Contacts of the helix formed by residues 221 - 233 (chain B) in PDB entry 4JU5
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 221 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171B GLN* 3.7 18.8 - - - +
219B GLU* 3.1 28.6 + - - +
220B VAL* 1.3 79.5 - - - +
222B LYS* 1.3 66.0 + - - +
223B GLU* 3.9 5.4 + - - +
224B ASN* 3.1 31.1 + - - +
225B LEU* 2.9 25.8 + - - +
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Residues in contact with LYS 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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171B GLN* 3.1 31.2 + - - +
174B GLN* 3.1 44.9 + - + +
175B ALA* 4.0 20.6 - - - +
178B ALA* 4.9 5.3 - - + +
221B THR* 1.3 71.5 - - - +
223B GLU* 1.3 58.9 + - + +
225B LEU* 3.3 5.1 + - - +
226B LEU* 2.9 50.9 + - + +
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Residues in contact with GLU 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 THR* 3.2 6.1 + - - +
222B LYS* 1.3 77.1 - - + +
224B ASN* 1.3 63.1 + - - +
226B LEU* 4.0 7.4 - - - +
227B ASP* 3.1 37.8 + - - +
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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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216B PHE* 3.6 13.3 - - + -
219B GLU* 2.8 43.1 + - - +
221B THR* 3.1 21.1 + - - +
223B GLU* 1.3 79.0 - - - +
225B LEU* 1.3 56.6 + - - +
227B ASP* 3.5 9.1 + - - +
228B PHE* 2.9 28.8 + - - +
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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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171B GLN 4.1 2.0 - - - +
172B PHE* 3.5 43.5 - - + +
175B ALA* 3.9 16.6 - - + -
203B VAL* 3.6 32.3 - - + -
216B PHE* 3.7 26.0 - - + -
220B VAL* 4.0 14.4 - - + -
221B THR 2.9 18.0 + - - +
222B LYS 3.6 4.5 - - - +
223B GLU 3.3 0.2 - - - -
224B ASN* 1.3 75.0 - - - +
226B LEU* 1.3 59.2 + - - +
228B PHE* 3.3 4.1 + - + +
229B ILE* 2.8 40.6 + - + +
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Residues in contact with LEU 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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175B ALA* 3.8 28.3 - - + +
178B ALA* 4.1 15.7 - - + -
179B ILE* 3.8 26.5 - - + -
222B LYS* 2.9 41.3 + - + +
223B GLU* 4.1 6.3 - - - +
225B LEU* 1.3 73.8 - - - +
227B ASP* 1.3 60.3 + - - +
229B ILE* 3.9 4.7 - - + +
230B LYS* 3.0 43.6 + - + +
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Residues in contact with ASP 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 GLU* 3.1 24.9 + - - +
224B ASN* 3.6 9.5 - - - +
226B LEU* 1.3 77.5 - - - +
228B PHE* 1.3 57.9 + - - +
230B LYS* 3.5 11.2 + - - +
231B HIS* 2.9 25.3 + - - +
252B GLU* 3.2 38.9 - - - +
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Residues in contact with PHE 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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157B VAL* 5.7 0.4 - - + -
203B VAL* 4.3 12.8 - - + -
205B LEU* 3.9 26.7 - - + -
214B ASN* 3.3 30.5 - - + -
215B ASN 3.8 7.4 - - - -
216B PHE* 3.5 50.9 - + + -
217B GLU 5.2 0.9 - - - -
224B ASN 2.9 18.6 + - - +
225B LEU* 3.5 7.6 - - + +
227B ASP* 1.3 74.4 - - - +
229B ILE* 1.3 74.5 + - + +
231B HIS* 3.4 2.0 + - - -
232B ASN* 2.8 55.5 + - - +
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Residues in contact with ILE 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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157B VAL* 4.3 16.2 - - + -
175B ALA* 5.2 2.2 - - + -
179B ILE* 3.8 21.3 - - + -
182B ILE* 3.7 28.5 - - + -
184B PHE* 3.7 33.9 - - + -
203B VAL* 6.0 1.3 - - + -
205B LEU* 4.1 12.0 - - + +
225B LEU* 2.8 29.9 + - + +
226B LEU* 4.0 7.6 - - + +
228B PHE* 1.3 86.8 - - + +
230B LYS* 1.3 55.7 + - + +
232B ASN 3.8 0.3 - - - -
233B GLN* 2.9 38.6 + - - +
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Residues in contact with LYS 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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179B ILE* 5.7 4.9 - - + -
226B LEU* 3.0 32.3 + - + +
227B ASP* 3.9 15.1 + - - +
229B ILE* 1.3 79.4 - - + +
231B HIS* 1.3 61.0 + - - +
232B ASN 3.3 0.9 + - - -
233B GLN* 3.9 21.6 + - - +
234B LEU* 4.2 14.0 - - - +
247B LYS* 5.0 2.4 - - - +
250B GLY* 3.3 39.9 + - - +
251B GLY* 4.5 7.8 + - - -
252B GLU* 4.5 5.2 + - - +
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Residues in contact with HIS 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 ASP 2.9 19.4 + - - +
228B PHE* 4.6 1.1 - - - -
229B ILE 3.4 0.4 - - - -
230B LYS* 1.3 75.6 - - - +
232B ASN* 1.3 78.9 + - - +
234B LEU* 5.3 2.9 - - - +
251B GLY* 5.3 0.9 - - - -
252B GLU* 3.4 25.1 + - - +
253B ILE* 3.5 35.2 - - + +
284B GLY* 3.7 19.7 + - - -
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Residues in contact with ASN 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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205B LEU* 3.7 10.6 - - + +
207B LYS* 3.0 31.4 + - - +
211B GLU* 4.8 1.9 - - - +
214B ASN* 3.4 37.6 + - + +
228B PHE* 2.8 44.9 + - + +
229B ILE 3.8 0.9 - - - +
230B LYS 3.2 0.2 - - - -
231B HIS* 1.3 99.6 + - - +
233B GLN* 1.3 62.3 + - - +
234B LEU 3.3 5.1 + - - -
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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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155B VAL* 3.7 16.7 - - + +
179B ILE* 5.6 2.5 - - - +
181B ASP* 3.3 24.3 - - - +
182B ILE* 3.4 27.1 - - + +
205B LEU* 4.3 7.2 - - - -
209B PHE* 3.5 18.3 - - - -
229B ILE* 2.9 23.9 + - + +
230B LYS* 3.9 22.4 + - - +
232B ASN* 1.3 77.9 - - - +
234B LEU* 1.3 64.2 + - + +
235B PRO* 4.2 1.2 - - - +
247B LYS* 3.7 31.7 + - + +
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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