Contacts of the helix formed by residues 474 - 480 (chain F) in PDB entry 1ZM9
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 ASP 474 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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439F TYR* 4.1 1.1 - - - -
472F ALA* 3.2 6.2 - - + +
473F GLY* 1.3 76.9 - - - +
475F PRO* 1.3 77.2 - - - +
476F ALA* 3.0 27.4 + - - +
477F LEU* 3.1 19.8 + - + +
478F ALA 3.4 6.8 + - - -
551F ARG* 4.1 21.1 - - + +
552F LEU 5.1 3.3 + - - +
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Residues in contact with PRO 475 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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439F TYR* 3.4 39.7 - - + -
473F GLY 3.7 2.2 - - - +
474F ASP* 1.3 87.7 - - - +
476F ALA* 1.3 57.3 + - - +
478F ALA* 2.8 4.6 + - + +
479F TYR* 2.6 34.9 + - - +
498F LEU* 3.9 7.0 - - + +
571F ILE* 3.8 17.3 - - + -
582F LEU* 3.6 21.3 - - + -
587F ILE* 4.1 14.4 - - + -
592F GLN* 6.1 3.4 - - - +
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Residues in contact with ALA 476 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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474F ASP* 3.0 19.7 + - - +
475F PRO* 1.3 82.8 - - + +
477F LEU* 1.3 64.2 + - - +
479F TYR* 3.0 15.7 + - - +
480F GLY* 3.4 5.4 + - - -
551F ARG* 3.9 16.2 + - - +
582F LEU* 3.2 28.0 + - + +
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Residues in contact with LEU 477 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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472F ALA* 3.8 8.5 - - + -
474F ASP* 3.1 12.3 + - + +
476F ALA* 1.3 80.3 - - - +
478F ALA* 1.3 60.7 + - - +
480F GLY* 3.7 4.2 + - - -
481F TYR* 3.4 26.4 - - + +
546F GLU* 3.7 28.5 - - + +
551F ARG* 3.6 44.7 - - + +
552F LEU 3.3 33.4 - - - +
553F GLU* 4.2 4.5 - - + +
702F P34 4.1 14.8 - - + -
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Residues in contact with ALA 478 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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439F TYR* 3.8 31.9 - - + +
441F GLY* 4.1 1.6 - - - -
472F ALA* 4.3 1.7 - - + +
474F ASP 3.4 4.3 + - - +
475F PRO 2.8 11.9 + - - +
477F LEU* 1.3 71.5 - - - +
479F TYR* 1.3 54.5 + - - +
480F GLY 2.7 4.4 + - - -
481F TYR* 2.6 35.9 + - - +
482F ALA 3.7 2.3 + - - -
498F LEU* 3.8 11.0 - - + -
702F P34 3.5 28.0 - - + +
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Residues in contact with TYR 479 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475F PRO 2.6 14.5 + - - +
476F ALA 3.2 12.6 - - - +
478F ALA* 1.3 72.3 - - - +
480F GLY* 1.3 61.2 + - - +
481F TYR 3.1 0.9 + - - -
482F ALA* 3.3 16.7 + - + +
498F LEU* 4.2 23.1 - - + +
571F ILE* 4.5 0.4 - - + -
572F PRO 3.7 18.4 + - - -
573F THR* 3.9 14.4 - - + -
574F ASP* 3.5 27.3 + - - +
577F ASN 5.6 1.7 + - - -
579F GLY 6.2 0.9 - - - -
580F GLY 3.6 22.9 - - - -
581F ASP* 4.3 1.9 + - - -
582F LEU* 3.4 59.0 - - + +
583F ASP 5.6 0.3 + - - -
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Residues in contact with GLY 480 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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580E PRO* 4.1 19.1 - - - +
704E GLN* 5.8 0.2 + - - -
476F ALA 3.4 7.0 + - - -
477F LEU 3.7 5.5 + - - -
478F ALA 2.7 7.3 + - - -
479F TYR* 1.3 78.1 - - - +
481F TYR* 1.3 61.7 + - - -
482F ALA 3.4 0.6 + - - -
483F GLN* 3.8 20.4 - - - +
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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