Contacts of the helix formed by residues 221 - 234 (chain A) in PDB entry 6UPR
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 ASP 221 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219A ASP 5.3 0.2 - - - +
220A GLU* 1.3 82.6 - - - +
222A GLU* 1.3 68.7 + - - +
223A ASP* 3.1 16.7 - - + +
224A PHE* 3.4 12.0 + - - +
225A LYS* 3.1 21.0 + - - +
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Residues in contact with GLU 222 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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220A GLU 4.6 0.5 - - - +
221A ASP* 1.3 75.8 - - - +
223A ASP* 1.3 59.8 + - - +
225A LYS* 3.2 34.1 + - - +
226A GLU* 3.0 30.8 + - - +
229A ARG* 4.8 2.1 + - - -
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Residues in contact with ASP 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 ASP* 3.1 13.1 - - + +
222A GLU* 1.3 81.3 - - - +
224A PHE* 1.3 62.2 + - - +
226A GLU* 3.4 8.2 + - - +
227A GLN* 3.1 23.9 + - - +
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Residues in contact with PHE 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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214A PRO 6.1 0.2 - - - -
216A ALA* 3.8 20.4 - - + -
220A GLU* 3.7 31.6 - - + -
221A ASP* 3.4 11.3 + - - +
222A GLU 3.4 0.2 - - - -
223A ASP* 1.3 80.1 - - - +
225A LYS* 1.3 55.6 + - - +
227A GLN* 4.0 22.1 - - - +
228A THR* 2.7 49.7 + - + -
282A THR* 5.0 15.7 - - + -
283A HIS* 5.2 13.5 - + - -
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Residues in contact with LYS 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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216A ALA* 4.4 23.0 + - + +
217A GLU 4.3 1.8 + - - +
218A SER* 3.5 36.6 + - - +
219A ASP 4.6 1.6 - - - +
220A GLU* 3.5 22.4 - - + +
221A ASP 3.1 12.3 + - - +
222A GLU* 3.2 33.2 - - - +
223A ASP 3.2 0.2 - - - -
224A PHE* 1.3 77.3 - - - +
226A GLU* 1.3 61.6 + - - +
228A THR* 3.4 3.5 + - - -
229A ARG* 3.2 50.3 + - - +
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Residues in contact with GLU 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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222A GLU 3.0 17.8 + - - +
223A ASP* 4.0 7.6 - - - +
225A LYS* 1.3 74.9 - - - +
227A GLN* 1.3 67.2 + - - +
229A ARG* 3.3 20.3 - - + +
230A LEU* 3.1 38.3 + - + +
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Residues in contact with GLN 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 ASP 3.1 17.3 + - - +
224A PHE* 4.0 22.6 - - - +
226A GLU* 1.3 77.7 - - - +
228A THR* 1.3 59.1 + - - +
230A LEU* 3.4 8.3 + - + +
231A LEU* 3.0 48.1 + - + +
278A THR* 3.5 31.2 - - + +
282A THR* 4.1 15.8 + - - +
283A HIS* 5.9 0.3 + - - -
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Residues in contact with THR 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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213A LEU* 5.3 5.2 - - + -
214A PRO 3.6 24.2 - - - +
216A ALA* 3.9 15.6 - - - +
224A PHE* 2.7 45.1 + - + -
225A LYS 3.8 4.7 - - - -
226A GLU 3.2 0.4 - - - -
227A GLN* 1.3 78.4 + - - +
229A ARG* 1.3 62.5 + - - +
231A LEU* 3.3 9.2 + - - +
232A LYS* 3.2 37.2 + - + +
283A HIS* 5.3 7.5 + - + -
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Residues in contact with ARG 229 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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222A GLU* 4.8 2.4 + - - -
225A LYS* 3.2 57.5 + - - +
226A GLU* 3.3 24.2 - - + +
228A THR* 1.3 77.7 - - - +
230A LEU* 1.3 56.5 + - - +
232A LYS* 4.2 11.9 - - - +
233A ALA* 3.2 27.5 + - - +
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Residues in contact with LEU 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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226A GLU* 3.1 36.8 + - + +
227A GLN* 3.6 7.4 - - - +
229A ARG* 1.3 77.0 - - + +
231A LEU* 1.3 68.4 + - + +
233A ALA* 3.3 12.4 + - + +
234A SER* 3.1 23.1 + - - +
275A LYS* 3.3 36.8 - - - +
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Residues in contact with LEU 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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213A LEU* 3.7 20.0 - - + -
227A GLN* 3.0 32.6 + - + +
228A THR* 3.3 3.3 + - - +
230A LEU* 1.3 77.3 - - + +
232A LYS* 1.3 63.3 + - - +
234A SER* 3.3 8.5 + - - -
235A ILE* 3.6 5.7 - - - +
237A PHE* 3.4 23.7 - - + -
275A LYS* 3.5 44.4 - - + +
278A THR* 4.3 16.2 - - + -
279A MET* 3.9 29.2 - - + +
282A THR* 4.7 0.9 - - - +
283A HIS* 4.5 8.3 - - - +
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Residues in contact with LYS 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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212A HIS* 6.2 0.7 - - + -
213A LEU* 3.8 41.7 - - + +
215A ASP* 3.7 35.6 + - - +
228A THR* 3.2 33.0 + - - +
229A ARG* 4.2 9.2 - - - +
230A LEU 3.3 0.2 - - - -
231A LEU* 1.3 76.2 - - - +
233A ALA* 1.3 61.4 + - - +
234A SER 3.5 0.5 + - - -
235A ILE* 3.6 22.5 + - + +
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Residues in contact with ALA 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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196A LYS* 5.8 1.2 - - - +
229A ARG 3.2 19.6 + - - +
230A LEU* 3.8 9.6 - - + +
231A LEU 3.2 0.6 - - - -
232A LYS* 1.3 77.9 - - - +
234A SER* 1.3 58.2 + - - +
235A ILE 3.4 3.2 - - - +
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Residues in contact with SER 234 (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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196A LYS* 3.1 30.8 + - - +
230A LEU* 3.1 18.2 + - - +
231A LEU 3.3 6.5 + - - -
232A LYS 3.2 0.6 - - - -
233A ALA* 1.3 77.6 - - - +
235A ILE* 1.3 59.4 + - - +
236A PRO 3.1 11.8 - - - +
237A PHE* 3.5 13.2 + - - -
272A ASP* 4.3 2.7 - - - -
275A LYS* 3.2 35.5 + - - -
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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