Contacts of the helix formed by residues 421 - 427 (chain A) in PDB entry 2OZO
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 PRO 421 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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420A GLY* 1.3 85.8 - - - +
422A LEU* 1.3 65.9 + - - +
423A HIS* 3.5 28.0 - - + +
424A LYS* 3.2 26.8 + - + +
425A PHE* 3.1 20.8 + - - +
465A ARG* 4.0 14.6 - - + +
467A VAL 3.4 8.7 - - - +
468A LEU* 4.0 2.4 - - + -
615A ANP 3.0 35.9 - - + +
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Residues in contact with LEU 422 (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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420A GLY 3.7 0.4 + - - -
421A PRO* 1.3 72.9 - - - +
423A HIS* 1.3 61.5 + - - +
425A PHE* 3.6 6.6 + - + +
426A LEU* 3.2 45.1 + - + +
438A VAL* 5.8 1.1 - - + -
441A LEU* 3.8 34.5 - - + -
442A LEU* 4.6 12.8 - - + -
445A VAL* 5.4 1.3 - - + -
464A ALA* 3.7 8.6 + - + +
467A VAL* 2.9 42.2 + - + +
469A LEU* 4.2 12.3 - - + +
528A THR* 4.8 8.7 - - + -
532A ALA* 3.8 23.1 - - + -
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Residues in contact with HIS 423 (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 PRO* 3.5 18.4 - - + +
422A LEU* 1.3 78.2 - - - +
424A LYS* 1.3 80.7 + - + +
426A LEU* 3.6 1.5 + - - -
427A VAL* 3.0 30.8 + - + +
464A ALA* 3.5 18.0 - - + +
465A ARG* 3.4 42.9 + - + -
531A GLU* 4.2 13.9 - - + +
532A ALA* 6.3 0.4 - - - +
536A GLY* 3.8 22.0 - - - +
538A LYS* 5.1 15.6 - - - -
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Residues in contact with LYS 424 (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 PRO* 3.2 29.9 + - + +
423A HIS* 1.3 100.2 + - + +
425A PHE* 1.3 64.2 + - - +
426A LEU 3.3 1.0 + - - -
427A VAL* 3.7 18.4 + - + +
429A LYS* 5.8 1.0 - - - -
615A ANP 4.1 12.1 + - - -
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Residues in contact with PHE 425 (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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419A GLY 4.8 8.7 - - - +
421A PRO 3.1 13.2 + - - +
422A LEU* 3.9 6.3 - - + +
423A HIS 3.3 0.4 - - - -
424A LYS* 1.3 79.3 - - - +
426A LEU* 1.3 81.1 + - + +
429A LYS* 3.2 45.3 - - - +
432A GLU* 5.3 0.2 - - - -
433A ILE* 3.5 33.9 - - + -
441A LEU* 4.9 9.0 - - + -
469A LEU* 3.2 36.3 - - + -
472A ARG* 4.2 20.9 - - + -
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Residues in contact with LEU 426 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422A LEU* 3.2 35.9 + - + +
423A HIS* 3.6 1.5 + - - +
424A LYS 3.2 0.8 - - - -
425A PHE* 1.3 104.4 - - + +
427A VAL* 1.3 68.1 + - - +
428A GLY 3.2 0.7 + - - -
429A LYS* 3.0 15.6 + - - +
433A ILE* 4.1 13.5 - - + -
438A VAL* 4.1 24.9 - - + -
441A LEU* 5.6 0.9 - - + -
532A ALA* 3.7 36.6 - - + +
535A TYR* 3.6 30.4 - - + +
536A GLY 4.2 4.3 - - - +
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Residues in contact with VAL 427 (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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423A HIS* 3.0 22.6 + - + +
424A LYS* 3.7 13.8 + - - +
425A PHE 3.7 1.4 - - - -
426A LEU* 1.3 75.5 - - - +
428A GLY* 1.3 64.1 + - - +
429A LYS* 2.9 14.6 + - - +
535A TYR 4.0 7.2 - - - +
536A GLY* 4.1 18.2 - - - +
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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