Contacts of the helix formed by residues 222 - 232 (chain B) in PDB entry 3EJW
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 THR 222 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14B GLY* 4.5 1.0 - - - -
15B PHE* 3.5 41.6 + - + +
196B ALA* 5.8 0.4 - - + +
221B SER* 1.3 84.9 + - - +
223B PRO* 1.3 69.6 - - + +
224B ASN* 4.2 0.6 - - - +
225B VAL* 3.2 28.6 + - - +
226B MET* 3.0 24.4 + - - +
238B PHE* 4.2 1.6 - - - -
240B LEU* 3.9 14.1 - - + -
243B VAL* 4.7 1.8 - - + -
315B PHE* 3.5 27.3 + - + +
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Residues in contact with PRO 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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221B SER 4.2 3.4 - - - +
222B THR* 1.3 82.4 - - - +
224B ASN* 1.3 55.6 + - - +
227B ARG* 2.9 46.8 + - - +
238B PHE* 3.9 11.4 - - + -
240B LEU* 4.5 0.2 - - + -
305B PHE* 3.5 31.6 - - + -
310B ILE* 3.8 19.4 - - + +
313B PHE* 4.0 12.1 - - + +
315B PHE* 3.2 39.0 - - + +
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Residues in contact with ASN 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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18B SER* 5.5 0.6 + - - -
222B THR* 4.9 1.3 - - - +
223B PRO* 1.3 76.4 - - - +
225B VAL* 1.3 62.8 + - + +
227B ARG* 2.9 36.5 + - - +
228B PRO* 4.3 4.0 - - - +
314B ASP* 2.9 28.2 + - - +
315B PHE* 3.0 36.4 + - - +
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Residues in contact with VAL 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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14B GLY* 4.6 16.8 - - - +
196B ALA 4.9 1.1 - - - +
200B PRO* 3.8 32.5 - - + -
221B SER* 4.3 7.2 - - - +
222B THR* 3.2 22.2 + - - +
223B PRO 3.2 0.6 - - - -
224B ASN* 1.3 79.5 - - + +
226B MET* 1.3 62.1 + - - +
227B ARG 3.4 0.2 - - - -
228B PRO* 3.6 10.9 - - - +
229B TYR* 3.7 11.7 - - + -
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Residues in contact with MET 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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199B LEU* 3.7 17.5 - - + -
200B PRO* 3.8 39.0 - - + -
203B ALA* 4.4 4.0 - - + -
221B SER* 3.8 13.7 - - - -
222B THR 3.0 18.3 + - - +
225B VAL* 1.3 76.1 - - - +
227B ARG* 1.3 65.7 + - - +
228B PRO* 3.3 1.8 - - - -
229B TYR* 2.9 33.7 + - + +
230B ILE* 3.1 11.8 + - + +
235B ILE* 3.5 29.6 - - + -
238B PHE* 3.4 33.4 - - + -
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Residues in contact with ARG 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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223B PRO* 2.9 23.9 + - - +
224B ASN* 2.9 30.3 + - - +
226B MET* 1.3 75.5 - - - +
228B PRO* 1.3 65.6 - - + +
230B ILE* 3.1 2.9 + - - +
231B GLU* 2.8 50.5 + - + +
310B ILE* 2.7 45.5 + - + +
311B GLY* 3.7 9.1 - - - -
313B PHE 2.8 25.0 + - - -
314B ASP* 5.4 0.2 - - - +
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Residues in contact with PRO 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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224B ASN 4.3 4.5 - - - +
225B VAL 3.6 13.2 - - - +
226B MET 3.4 5.2 - - - +
227B ARG* 1.3 96.1 - - + +
229B TYR* 1.3 61.8 + - + +
231B GLU* 3.2 6.8 + - + +
232B ARG* 2.9 63.7 + - + +
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Residues in contact with TYR 229 (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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200B PRO* 3.9 24.7 + - + +
203B ALA* 3.6 22.0 - - + -
204B GLN* 2.7 44.7 + - - +
207B GLU* 3.4 23.3 - - - -
225B VAL* 3.7 19.3 - - + -
226B MET* 2.9 29.5 + - + +
228B PRO* 1.3 79.5 - - + +
230B ILE* 1.3 59.2 + - - +
232B ARG* 3.5 14.3 + - - -
233B GLY 3.3 1.7 + - - -
234B THR* 2.9 37.0 + - + -
235B ILE* 3.5 6.5 + - + -
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Residues in contact with ILE 230 (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 MET* 3.1 15.4 + - + +
227B ARG 3.6 6.7 - - - +
229B TYR* 1.3 74.3 - - - +
231B GLU* 1.3 65.1 + - - +
233B GLY* 3.1 13.7 + - - -
235B ILE* 3.6 33.6 - - + +
236B GLN 4.0 14.4 - - - +
238B PHE* 3.8 31.9 - - + -
305B PHE 4.1 6.7 - - - +
306B THR* 3.9 3.6 - - - +
307B LYS* 3.4 44.8 - - + +
310B ILE* 3.8 15.9 - - + -
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Residues in contact with GLU 231 (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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227B ARG* 2.8 33.3 + - + +
228B PRO* 3.7 7.2 - - + +
230B ILE* 1.3 78.5 - - - +
232B ARG* 1.3 62.4 + - + +
233B GLY 3.2 1.1 + - - -
307B LYS* 3.3 45.4 + - - +
310B ILE* 3.9 22.6 - - - +
311B GLY* 6.1 0.2 - - - -
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Residues in contact with ARG 232 (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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204B GLN* 4.6 2.4 + - - -
207B GLU* 2.8 39.5 + - - -
228B PRO* 2.9 40.6 + - - +
229B TYR* 3.5 20.4 - - - +
230B ILE 3.2 0.2 - - - -
231B GLU* 1.3 78.6 - - + +
233B GLY* 1.3 59.6 + - - +
234B THR* 3.2 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