Contacts of the helix formed by residues 219 - 230 (chain B) in PDB entry 3A4T
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 219 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209B TYR* 4.6 0.2 - - - -
211B THR* 3.3 13.5 - - - +
213B SER 3.2 19.3 + - - +
214B MET* 2.9 21.0 - - - -
215B GLU 2.8 19.8 + - - +
216B VAL 2.9 4.8 + - - -
217B GLU 3.3 0.8 - - - -
218B GLU* 1.3 93.8 + - - +
220B GLU* 1.3 78.8 + - - +
222B VAL* 3.0 18.9 + - - +
223B ILE* 3.3 9.5 + - - +
258B ARG* 3.0 7.8 + - - -
267B PHE* 3.2 37.2 - - + +
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Residues in contact with GLU 220 (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 VAL* 3.0 18.1 + - + +
219B ASN* 1.3 80.0 - - - +
221B GLU* 1.3 56.9 + - - +
223B ILE* 3.2 2.8 + - - +
224B LYS* 2.9 33.5 + - + +
251B GLY* 3.1 4.9 - - - -
252B TYR* 2.5 45.7 + - + +
253B ILE* 3.7 29.7 - - + +
256B THR* 4.5 0.4 - - - +
258B ARG* 2.7 43.7 + - - -
267B PHE* 3.6 17.3 - - + -
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Residues in contact with GLU 221 (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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191B LYS* 2.9 27.8 + - - +
216B VAL* 3.0 14.3 + - + +
217B GLU* 3.3 46.3 - - - +
220B GLU* 1.3 77.5 - - - +
222B VAL* 1.3 57.0 + - - +
224B LYS* 3.8 23.3 - - - +
225B TYR* 3.2 29.8 + - - +
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Residues in contact with VAL 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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187B SER* 4.1 9.0 - - - +
190B GLN* 3.5 38.8 - - + +
191B LYS* 4.4 5.2 - - + +
194B ILE* 4.1 14.5 - - + +
209B TYR* 3.8 26.0 - - + +
217B GLU 3.6 8.3 - - - +
218B GLU 3.5 24.9 - - - +
219B ASN 3.0 8.9 + - - +
221B GLU* 1.3 77.4 - - - +
223B ILE* 1.3 62.0 + - - +
225B TYR* 3.5 7.9 + - - +
226B ILE* 3.3 21.0 + - - +
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Residues in contact with ILE 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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194B ILE* 3.8 24.0 - - + -
209B TYR* 3.9 17.0 - - + -
219B ASN 3.3 10.9 + - - +
220B GLU* 3.2 6.5 + - - +
222B VAL* 1.3 75.6 - - - +
224B LYS* 1.3 58.2 + - - +
226B ILE* 3.1 8.1 - - - +
227B LEU* 3.0 40.2 + - + +
235B LEU* 3.7 28.7 - - + -
253B ILE* 3.9 16.8 - - + -
256B THR* 4.7 1.8 - - + -
267B PHE* 4.0 10.5 - - + -
269B ALA* 3.8 27.8 - - + -
271B LEU* 4.5 11.2 - - + -
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Residues in contact with LYS 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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220B GLU* 2.9 18.5 + - + +
221B GLU* 3.8 24.0 - - - +
223B ILE* 1.3 74.2 - - - +
225B TYR* 1.3 63.4 + - - +
227B LEU* 3.4 7.0 + - - +
228B GLN* 3.2 24.4 + - - +
253B ILE* 4.0 14.6 - - + +
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Residues in contact with TYR 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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191B LYS* 3.7 63.6 + - + +
192B GLU* 5.0 2.1 + - - -
194B ILE* 4.4 3.4 - - + -
195B ASP* 4.6 9.9 - - + +
221B GLU* 3.2 19.4 + - - +
222B VAL 3.5 6.5 - - - +
224B LYS* 1.3 81.6 - - - +
226B ILE* 1.3 67.1 + - + +
228B GLN* 4.1 6.5 - - + +
229B LYS* 3.0 69.6 + - + +
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Residues in contact with ILE 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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194B ILE* 4.0 33.0 - - + +
195B ASP* 3.8 31.2 - - + +
198B ILE* 3.9 19.7 - - + -
222B VAL 3.3 2.2 + - - +
223B ILE* 3.1 23.3 - - - +
225B TYR* 1.3 82.3 - - + +
227B LEU* 1.3 64.3 + - + +
229B LYS* 4.3 3.8 - - + -
230B ARG* 3.0 59.2 + - + +
233B VAL* 4.6 4.9 - - + +
271B LEU* 4.1 16.6 - - + -
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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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223B ILE* 3.0 42.7 + - + +
224B LYS* 4.0 7.4 - - - +
225B TYR 3.2 0.4 - - - -
226B ILE* 1.3 75.4 - - + +
228B GLN* 1.3 61.7 + - - +
230B ARG 3.1 20.5 - - - +
233B VAL* 3.5 31.6 - - + +
234B GLU* 4.6 0.4 - - - -
235B LEU* 4.4 22.7 - - + +
253B ILE* 4.8 10.5 - - + -
271B LEU* 4.1 14.1 - - + -
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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 LYS 3.2 13.7 + - - +
225B TYR* 4.2 7.9 - - + +
227B LEU* 1.3 75.9 - - - +
229B LYS* 1.3 92.7 + - - +
230B ARG* 3.1 2.6 + - - -
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Residues in contact with LYS 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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195B ASP* 4.5 19.1 - - + +
225B TYR* 3.0 60.9 + - + +
226B ILE* 3.8 6.1 - - + +
228B GLN* 1.3 97.4 + - - +
230B ARG* 1.3 66.9 + - + +
231B ASN 4.0 1.2 + - - -
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Residues in contact with ARG 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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195B ASP* 2.8 27.8 + - - +
198B ILE* 3.3 31.9 - - - +
199B ASP* 2.9 31.1 + - - +
226B ILE* 3.0 31.3 + - + +
227B LEU 3.1 17.3 - - - +
228B GLN 3.1 2.6 - - - -
229B LYS* 1.3 86.7 - - + +
231B ASN* 1.3 61.1 + - - +
232B ASP* 3.0 34.5 + - - +
233B VAL* 4.0 18.4 + - + +
273B LYS* 4.5 7.7 - - - +
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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