Contacts of the strand formed by residues 439 - 443 (chain C) in PDB entry 4ZTZ
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 PHE 439 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382C LYS 3.2 5.1 + - - +
383C VAL* 3.2 9.5 - - + +
384C ALA 3.2 14.6 + - - -
437C ILE* 3.2 16.0 - - - +
438C LEU* 1.3 90.1 - - + +
440C THR* 1.3 60.4 + - - +
455C LEU* 3.6 27.4 - - + -
456C ARG 3.4 2.0 - - - -
457C SER* 3.6 36.3 - - - -
474C PHE* 3.9 23.1 - + - -
475C LEU* 3.6 27.1 - - + -
478C TYR* 3.5 51.6 - + - -
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Residues in contact with THR 440 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384C ALA* 3.4 5.8 - - + +
429C TYR* 3.2 24.3 + - + -
432C TYR* 3.6 43.3 - - + -
433C ASP* 5.2 1.6 - - - +
437C ILE* 3.8 9.0 - - + +
439C PHE* 1.3 76.0 - - - +
441C VAL* 1.3 62.3 + - - +
454C HIS 3.4 4.7 - - - +
455C LEU* 3.5 1.2 - - - +
456C ARG* 2.9 59.3 + - - +
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Residues in contact with VAL 441 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383C VAL* 3.8 24.2 - - + -
384C ALA 2.6 14.1 + - - +
385C LEU* 3.1 17.4 - - + +
386C ASP* 3.0 27.2 + - - +
402C LEU* 4.2 6.1 - - + -
440C THR* 1.3 78.0 - - - +
442C LEU* 1.3 64.2 + - - +
443C VAL* 4.5 0.4 - - + -
453C ILE* 3.7 38.8 - - + -
454C HIS 3.5 2.9 - - - -
455C LEU* 3.9 16.2 - - + -
471C LEU* 3.9 18.6 - - + -
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Residues in contact with LEU 442 (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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386C ASP* 3.9 11.7 - - + +
387C VAL 3.4 35.2 - - - +
388C GLY* 3.7 10.8 - - - +
422C GLN* 4.9 5.2 - - + +
425C LEU* 4.3 23.1 - - + -
428C LEU* 6.0 4.0 - - + -
429C TYR* 5.2 8.3 - - + +
441C VAL* 1.3 75.1 - - - +
443C VAL* 1.3 62.9 + - - +
444C THR* 3.7 6.6 + - - +
453C ILE* 3.3 6.2 - - - +
454C HIS* 2.9 62.4 + - + +
463C LYS* 6.0 0.7 - - - +
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Residues in contact with VAL 443 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385C LEU* 4.8 4.9 - - + -
386C ASP 3.0 18.4 + - - +
387C VAL* 3.5 7.5 - - + +
388C GLY 3.4 16.6 + - - -
395C LEU* 4.1 11.2 - - + +
398C VAL* 4.1 23.3 - - + -
399C CYS* 3.6 24.9 - - - -
402C LEU* 4.9 4.5 - - + -
441C VAL* 4.5 6.3 - - + -
442C LEU* 1.3 70.9 - - - +
444C THR* 1.3 69.7 + - - +
447C THR* 4.0 18.8 - - + -
448C LEU* 4.9 1.6 - - + -
453C ILE* 3.6 21.5 - - + -
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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