + - - +
461A VAL* 4.3 26.0 - - + -
463A PHE* 5.8 2.2 - - - +
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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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445A THR* 5.9 1.6 - - + -
449A GLU 2.9 15.8 + - - +
450A ALA* 3.8 8.1 - - - +
451A VAL 3.1 0.4 - - - -
452A LYS* 1.3 76.4 - - - +
454A ALA* 1.3 58.2 + - - +
455A VAL 5.0 0.9 - - - -
551A GLN* 4.5 15.4 - - - +
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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