Contacts of the strand formed by residues 221 - 228 (chain B) in PDB entry 4X3G
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 221 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185B PHE* 3.9 18.4 - + + -
187B PHE* 3.5 37.2 - + - -
189B PHE* 3.6 26.7 - + + -
211B LEU* 4.1 11.0 - - + -
217B GLN 3.2 29.8 - - - -
218B ALA* 3.1 14.2 + - - +
219B GLU 4.3 0.7 - - - +
220B ASN* 1.3 82.5 - - + +
222B ALA* 1.3 62.2 + - - +
239B THR* 3.8 11.4 + - - +
240B PRO* 3.4 26.5 - - + +
279B ILE* 4.5 1.3 - - + -
280B SER 3.4 14.1 - - - +
281B MET* 3.6 36.8 - - + -
282B CYS* 3.7 9.1 - - - -
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Residues in contact with ALA 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221B PHE* 1.3 75.3 - - - +
223B TYR* 1.3 58.8 + - - +
238B ALA 3.4 11.4 - - - +
239B THR* 5.4 1.6 - - - +
240B PRO* 4.2 2.2 - - - -
278B THR 4.1 0.3 - - - +
279B ILE* 3.8 1.3 - - - -
280B SER* 2.7 56.1 + - - +
282B CYS* 4.4 14.6 - - + -
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Residues in contact with TYR 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208B ILE* 3.5 23.2 - - + +
209B VAL* 3.5 35.7 - - + -
222B ALA* 1.3 74.5 - - - +
224B ARG* 1.4 62.0 + - - +
225B LEU* 3.6 30.7 - - + -
236B TRP* 2.9 31.6 + + - -
237B GLU* 3.5 4.0 - - - +
238B ALA* 2.9 52.1 + - + +
239B THR 3.7 19.3 - - - -
240B PRO* 3.5 24.4 - - + +
255B ASP 4.9 0.7 + - - -
256B CYS* 4.5 0.3 - - - -
278B THR 3.4 5.4 - - - -
279B ILE* 4.0 20.9 - - + +
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Residues in contact with ARG 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162B ASP* 4.9 3.8 + - - -
223B TYR* 1.4 74.3 - - - +
225B LEU* 1.3 68.1 + - - +
226B GLU* 3.7 22.4 + - + +
235B THR* 3.7 28.5 - - + -
236B TRP 3.4 3.4 - - - -
237B GLU* 3.7 26.2 + - + +
276B ASN 3.4 1.4 - - - +
277B VAL* 3.4 11.8 - - - +
278B THR* 2.7 73.8 + - + +
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Residues in contact with LEU 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165B PHE* 5.8 2.5 - - + -
191B LEU* 6.4 0.2 - - + -
207B ALA* 3.3 42.2 - - + +
208B ILE 4.0 1.8 - - - +
209B VAL* 4.2 9.0 - - + -
223B TYR* 3.6 24.9 - - + -
224B ARG* 1.3 74.3 - - - +
226B GLU* 1.3 59.4 + - - +
227B LEU 4.3 0.2 - - - -
234B LEU 3.7 1.1 - - - +
235B THR* 3.2 5.9 - - - +
236B TRP* 2.8 40.4 + - + +
257B LEU* 3.9 24.3 - - + +
275B ILE* 3.8 12.6 - - + -
276B ASN 3.5 1.6 - - - -
277B VAL* 3.7 32.8 - - + -
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Residues in contact with GLU 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224B ARG* 3.7 29.0 + - - +
225B LEU* 1.3 73.3 - - - +
227B LEU* 1.3 64.9 + - - +
228B ASN* 2.8 27.3 + - - +
233B ARG* 3.4 25.4 + - + -
234B LEU 3.4 2.2 - - - -
235B THR* 3.8 20.0 + - + +
274B GLY 4.0 0.7 - - - +
275B ILE* 3.8 3.4 - - - +
276B ASN* 2.9 54.5 + - + +
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Residues in contact with LEU 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226B GLU* 1.3 73.2 - - - +
228B ASN* 1.3 60.1 + - - +
233B ARG* 3.3 4.2 - - - +
234B LEU* 2.9 59.0 + - + +
257B LEU* 4.1 13.5 - - + -
259B PHE* 4.1 27.6 - - + -
264B ALA* 6.1 0.2 - - - -
267B PHE* 3.2 33.8 - - + -
273B LEU* 4.0 14.4 - - + -
274B GLY 3.9 10.5 - - - +
275B ILE* 3.8 35.7 - - + -
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Residues in contact with ASN 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226B GLU* 2.8 29.5 + - - -
227B LEU* 1.3 71.6 - - - +
229B GLY* 1.3 62.8 + - - +
232B ARG 3.4 13.6 - - - +
233B ARG* 3.4 26.6 + - - +
267B PHE* 3.6 15.8 - - - +
274B GLY 4.7 4.1 + - - +
276B ASN* 4.3 11.5 + - - +
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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