Contacts of the helix formed by residues 223 - 236 (chain B) in PDB entry 4EEM
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 ASN 223 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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216B GLN* 3.1 12.4 + - - +
221B ILE 3.7 0.2 + - - -
222B PHE* 1.3 76.9 - - - +
224B ARG* 1.3 61.7 + - - +
225B ALA* 3.5 5.5 + - - +
226B LYS* 3.0 28.5 + - + +
227B LEU* 3.2 22.7 + - - +
305B ASN 2.8 28.2 + - - +
307B TYR 3.1 24.1 + - - +
308B TRP* 3.5 35.3 - - + -
394B ILE* 4.4 3.6 - - + -
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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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183B PRO* 3.9 15.3 - - + +
222B PHE* 3.7 24.3 - - + -
223B ASN* 1.3 71.5 + - - +
225B ALA* 1.3 62.6 + - - +
227B LEU* 3.2 7.6 + - - +
228B LEU* 3.1 44.0 + - + +
246B PHE* 5.0 5.5 + - - +
247B SER 5.2 0.4 - - - -
248B ASP* 2.7 35.0 + - - +
287B GLY* 4.8 1.4 - - - -
288B GLY 3.5 24.4 + - - +
290B SER* 6.0 0.2 + - - -
307B TYR 4.7 2.0 + - - -
309B GLY 5.6 2.6 + - - -
313B GLU* 2.9 37.7 + - - +
314B ASP* 4.5 7.9 - - - +
317B ILE* 5.0 4.9 - - - +
349B ASN* 6.3 0.2 - - - +
403B UDP 4.3 8.1 - - - -
412B GOL 3.5 21.4 + - - +
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Residues in contact with ALA 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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223B ASN* 3.4 5.1 + - - +
224B ARG* 1.3 76.2 - - - +
226B LYS* 1.3 66.8 + - - +
228B LEU* 3.1 14.8 + - - +
229B ASN* 3.0 23.6 + - - -
303B PHE* 4.1 12.8 - - + +
304B PRO* 3.3 22.2 - - + +
307B TYR* 5.3 1.3 + - + -
313B GLU* 3.5 33.2 - - + +
317B ILE* 4.8 2.9 - - + -
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Residues in contact with LYS 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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223B ASN* 3.0 30.0 + - + +
225B ALA* 1.3 77.0 - - - +
227B LEU* 1.3 63.1 + - - +
229B ASN* 3.2 3.8 + - - +
230B VAL* 3.1 22.2 + - - +
304B PRO 3.9 1.4 + - - -
305B ASN* 3.7 42.0 - - - +
308B TRP* 4.6 6.5 - - + -
374B LEU* 4.0 14.6 - - + -
375B THR* 3.0 33.3 + - - +
394B ILE* 2.5 48.0 + - + +
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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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183B PRO* 4.1 8.7 - - + -
184B PHE 4.0 10.3 - - - +
214B ILE* 3.5 24.9 - - + +
216B GLN* 3.6 29.8 - - + +
222B PHE* 3.4 40.6 - - + -
223B ASN 3.2 14.6 + - - +
224B ARG 3.5 4.9 - - - +
225B ALA 3.2 0.6 - - - -
226B LYS* 1.3 76.0 - - - +
228B LEU* 1.3 64.0 + - - +
230B VAL* 3.2 3.8 + - - -
231B GLY 3.0 17.5 + - - -
392B VAL* 3.7 26.0 - - + -
394B ILE* 4.0 13.9 - - + -
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Residues in contact with LEU 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B ILE* 3.9 22.6 - - + +
183B PRO* 3.8 32.8 - - + -
224B ARG* 3.1 46.4 + - + +
225B ALA* 3.1 10.0 + - - +
227B LEU* 1.3 77.0 - - - +
229B ASN* 1.3 56.4 + - - +
231B GLY* 3.2 2.8 + - - -
232B PHE* 3.0 23.0 + - - +
246B PHE* 3.7 41.7 - - + -
303B PHE* 3.7 19.7 - - + -
317B ILE* 5.2 1.8 - - + -
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Residues in contact with ASN 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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225B ALA 3.0 13.3 + - - -
226B LYS 3.2 8.3 + - - +
228B LEU* 1.3 71.2 - - - +
230B VAL* 1.3 67.6 + - - +
232B PHE* 3.1 4.5 + - - +
233B GLN* 3.0 23.4 + - - +
297B PHE* 3.2 19.8 - - - -
302B GLY* 3.9 0.3 - - - -
303B PHE* 2.7 51.5 + - - +
