Contacts of the strand formed by residues 242 - 246 (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 ARG 242 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233E TYR* 4.3 11.4 - - - +
458E GLY* 3.9 17.2 + - - +
459E ASP* 3.6 39.3 + - + +
461E HIS* 5.2 5.3 + - - -
139F MET* 3.2 22.5 - - + +
218F LYS 3.5 14.9 + - - +
219F ALA* 3.5 9.9 - - + -
220F VAL 3.1 20.0 + - - -
240F GLY 3.8 2.4 + - - -
241F LYS* 1.3 74.7 - - - +
243F CYS* 1.3 65.4 + - - +
469F ARG 3.2 7.5 + - - -
470F PHE* 2.8 49.9 + - + +
472F THR 2.9 18.4 + - - -
473F LYS* 3.7 25.5 - - - +
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Residues in contact with CYS 243 (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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233E TYR* 5.0 2.0 + - - -
459E ASP* 4.5 5.1 + - - +
220F VAL* 3.3 17.3 - - + +
232F ILE* 4.2 14.1 - - - -
233F TYR* 3.5 51.6 - - + +
236F ALA* 3.8 21.5 - - + -
237F SER* 5.3 2.0 - - - +
241F LYS 4.3 0.9 - - - +
242F ARG* 1.3 80.4 - - - +
244F GLN* 1.3 73.5 + - - +
245F ALA* 4.3 1.1 - - - -
457F PHE 4.2 0.5 - - - +
458F GLY* 4.4 4.5 - - - -
459F ASP 5.4 0.2 + - - -
470F PHE* 3.5 12.4 - - - -
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Residues in contact with GLN 244 (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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158F MET* 5.6 0.7 - - - +
220F VAL 3.1 5.0 + - - +
221F SER* 2.8 28.0 + - - +
222F PHE 2.9 26.8 + - - +
243F CYS* 1.3 75.1 - - - +
245F ALA* 1.3 62.6 + - - +
246F LEU* 4.6 10.5 - - + +
456F LEU* 5.8 1.1 - - + -
457F PHE 3.6 7.6 - - - +
458F GLY* 5.2 1.3 - - - -
460F LEU 2.7 38.7 + - - +
461F HIS 2.9 21.7 + - - +
462F ALA* 4.5 8.1 - - - +
463F TYR 5.2 1.2 + - - -
467F ALA* 5.5 1.8 - - - +
470F PHE* 3.6 33.7 - - + +
471F TYR* 3.9 6.4 + - - -
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Residues in contact with ALA 245 (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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222F PHE* 3.3 14.1 - - + -
229F ALA* 3.8 32.3 - - + +
233F TYR* 4.3 7.9 - - + +
243F CYS* 4.3 4.5 - - - -
244F GLN* 1.3 75.6 - - - +
246F LEU* 1.3 65.5 + - - +
456F LEU* 3.5 2.1 - - - -
457F PHE* 2.9 46.2 + - + +
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Residues in contact with LEU 246 (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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157F TRP* 4.3 7.2 - - + -
222F PHE* 2.8 25.3 + - - +
223F VAL* 4.3 14.1 - - + -
224F GLY 3.0 24.8 + - - +
229F ALA* 4.1 1.6 - - - -
244F GLN* 4.6 11.2 - - + -
245F ALA* 1.3 83.5 - - - +
247F GLY* 1.3 62.1 + - - +
410F ASN* 5.6 2.7 - - - +
449F PHE* 3.4 48.9 - - + +
450F GLY* 4.4 1.6 - - - -
451F GLY 5.3 0.9 - - - +
455F SER 3.6 5.8 - - - +
456F LEU* 3.8 24.0 - - + -
462F ALA* 3.9 19.1 - - + +
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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