Contacts of the strand formed by residues 235 - 241 (chain D) in PDB entry 4JZJ
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 235 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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207D LEU* 4.0 13.2 - - + -
227D MET* 3.8 45.3 - - + -
229D SER* 3.8 19.1 - - - -
232D ASN* 3.8 35.9 - - + -
233D ARG* 4.2 1.8 - - - -
234D LYS* 1.3 78.9 - - - +
236D ARG* 1.3 61.9 + - - +
237D TYR* 3.7 29.5 - - + +
254D ARG 3.9 10.7 - - - +
255D ASP* 4.0 11.5 + - - +
273D ALA* 4.1 12.3 - - + -
274D ARG 3.5 6.3 - - - -
275D GLU* 4.0 20.2 - - + -
276D ARG* 5.7 1.5 + - - -
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Residues in contact with ARG 236 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235D PHE* 1.3 75.1 - - - +
237D TYR* 1.3 73.9 + - - +
238D GLU* 4.0 10.7 + - + +
252D GLN* 5.2 4.9 - - - +
253D VAL 3.6 15.5 - - - +
254D ARG* 4.3 15.5 - - + +
273D ALA* 3.5 1.9 - - - +
274D ARG* 3.0 77.9 + - + +
276D ARG* 4.4 20.6 - - - +
279D GLU* 2.8 33.5 + - - -
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Residues in contact with TYR 237 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210D PRO* 3.8 17.7 - - + -
225D TRP* 3.5 37.2 - + + -
227D MET* 3.1 37.8 + - + +
235D PHE* 3.7 21.2 - - + +
236D ARG* 1.3 87.5 - - - +
238D GLU* 1.3 70.3 + - - +
239D LEU* 4.3 3.6 - - + -
252D GLN* 3.6 4.5 - - - +
253D VAL* 3.3 33.0 + - + +
255D ASP 3.8 17.7 - - - -
256D ARG 4.1 7.2 - - - -
257D THR* 3.9 11.3 - - + +
271D ILE* 4.2 12.1 - - + -
272D ARG 3.3 8.1 - - - +
273D ALA* 3.9 13.9 - - + -
274D ARG* 5.8 0.4 - - - -
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Residues in contact with GLU 238 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236D ARG* 4.0 8.2 + - + +
237D TYR* 1.3 83.3 - - - +
239D LEU* 1.3 62.0 + - - +
250D THR* 5.5 7.2 - - + -
251D GLU 3.6 5.4 - - - +
252D GLN* 3.3 29.4 + - + -
271D ILE* 3.4 1.2 - - - -
272D ARG* 2.9 50.7 + - + +
274D ARG* 3.3 32.7 + - - -
284D TRP* 3.1 32.5 - - + -
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Residues in contact with LEU 239 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212D MET* 3.5 32.1 - - + -
223D MET* 4.6 1.8 - - + -
225D TRP* 3.8 18.2 - - + -
237D TYR* 4.5 0.4 - - + -
238D GLU* 1.3 79.1 - - - +
240D GLN* 1.3 60.9 + - - +
241D ILE* 3.9 17.4 + - + +
250D THR* 3.3 6.4 + - - +
251D GLU* 2.9 43.1 + - + +
253D VAL* 3.8 28.7 - - + -
259D PHE* 4.8 12.3 - - + -
269D VAL* 4.2 7.4 - - + -
270D GLN 3.4 3.8 - - - +
271D ILE* 3.6 21.5 - - + -
284D TRP* 4.8 0.7 - - - -
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Residues in contact with GLN 240 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238D GLU 3.9 0.8 + - - -
239D LEU* 1.3 72.4 - - - +
241D ILE* 1.3 60.4 + - - +
248D VAL* 3.8 29.7 - - + +
249D ILE 3.7 5.6 - - - +
250D THR* 4.3 9.2 + - - +
268D THR 3.8 1.6 - - - +
269D VAL* 3.4 5.2 - - - -
270D GLN* 2.8 62.0 + - + +
284D TRP* 4.1 25.6 + - + -
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Residues in contact with ILE 241 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223D MET* 5.0 3.8 - - - -
239D LEU* 4.1 18.4 - - + +
240D GLN* 1.3 77.9 - - - +
242D GLN* 1.3 63.4 + - - +
248D VAL* 4.4 1.3 - - - -
249D ILE* 2.7 54.7 + - + +
251D GLU* 4.4 12.6 - - + -
259D PHE* 4.1 26.9 - - + -
261D LEU* 4.5 19.3 - - + -
267D TYR* 3.6 32.3 - - + -
268D THR 3.9 2.2 - - - +
269D VAL* 4.1 13.7 - - + -
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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