Contacts of the strand formed by residues 222 - 232 (chain C) in PDB entry 4J2X
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 GLN 222 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218C ARG* 3.3 11.2 - - - +
219C LEU 3.3 10.2 + - - +
220C ARG 3.2 12.6 + - - +
221C SER* 1.3 75.4 - - - +
223C THR* 1.4 65.6 + - - +
224C VAL* 4.2 14.8 - - + +
225C SER* 2.7 29.1 + - - +
12E C 4.0 0.2 + - - -
13E A 2.8 48.2 + - - +
14E G 3.3 56.8 + - - +
6F G 3.7 9.5 + - - +
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Residues in contact with THR 223 (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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92C PHE* 5.3 5.4 - - + +
94C CYS* 4.9 2.9 - - - -
218C ARG* 4.5 0.3 + - - -
221C SER 3.8 4.2 + - - -
222C GLN* 1.4 71.2 + - - +
224C VAL* 1.3 72.0 + - + +
226C THR* 2.6 29.9 + - - +
6F G 3.5 26.7 + - - +
7F T 2.6 36.6 + - - -
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Residues in contact with VAL 224 (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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222C GLN* 4.2 22.4 - - + +
223C THR* 1.3 82.7 - - + +
225C SER* 1.3 59.2 + - - +
226C THR 3.5 4.0 + - - +
240C SER* 5.6 3.8 - - - -
14E G 4.0 9.6 - - + +
15E T 3.7 43.7 - - - +
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Residues in contact with SER 225 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217C ASN* 3.7 6.8 - - - +
218C ARG* 4.5 0.5 - - - -
219C LEU* 2.8 45.2 + - - -
220C ARG* 6.3 0.4 - - - -
222C GLN* 2.7 23.1 + - - -
224C VAL* 1.3 77.1 - - - +
226C THR* 1.4 65.0 + - - +
227C ARG* 3.2 16.4 + - - +
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Residues in contact with THR 226 (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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94C CYS* 4.9 0.6 - - - -
216C PHE* 3.7 20.9 - - + -
217C ASN 3.2 8.1 - - - +
218C ARG* 2.8 35.7 + - - +
223C THR* 2.6 24.0 + - - -
224C VAL 3.3 3.2 - - - +
225C SER* 1.4 75.1 + - - +
227C ARG* 1.3 61.0 + - - +
228C TYR* 3.5 37.3 - - + +
239C SER 4.2 0.2 - - - +
240C SER* 3.8 22.7 - - - +
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Residues in contact with ARG 227 (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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216C PHE* 3.3 1.8 - - - -
217C ASN* 2.8 33.7 + - - +
225C SER 3.4 14.8 - - - +
226C THR* 1.3 72.5 - - - +
228C TYR* 1.3 60.4 + - - +
238C ALA* 3.4 31.5 + - + -
239C SER 3.1 6.1 - - - +
240C SER* 4.1 23.6 + - - +
326C LEU* 4.2 14.5 - - + +
328C GLN* 3.5 41.8 + - - +
329C GLU* 3.5 29.1 + - - +
354C TRP* 4.1 2.9 - - - -
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Residues in contact with TYR 228 (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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94C CYS* 3.4 24.4 - - + +
95C PRO* 3.7 21.8 - - + -
96C PRO* 3.5 23.2 - - + +
214C ALA* 5.7 1.1 - - + -
215C LEU 3.4 5.8 - - - +
216C PHE* 3.4 32.1 - + + -
226C THR* 3.5 25.1 - - + +
227C ARG* 1.3 72.4 - - - +
229C LEU* 1.4 64.8 + - - +
230C HIS* 3.3 0.9 + - - +
238C ALA* 4.2 2.7 - - - -
239C SER* 2.7 46.1 + - - -
240C SER 4.5 10.5 - - - -
241C GLN 5.5 1.1 - - - -
242C GLN 3.3 19.7 - - - +
243C TRP* 3.4 25.1 - + + -
354C TRP* 4.8 0.4 - - - -
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Residues in contact with LEU 229 (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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215C LEU* 2.8 41.0 + - + +
228C TYR* 1.4 71.0 - - - +
230C HIS* 1.3 59.2 + - - +
236C PHE* 3.9 17.5 - - + -
237C HIS 3.6 9.0 - - - +
238C ALA* 4.7 0.4 - - - +
243C TRP* 3.9 0.5 - - - +
244C GLY 3.0 22.0 + - - +
246C PHE* 3.3 31.1 - - + -
276C LEU* 4.6 3.6 - - + -
285C LEU* 4.1 22.4 - - + -
324C LEU* 4.5 9.0 - - + -
331C ILE* 3.7 37.0 - - + -
354C TRP* 4.1 13.9 - - + -
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Residues in contact with HIS 230 (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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100C TYR* 5.8 2.7 - - - -
228C TYR 3.8 8.5 - - - +
229C LEU* 1.3 77.4 - - - +
231C VAL* 1.3 80.1 + - - +
232C GLU* 3.6 10.7 - - + +
236C PHE* 3.4 4.4 - - - +
237C HIS* 2.7 68.5 + + + -
239C SER* 4.0 4.9 - - - -
242C GLN* 3.6 44.8 + - + +
243C TRP 3.6 22.1 + - - -
244C GLY* 3.8 4.1 + - - +
246C PHE* 4.1 5.6 - - - -
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Residues in contact with VAL 231 (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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230C HIS* 1.3 89.9 + - - +
232C GLU* 1.3 59.1 + - - +
233C GLY 4.1 3.7 + - - +
235C ASN 3.5 16.6 - - - +
236C PHE* 3.7 34.1 - - + +
244C GLY* 5.5 0.4 - - - -
246C PHE* 4.0 3.5 - - + -
278C CYS* 3.8 25.6 - - + -
280C VAL* 5.8 0.5 - - - +
281C THR* 3.6 34.2 - - + +
283C MET* 3.8 27.6 - - + -
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Residues in contact with GLU 232 (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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230C HIS* 3.6 9.0 - - + +
231C VAL* 1.3 72.5 - - - +
233C GLY* 1.3 67.3 + - - +
234C GLY 3.6 1.4 + - - -
235C ASN* 3.2 18.3 + - - +
237C HIS* 3.4 33.8 + - + -
242C GLN* 3.4 23.3 + - - +
329C GLU* 5.1 1.9 - - - +
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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