Contacts of the strand formed by residues 433 - 436 (chain F) in PDB entry 4ZZ7
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 MET 433 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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476E THR* 3.4 9.2 - - - +
281F MET* 3.7 20.2 - - + +
410F ASN* 3.2 30.2 + - - +
411F GLY* 3.3 4.5 - - - -
412F THR 3.0 25.8 + - - -
431F VAL* 3.4 1.9 - - - +
432F GLY* 1.3 82.5 - - - +
434F VAL* 1.3 61.3 + - - +
441F PRO* 3.5 20.6 - - + +
443F PRO* 3.4 36.8 - - + -
449F PHE* 3.6 27.1 - - + -
450F GLY 3.4 32.5 - - - +
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Residues in contact with VAL 434 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475E LYS* 4.0 16.6 - - + -
476E THR 3.0 6.9 + - - -
477E VAL* 3.3 11.0 - - + +
478E THR 2.8 28.9 + - - +
412F THR* 3.5 6.1 - - + -
425F PHE* 3.9 19.1 - - + -
426F SER* 3.6 33.0 - - - -
429F ILE* 3.7 17.3 - - + -
431F VAL 3.5 20.6 - - - +
433F MET* 1.3 76.6 - - - +
435F GLY* 1.3 61.2 + - - +
436F ILE* 4.1 4.5 - - + -
441F PRO* 3.6 5.1 - - - +
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Residues in contact with GLY 435 (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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478E THR 3.6 3.4 - - - -
412F THR 2.6 14.9 + - - -
413F CYS* 3.3 1.6 - - - -
414F ILE* 3.0 24.7 + - - +
425F PHE* 3.9 1.7 - - - -
434F VAL* 1.3 73.8 - - - +
436F ILE* 1.3 69.1 + - - +
437F ASN 3.9 1.3 - - - -
438F ILE* 3.5 22.7 - - - -
441F PRO* 3.5 9.1 - - - +
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Residues in contact with ILE 436 (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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477E VAL* 4.0 9.4 - - + -
478E THR 2.9 16.9 + - - +
479E GLN* 3.9 28.5 - - + +
480E ARG* 3.0 22.3 + - - +
481E TRP* 4.2 6.7 - - + -
414F ILE* 3.6 19.1 - - + +
416F THR* 5.0 2.5 - - + -
422F ALA* 3.8 29.2 - - + +
425F PHE* 4.4 0.2 - - + -
426F SER* 4.0 26.2 - - - +
434F VAL* 4.1 6.3 - - + -
435F GLY* 1.3 80.4 - - - +
437F ASN* 1.3 81.1 + - - +
438F ILE* 3.3 2.2 + - - +
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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