Contacts of the helix formed by residues 222 - 234 (chain B) in PDB entry 4BJ3
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 222 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187B TYR* 3.7 4.9 - - - +
188B ALA 3.0 12.9 + - - +
189B ASN* 2.8 30.9 + - - +
191B PRO* 5.9 2.1 - - + +
220B LEU* 4.3 18.9 - - - +
221B THR* 1.3 70.2 - - - +
223B THR* 1.3 64.9 + - - +
224B PHE 3.5 1.8 - - - -
225B GLY* 4.5 7.2 - - - -
226B ALA* 3.1 21.8 + - - +
258B HIS* 4.2 10.6 - - - +
259B ASP* 3.3 24.5 - - - +
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Residues in contact with THR 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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187B TYR* 3.0 33.9 + - + +
221B THR* 3.1 13.6 + - - +
222B ASN* 1.3 70.1 - - - +
224B PHE* 1.3 63.1 + - + +
226B ALA* 3.1 5.5 + - - +
227B ILE* 2.9 36.6 + - + +
251B VAL* 4.6 4.0 - - + -
253B THR* 4.0 9.7 + - + +
255B GLY 5.9 0.2 - - - -
257B SER* 3.6 24.4 - - - -
259B ASP* 3.3 2.6 + - - -
303B ILE* 4.0 27.1 - - + -
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Residues in contact with PHE 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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223B THR* 1.3 82.0 - - + +
225B GLY* 1.3 56.5 + - - +
226B ALA 3.2 0.2 - - - -
227B ILE* 3.8 12.1 - - + -
228B GLN* 3.1 28.2 + - - +
257B SER* 3.8 18.6 - - - -
259B ASP* 3.1 27.2 + - - +
260B GLY* 3.9 10.1 - - - -
262B MET* 3.6 37.2 - - + +
263B LEU* 3.6 39.9 - - + -
266B VAL* 3.9 17.3 - - + +
267B ILE* 4.4 6.3 - - + -
299B GLU* 5.4 8.1 - - + -
303B ILE* 4.1 26.2 - - + -
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Residues in contact with GLY 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B PRO* 4.7 6.1 - - - +
222B ASN* 3.4 8.5 + - - -
223B THR 3.2 1.0 - - - -
224B PHE* 1.3 77.7 - - - +
226B ALA* 1.3 58.2 + - - +
228B GLN* 4.2 8.8 - - - +
229B TYR* 3.7 16.5 + - - +
259B ASP* 3.2 17.7 + - - -
262B MET* 4.4 10.1 - - - -
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Residues in contact with ALA 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B VAL* 4.3 7.9 - - + +
185B ILE* 5.7 1.6 - - - +
187B TYR* 3.5 38.1 - - + -
191B PRO* 3.9 17.5 - - + +
222B ASN 3.1 14.5 + - - +
223B THR 3.1 4.6 + - - +
225B GLY* 1.3 77.4 - - - +
227B ILE* 1.3 64.5 + - - +
228B GLN 3.2 1.3 - - - -
229B TYR* 3.2 5.6 + - - +
230B ALA* 3.2 21.1 + - - +
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Residues in contact with ILE 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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149B VAL* 4.7 6.7 - - + -
223B THR* 2.9 34.5 + - + +
224B PHE* 3.6 13.0 + - + +
226B ALA* 1.3 76.0 - - - +
228B GLN* 1.3 62.4 + - - +
230B ALA* 3.2 9.2 + - - +
231B ARG* 3.1 19.8 + - - +
249B MET* 3.6 25.4 - - + +
251B VAL* 3.9 35.0 - - + -
266B VAL* 3.7 17.9 - - + -
267B ILE* 5.5 4.5 - - + -
270B CYS* 4.3 6.7 - - - -
277B ARG* 5.6 2.7 - - - -
303B ILE* 4.1 18.4 - - + -
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Residues in contact with GLN 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 PHE 3.1 18.5 + - - +
225B GLY* 4.2 9.8 - - - +
226B ALA 3.2 0.2 - - - -
227B ILE* 1.3 78.8 - - - +
229B TYR* 1.3 61.4 + - - +
231B ARG* 3.2 45.1 + - - +
232B LYS* 3.1 35.6 + - + +
262B MET* 5.1 7.2 - - - +
266B VAL* 4.4 20.7 - - + +
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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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185B ILE* 5.1 11.7 - - + -
191B PRO* 4.1 33.4 - - + -
193B VAL* 4.4 25.4 - - + +
225B GLY 3.7 11.9 + - - +
226B ALA 3.2 11.2 + - - +
228B GLN* 1.3 78.6 - - - +
230B ALA* 1.3 64.9 + - + +
232B LYS* 3.4 6.6 + - - -
233B TYR* 3.2 58.1 + + + +
234B ALA* 4.0 3.5 + - + -
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Residues in contact with ALA 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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147B VAL* 5.0 4.3 - - + -
149B VAL* 3.9 14.1 - - + -
185B ILE* 5.5 4.9 - - + -
226B ALA 3.2 11.7 + - - +
227B ILE 3.5 8.5 - - - +
228B GLN 3.2 0.2 - - - -
229B TYR* 1.3 78.9 - - + +
231B ARG* 1.3 64.0 + - - +
232B LYS 3.1 2.9 + - - -
234B ALA* 3.2 35.9 + - + +
235B TYR* 3.2 13.0 - - - -
249B MET* 3.8 20.2 - - - -
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Residues in contact with ARG 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 ILE 3.1 11.7 + - - +
228B GLN* 3.2 44.2 + - - +
230B ALA* 1.3 76.9 - - - +
232B LYS* 1.3 90.3 + - - +
235B TYR* 4.0 20.0 - - - +
247B LYS* 5.6 2.3 + - - -
249B MET* 5.1 1.1 - - + -
266B VAL* 4.8 7.5 + - - +
269B GLN* 3.3 54.0 + - - +
270B CYS* 4.8 7.9 - - - -
273B ASP* 3.6 22.1 + - - +
275B ILE* 4.0 20.4 - - + +
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Residues in contact with LYS 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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228B GLN* 3.1 33.7 + - + +
229B TYR* 3.9 3.1 - - - +
230B ALA 3.1 0.2 - - - -
231B ARG* 1.3 108.9 - - - +
233B TYR* 1.3 110.7 + - + +
234B ALA 3.9 0.2 - - - -
235B TYR* 4.9 2.3 - - - +
236B SER* 4.4 9.2 + - - -
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Residues in contact with TYR 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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196B ASN* 4.8 0.2 + - - -
229B TYR* 3.2 51.2 + + + +
232B LYS* 1.3 123.8 + - + +
234B ALA* 1.3 57.4 + - - +
235B TYR 3.2 2.7 - - - -
236B SER* 2.8 17.7 + - - +
239B SER* 2.6 28.8 + - - -
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Residues in contact with ALA 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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147B VAL* 4.4 20.3 - - + +
185B ILE* 5.2 12.1 - - + -
196B ASN* 4.8 9.1 + - - +
197B LEU* 3.4 23.0 - - - +
229B TYR* 4.0 4.9 + - + -
230B ALA* 3.2 32.8 + - + +
233B TYR* 1.3 79.0 - - - +
235B TYR* 1.3 60.6 + - + +
236B SER 3.4 1.3 - - - -
239B SER* 3.5 10.6 - - - -
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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