Contacts of the strand formed by residues 232 - 238 (chain C) in PDB entry 2JIF
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 ILE 232 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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176C LEU* 5.6 0.7 - - + -
186C PHE* 3.7 42.6 - - + +
188C LEU* 4.1 18.4 - - + -
220C MET* 3.8 28.9 - - + -
221C ALA 3.6 6.5 - - - +
222C ASN* 3.9 16.8 - - - +
229C TYR* 3.1 30.4 + - + +
230C LYS 3.4 0.2 - - - -
231C GLY* 1.3 75.4 - - - +
233C THR* 1.3 60.8 + - - +
280C GLY 3.2 12.5 - - - +
282C GLY 2.9 19.9 + - - -
283C TYR* 3.6 18.6 + - + +
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Residues in contact with THR 233 (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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219C VAL 3.4 1.6 - - - +
220C MET* 3.3 5.0 - - - -
221C ALA 2.8 35.8 + - - +
223C VAL* 3.4 17.5 - - + +
231C GLY 3.2 10.0 + - - -
232C ILE* 1.3 71.1 - - - +
234C SER* 1.3 64.3 + - - +
235C PHE* 3.6 22.8 - - + -
275C ILE* 3.9 25.6 - - + -
278C GLN 4.7 1.8 - - - +
279C ILE* 3.6 14.1 - - + +
280C GLY 3.0 20.0 + - - +
282C GLY* 4.0 6.3 - - - +
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Residues in contact with SER 234 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149C LEU* 5.6 0.2 - - - +
218C LEU* 4.3 10.5 - - - +
219C VAL 3.5 4.9 - - - -
220C MET* 3.2 22.6 - - - -
233C THR* 1.3 73.6 - - - +
235C PHE* 1.3 61.4 + - - +
275C ILE* 3.6 8.1 - - - +
276C LEU* 2.8 50.7 + - - +
278C GLN 5.5 0.2 + - - -
282C GLY* 3.4 16.5 + - - -
285C TYR* 3.8 13.7 - - - +
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Residues in contact with PHE 235 (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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192C ALA* 3.6 31.4 - - + -
199C TYR* 3.8 23.6 - + + -
201C LEU* 4.4 8.5 - - + -
217C PHE 3.2 4.9 - - - +
218C LEU* 3.4 3.9 - - - -
219C VAL 2.8 46.6 + - - +
221C ALA* 4.0 12.3 - - + -
223C VAL* 4.0 6.3 - - + -
233C THR* 3.6 33.4 - - + -
234C SER* 1.3 75.1 - - - +
236C LEU* 1.3 64.4 + - - +
237C VAL* 3.7 16.4 + - + +
270C VAL* 4.0 22.0 - - + -
271C PRO 5.5 0.2 - - - -
274C ASN 3.6 2.0 - - - -
275C ILE* 3.6 28.5 - - + -
276C LEU* 5.2 0.4 - - - -
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Residues in contact with LEU 236 (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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150C ILE* 4.3 24.0 - - + -
158C GLN* 3.9 31.6 - - + +
162C TYR* 3.8 29.8 - - + +
216C LEU* 4.0 21.8 - - + -
217C PHE 3.7 1.3 - - - -
218C LEU* 4.3 19.3 - - + -
235C PHE* 1.3 72.6 - - - +
237C VAL* 1.3 63.0 + - - +
270C VAL* 3.7 3.8 - - - +
274C ASN* 2.9 44.7 + - + +
276C LEU* 4.3 19.1 - - + -
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Residues in contact with VAL 237 (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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201C LEU* 4.4 4.3 - - + -
216C LEU* 3.6 4.3 - - - +
217C PHE* 2.8 41.9 + - + +
219C VAL* 3.7 26.7 - - + -
235C PHE* 4.0 11.2 - - + +
236C LEU* 1.3 78.1 - - - +
238C ASP* 1.3 75.9 + - - +
241C THR* 4.3 3.4 - - + -
244C LEU* 4.1 12.8 - - + -
265C PHE* 4.8 2.9 - - + -
268C VAL* 4.1 24.0 - - + -
269C LYS 5.9 0.4 - - - +
270C VAL* 3.9 22.2 - - + -
274C ASN* 5.1 0.2 - - - +
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Residues in contact with ASP 238 (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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162C TYR* 3.1 33.8 + - - -
170C LYS* 4.8 6.5 + - - -
215C GLY 3.6 7.7 - - - +
216C LEU* 4.4 1.9 - - - +
236C LEU 4.2 0.4 + - - -
237C VAL* 1.3 80.2 - - - +
239C ARG* 1.3 67.0 + - - +
240C ASP* 3.3 10.8 + - + +
241C THR* 3.6 20.3 - - - +
244C LEU* 3.8 1.8 - - - +
274C ASN* 4.9 7.1 + - - +
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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