Contacts of the strand formed by residues 452 - 457 (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 LEU 452 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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444C THR* 4.8 1.0 - - - +
446C THR* 4.0 6.5 + - - +
447C THR* 2.5 33.1 + - - -
450C ASN* 2.8 37.5 + - + +
451C GLY* 1.3 79.0 - - - +
453C ILE* 1.3 55.2 + - - +
454C HIS* 5.6 1.1 - - - -
465C MET* 5.3 17.7 - - + +
466C MET* 3.9 7.9 - - - +
467C HIS* 3.8 29.6 - - + +
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Residues in contact with ILE 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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402C LEU* 3.7 13.7 - - + -
441C VAL* 3.7 17.7 - - + -
442C LEU 3.3 17.7 - - - +
443C VAL* 3.6 23.6 - - + -
447C THR* 3.9 13.0 - - + +
451C GLY 4.5 2.5 - - - +
452C LEU* 1.3 72.6 - - - +
454C HIS* 1.3 68.4 + - - +
455C LEU* 3.3 4.5 + - - +
465C MET* 3.2 7.0 - - - -
466C MET* 2.9 46.3 + - + +
468C ILE* 3.6 35.9 - - + -
471C LEU* 4.9 9.0 - - + -
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Residues in contact with HIS 454 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429C TYR* 5.1 4.0 + - - +
440C THR 3.4 4.3 - - - +
442C LEU* 2.9 63.0 + - + +
444C THR* 3.5 35.1 - - + +
446C THR* 4.7 4.8 + - - +
452C LEU 5.2 0.7 - - - -
453C ILE* 1.3 73.9 - - - +
455C LEU* 1.3 64.7 + - - +
456C ARG* 4.9 0.5 - - - +
464C GLU 3.6 5.6 + - - +
465C MET* 3.7 30.8 - - + +
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Residues in contact with LEU 455 (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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429C TYR* 5.2 0.3 + - - -
439C PHE* 3.6 31.9 - - + -
440C THR 3.6 7.2 - - - +
441C VAL* 3.9 13.7 - - + +
453C ILE* 3.3 5.3 + - + +
454C HIS* 1.3 75.8 - - - +
456C ARG* 1.3 71.2 + - - +
463C LYS* 3.7 2.8 - - - +
464C GLU* 2.8 47.8 + - + +
466C MET* 3.7 33.4 - - + -
471C LEU* 4.1 13.7 - - + -
474C PHE* 3.6 32.8 - - + -
475C LEU* 5.6 0.2 - - + -
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Residues in contact with ARG 456 (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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429C TYR* 3.5 58.9 - - + +
433C ASP* 2.9 36.5 + - - -
439C PHE* 3.4 5.3 - - - -
440C THR* 2.9 57.8 + - - +
455C LEU* 1.3 79.6 - - - +
457C SER* 1.3 88.7 + - - +
461C THR* 3.5 30.6 + - - +
462C MET 3.6 8.5 - - - +
463C LYS* 4.0 16.0 - - + +
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Residues in contact with SER 457 (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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438C LEU 3.6 0.6 + - - -
439C PHE* 3.6 29.6 - - - -
456C ARG* 1.3 95.4 + - - +
458C ARG* 1.3 68.8 + - - +
459C ASP* 3.6 9.0 + - - +
460C THR* 3.2 28.8 + - - +
461C THR* 3.3 12.0 - - - -
462C MET* 3.5 12.9 + - - +
478C TYR* 5.7 0.5 + - - -
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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