Contacts of the helix formed by residues 221 - 233 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171A GLN* 4.1 13.0 - - - +
219A GLU* 2.9 13.4 + - - +
220A VAL* 1.3 75.9 + - - +
222A LYS* 1.3 68.5 + - + +
223A GLU* 3.5 28.0 - - + +
224A ASN* 3.7 21.7 + - - +
225A LEU* 3.0 26.4 + - - +
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Residues in contact with LYS 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A GLN* 3.2 33.1 + - - +
174A GLN* 3.7 43.1 - - + +
175A ALA* 4.1 13.4 - - - +
178A ALA* 4.5 8.7 - - - -
221A THR* 1.3 74.6 - - + +
223A GLU* 1.3 83.6 + - - +
225A LEU* 3.3 3.3 + - - +
226A LEU* 3.0 51.6 + - + +
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Residues in contact with GLU 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221A THR* 3.2 16.8 - - + -
222A LYS* 1.3 107.2 + - - +
224A ASN* 1.3 64.6 + - - +
226A LEU* 3.7 10.6 + - - +
227A ASP* 3.2 23.7 + - - +
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Residues in contact with ASN 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216A PHE* 3.4 20.4 - - + -
219A GLU* 3.0 37.6 + - - +
221A THR* 3.3 20.7 + - - +
223A GLU* 1.3 80.4 - - - +
225A LEU* 1.3 57.3 + - - +
227A ASP* 3.4 9.0 + - - +
228A PHE* 3.1 21.1 + - - +
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Residues in contact with LEU 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A GLN 4.3 0.9 - - - -
172A PHE* 3.6 39.0 - - + +
175A ALA* 3.9 14.6 - - + -
203A VAL* 3.8 30.7 - - + -
216A PHE* 3.7 31.9 - - + -
220A VAL* 3.8 16.2 - - + -
221A THR 3.0 20.2 + - - +
222A LYS 3.7 4.0 - - - +
223A GLU 3.3 0.2 - - - -
224A ASN* 1.3 75.4 - - - +
226A LEU* 1.3 59.0 + - - +
228A PHE* 3.0 6.1 + - + +
229A ILE* 2.9 39.0 + - + +
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Residues in contact with LEU 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A ALA* 3.8 29.2 - - + +
178A ALA* 3.8 16.2 - - + -
179A ILE* 3.9 21.5 - - + +
222A LYS* 3.0 50.6 + - + +
223A GLU* 4.0 11.9 - - - +
225A LEU* 1.3 75.4 - - - +
227A ASP* 1.3 62.4 + - - +
229A ILE* 4.0 6.0 - - + +
230A LYS* 3.2 26.3 + - - +
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Residues in contact with ASP 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223A GLU 3.2 19.6 + - - +
224A ASN* 3.4 12.1 + - - +
226A LEU* 1.3 77.4 - - - +
228A PHE* 1.3 60.8 + - - +
230A LYS* 4.1 3.4 - - - +
231A HIS* 3.2 25.8 + - - +
252A GLU* 6.1 1.2 - - - +
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Residues in contact with PHE 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157A VAL* 5.7 0.2 - - + -
203A VAL* 4.4 12.3 - - + -
205A LEU* 3.9 27.4 - - + -
214A ASN* 3.3 27.8 - - + -
215A ASN 3.7 8.1 - - - -
216A PHE* 3.4 53.4 - + + -
217A GLU 5.1 0.9 - - - -
224A ASN 3.1 14.7 + - - +
225A LEU* 3.0 12.0 + - + +
227A ASP* 1.3 74.8 - - - +
229A ILE* 1.3 76.2 + - + +
231A HIS* 3.5 2.9 + - - +
232A ASN* 3.1 52.4 + - - +
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Residues in contact with ILE 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157A VAL* 4.5 7.6 - - + -
175A ALA* 5.3 2.0 - - + +
179A ILE* 3.7 23.8 - - + -
182A ILE* 3.8 23.1 - - + -
184A PHE* 3.7 34.3 - - + -
203A VAL* 6.4 0.2 - - + -
205A LEU* 3.9 14.6 - - + -
225A LEU* 2.9 27.7 + - + +
226A LEU* 4.0 6.7 - - + +
228A PHE* 1.3 84.3 - - + +
230A LYS* 1.3 53.4 + - - +
232A ASN 2.8 6.8 + - - -
233A GLN* 2.6 50.2 + - + +
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Residues in contact with LYS 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A ILE* 5.4 1.8 - - + +
226A LEU 3.2 16.0 + - - +
227A ASP* 4.2 4.0 - - - +
229A ILE* 1.3 78.5 - - - +
231A HIS* 1.3 59.4 + - - +
233A GLN* 3.9 15.3 - - - +
234A LEU* 3.4 24.1 - - - +
251A GLY* 6.0 4.1 - - - -
252A GLU* 6.1 5.6 - - + +
253A ILE* 5.4 5.2 - - - +
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Residues in contact with HIS 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227A ASP 3.2 17.7 + - - +
228A PHE* 3.8 5.8 - - - +
229A ILE 3.1 0.6 - - - -
230A LYS* 1.3 76.5 - - - +
232A ASN* 1.3 75.7 + - - +
234A LEU* 5.4 4.7 + - - +
253A ILE* 6.2 3.5 - - - +
284A GLY* 5.0 16.2 - - - -
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Residues in contact with ASN 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A LEU* 4.0 13.8 - - + +
207A LYS* 3.1 28.9 + - - +
211A GLU* 4.4 3.5 - - - +
214A ASN* 3.3 35.1 + - + +
228A PHE* 3.1 47.3 + - - +
229A ILE 2.8 3.0 + - - +
231A HIS* 1.3 96.2 - - - +
233A GLN* 1.3 64.4 + - - +
234A LEU 3.3 6.1 + - - +
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Residues in contact with GLN 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A VAL* 3.3 26.3 - - + +
179A ILE* 4.6 7.9 - - - +
181A ASP* 3.9 19.5 + - - +
182A ILE* 3.9 25.8 - - + +
205A LEU* 4.3 7.2 - - - -
209A PHE* 3.4 5.8 - - - -
229A ILE* 2.6 36.1 + - + +
230A LYS* 3.9 18.2 + - - +
231A HIS 3.7 0.8 - - - -
232A ASN* 1.3 72.8 - - - +
234A LEU* 1.3 69.5 + - + +
235A PRO* 4.5 0.3 - - - +
247A LYS* 4.6 18.9 + - + +
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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