Contacts of the helix formed by residues 446 - 454 (chain C) in PDB entry 1Z5S
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 LEU 446 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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437C PHE* 3.4 33.6 - - + -
442C SER 3.5 15.4 + - - +
443C PRO 4.3 7.2 - - - +
444C GLU 2.7 4.0 + - - -
445C LYS* 1.3 75.5 - - - +
447C LEU* 1.3 63.1 + - + +
449C LEU* 3.1 27.8 - - + +
453C SER* 4.1 11.6 + - - +
457C ILE* 3.5 20.0 - - + -
476C VAL* 5.0 3.4 - - + -
479C VAL* 4.4 7.0 - - + -
486C VAL* 4.6 1.1 - - + +
489C ALA* 3.8 23.1 - - + +
490C VAL* 3.6 36.1 - - + +
493C ALA* 5.0 7.0 - - + -
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Residues in contact with LEU 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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443C PRO 3.4 22.4 - - - +
444C GLU* 2.6 20.9 + - + +
446C LEU* 1.3 69.0 - - + +
448C ARG* 1.3 51.5 + - - +
449C LEU 2.6 18.2 + - - -
450C GLY* 3.1 15.7 + - - +
485C THR* 4.1 20.2 - - - +
486C VAL* 3.6 20.9 - - + -
489C ALA* 4.0 26.0 - - + -
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Residues in contact with ARG 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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433C ASP* 5.2 4.5 - - - +
444C GLU 3.0 9.3 + - - +
445C LYS* 3.6 15.5 - - - +
446C LEU 3.2 1.0 - - - -
447C LEU* 1.3 72.7 - - - +
449C LEU* 1.3 67.1 + - - +
450C GLY 3.6 0.9 - - - -
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Residues in contact with LEU 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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433C ASP* 3.4 39.5 - - + +
434C VAL* 4.3 13.7 - - + +
437C PHE* 4.6 9.4 - - + -
445C LYS 3.4 13.0 - - - +
446C LEU* 3.1 28.9 - - + +
447C LEU 2.6 4.8 + - - -
448C ARG* 1.3 81.0 - - - +
450C GLY* 1.3 65.7 + - - +
452C LYS* 3.9 15.4 + - - +
453C SER* 3.4 22.7 - - - -
456C LEU* 4.7 9.9 - - + +
457C ILE* 4.2 16.6 - - + -
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Residues in contact with GLY 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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447C LEU* 3.1 11.3 + - - +
448C ARG 3.6 1.6 - - - -
449C LEU* 1.3 80.2 - - - +
451C PRO* 1.3 68.4 - - - +
452C LYS* 3.0 10.3 + - - -
453C SER* 3.2 14.6 + - - -
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Residues in contact with PRO 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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450C GLY* 1.3 82.4 - - - +
452C LYS* 1.3 58.5 + - + +
453C SER* 3.2 7.9 + - - +
454C SER* 3.9 14.2 + - - -
455C VAL* 5.9 0.9 - - - +
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Residues in contact with LYS 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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449C LEU 4.0 9.9 - - - +
450C GLY 3.0 1.6 - - - -
451C PRO* 1.3 82.4 - - + +
453C SER* 1.3 56.1 + - - +
454C SER 3.6 0.7 - - - -
455C VAL* 4.3 5.9 - - - +
456C LEU* 2.8 33.5 + - + +
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Residues in contact with SER 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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446C LEU* 4.1 11.9 + - - +
447C LEU* 5.8 0.3 - - - -
449C LEU* 3.4 37.9 - - - -
450C GLY 3.2 10.5 + - - -
451C PRO* 3.2 2.0 - - - +
452C LYS* 1.3 76.0 - - - +
454C SER* 1.3 58.6 + - - +
455C VAL 2.5 18.4 + - - -
456C LEU* 3.0 15.2 + - - -
457C ILE* 3.1 24.7 + - - +
489C ALA* 5.5 6.4 + - - +
493C ALA* 5.4 1.0 - - - -
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Residues in contact with SER 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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451C PRO 3.9 10.9 + - - -
452C LYS 3.6 0.2 - - - -
453C SER* 1.3 80.2 + - - +
455C VAL* 1.3 67.8 + - - +
458C ALA* 4.4 2.5 - - - -
489C ALA 5.5 1.6 - - - -
492C ASP* 3.4 34.6 + - - +
493C ALA* 4.4 13.2 - - - +
496C ALA* 3.0 23.4 - - - +
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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