Contacts of the strand formed by residues 367 - 370 (chain J) 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 THR 367 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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273J PHE* 3.9 3.3 - - - -
305J MET* 4.4 3.8 - - - -
336J ILE* 3.7 31.2 - - + +
346J ILE* 5.4 0.4 - - - -
348J VAL 3.3 15.0 - - - -
349J ASP* 4.6 0.4 - - - -
350J GLY* 3.4 20.6 - - - +
364J VAL* 4.7 0.7 - - + -
365J GLY 2.9 18.6 - - - +
366J GLY* 1.3 71.9 - - - -
368J LEU* 1.3 59.7 + - - +
369J ILE* 4.0 7.7 - - - +
386J PRO 3.0 8.9 + - - +
387J VAL* 3.4 21.4 - - + +
388J LEU 3.0 24.3 + - - +
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Residues in contact with LEU 368 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298J VAL* 4.1 17.7 - - + +
301J MET* 3.6 30.7 - - + -
302J THR* 3.9 20.2 - - - +
305J MET* 3.6 20.9 - - + -
346J ILE* 3.7 1.7 - - - -
347J VAL* 2.9 29.0 + - + -
348J VAL* 3.2 23.8 + - + +
367J THR* 1.3 72.9 - - - +
369J ILE* 1.3 78.8 + - - +
370J ASP* 5.0 0.2 - - - -
388J LEU* 3.5 11.7 - - + +
390J VAL* 3.5 31.6 - - + -
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Residues in contact with ILE 369 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336J ILE* 4.6 11.2 - - + -
339J ALA* 4.0 20.9 - - + -
344J ALA* 3.5 31.6 - - + -
345J THR 3.8 2.5 - - - +
346J ILE* 4.0 20.2 - - + -
367J THR* 4.0 12.1 - - - +
368J LEU* 1.3 83.4 - - - +
370J ASP* 1.3 55.2 + - - +
372J VAL* 3.5 14.5 - - + +
378J SER* 5.9 0.2 - - - -
383J ILE* 5.3 2.0 - - + -
387J VAL* 3.6 27.4 - - + -
388J LEU 3.0 8.3 + - - +
389J GLN* 3.5 10.7 - - + +
390J VAL 2.8 31.9 + - - -
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Residues in contact with ASP 370 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298J VAL* 3.3 22.2 - - + +
344J ALA* 3.7 4.3 - - - +
345J THR* 2.9 30.6 + - - +
347J VAL* 3.6 22.4 - - + +
368J LEU* 4.2 0.8 - - + -
369J ILE* 1.3 74.5 - - - +
371J HIS* 1.3 106.2 + - + +
372J VAL 3.3 3.2 + - - -
390J VAL* 4.0 9.2 - - - +
392J ARG* 2.7 41.0 + - - -
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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