304B PRO 4.2 1.0 + - - -
305B ASN* 2.8 24.2 + - - +
370B GLY 4.4 3.4 - - - -
371B LEU* 4.9 6.2 - - + +
374B LEU* 3.8 20.9 - - + +
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Residues in contact with VAL 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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214B ILE* 4.0 15.9 - - + -
226B LYS 3.1 14.1 + - - +
227B LEU* 3.5 7.6 - - - +
229B ASN* 1.3 77.7 - - - +
231B GLY* 1.3 57.8 + - - +
233B GLN* 3.2 0.9 + - - +
234B GLU* 2.8 46.9 + - + +
374B LEU* 4.4 8.7 - - + -
376B TYR* 3.6 42.2 - - + -
390B ILE* 4.8 4.9 - - + -
392B VAL* 4.4 9.6 - - + -
394B ILE* 4.0 18.4 - - + -
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Residues in contact with GLY 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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181B ILE* 3.4 14.9 - - - +
214B ILE* 3.4 29.8 - - - +
227B LEU 3.0 10.9 + - - -
228B LEU 3.2 4.0 + - - -
230B VAL* 1.3 76.1 - - - +
232B PHE* 1.3 62.4 + - - +
234B GLU* 4.8 1.1 - - - -
235B ALA* 3.0 28.9 + - - +
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Residues in contact with PHE 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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181B ILE* 4.1 1.9 - - - +
228B LEU 3.0 11.1 + - - +
229B ASN 3.1 7.2 + - - +
231B GLY* 1.3 79.2 - - - +
233B GLN* 1.3 70.2 + - - +
236B LEU* 3.4 42.7 + - + +
244B PHE* 3.6 51.8 - + + -
246B PHE* 4.7 2.5 - - + -
294B LYS* 4.4 8.1 - - + -
297B PHE* 3.3 61.9 - + + -
298B LEU* 3.8 19.3 - - + -
371B LEU* 4.1 23.1 - - + -
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Residues in contact with GLN 233 (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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229B ASN 3.0 14.5 + - - +
230B VAL 3.9 2.0 - - - +
232B PHE* 1.3 89.5 - - + +
234B GLU* 1.3 62.1 + - - +
236B LEU* 3.7 11.2 + - - +
237B LYS* 3.7 22.7 + - - +
371B LEU* 3.7 22.7 - - + +
374B LEU* 4.2 14.2 + - + +
376B TYR* 3.2 34.3 + - - +
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Residues in contact with GLU 234 (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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212B TYR* 5.1 0.4 - - - -
230B VAL* 2.8 36.5 + - + +
231B GLY* 4.3 1.1 - - - +
233B GLN* 1.3 71.7 - - - +
235B ALA* 1.3 65.8 + - - +
237B LYS* 2.8 54.1 + - - +
238B ASP* 4.0 5.4 + - - +
376B TYR* 2.5 29.8 + - + +
378B VAL* 4.0 18.3 - - - +
381B VAL* 5.3 4.3 - - - +
390B ILE* 3.5 33.4 - - + +
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Residues in contact with ALA 235 (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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179B ALA* 3.7 30.1 - - + -
181B ILE* 4.2 1.1 - - + -
212B TYR* 3.9 30.1 - - + -
231B GLY 3.0 19.9 + - - +
232B PHE 4.1 2.5 - - - +
234B GLU* 1.3 76.9 - - - +
236B LEU* 1.3 64.2 + - - +
238B ASP* 3.0 13.9 + - - +
239B TYR 3.5 0.3 + - - -
241B TYR* 3.3 19.9 - - + -
244B PHE* 4.5 2.0 - - + -
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Residues in contact with LEU 236 (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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232B PHE* 3.4 51.6 + - + +
233B GLN* 3.8 8.3 - - - +
234B GLU 3.2 1.0 - - - -
235B ALA* 1.3 79.7 - - - +
237B LYS* 1.3 60.5 + - + +
238B ASP 3.2 0.2 - - - -
239B TYR 3.3 24.2 + - - +
240B ASP* 4.6 9.4 - - - +
241B TYR* 3.8 21.3 - - - +
244B PHE* 3.7 12.6 - - + -
294B LYS* 3.7 30.5 - - - +
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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