Contacts of the helix formed by residues 220 - 232 (chain A) in PDB entry 1FRP
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 220 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218A GLU 3.8 1.8 + - - -
219A PHE* 1.3 75.0 - - - +
221A PRO* 1.3 72.9 - - + +
222A ALA* 3.1 17.5 + - - +
223A ILE* 3.3 15.0 + - - +
224A THR* 2.9 21.8 + - - -
265A PRO* 5.0 1.7 - - - +
266A ALA* 4.8 11.5 + - - +
331A TYR* 3.0 30.7 + - - -
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Residues in contact with PRO 221 (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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219A PHE 4.5 1.1 - - - +
220A ASP* 1.3 88.4 - - + +
222A ALA* 1.3 57.6 + - - +
224A THR* 3.9 8.9 - - - +
225A GLU* 3.1 27.7 + - - +
334A HIS* 3.7 33.6 + - + +
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Residues in contact with ALA 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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220A ASP* 3.1 10.0 + - - +
221A PRO* 1.3 75.7 - - - +
223A ILE* 1.3 59.7 + - - +
226A TYR* 2.9 30.1 + - - +
327A LEU* 3.9 3.7 - - - +
330A ILE* 3.5 29.5 - - + +
331A TYR* 3.7 38.8 - - + -
334A HIS* 4.4 7.5 + - + +
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Residues in contact with ILE 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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211A ILE* 3.9 11.4 - - + -
219A PHE* 3.7 20.6 - - + -
220A ASP* 3.3 15.4 + - - +
222A ALA* 1.3 76.7 - - - +
224A THR* 1.3 57.7 + - - +
226A TYR* 3.0 5.9 + - - +
227A ILE* 2.9 49.4 + - + +
263A MET* 4.5 10.3 - - - -
265A PRO* 4.0 24.7 - - + -
317A ILE* 4.5 3.8 - - + -
327A LEU* 4.1 16.4 - - + -
331A TYR* 3.5 34.5 - - + +
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Residues in contact with THR 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 ALA 5.1 3.6 + - - +
219A PHE* 3.7 17.9 + - + +
220A ASP 2.9 18.9 + - - -
221A PRO* 3.9 8.6 - - - +
222A ALA 3.4 0.2 - - - -
223A ILE* 1.3 77.8 - - - +
225A GLU* 1.3 64.0 + - - +
227A ILE* 3.4 7.6 + - - +
228A GLN* 3.1 29.0 + - + +
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Residues in contact with GLU 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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221A PRO 3.1 15.2 + - - +
222A ALA 3.8 4.0 - - - +
224A THR* 1.3 80.5 - - - +
226A TYR* 1.3 57.3 + - - +
228A GLN* 3.2 10.6 - - + +
229A ARG* 3.0 42.9 + - + +
330A ILE* 3.8 13.3 - - + +
333A LYS* 3.5 25.8 + - - +
334A HIS* 2.9 28.3 + - - +
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Residues in contact with TYR 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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209A TYR* 5.0 0.4 - + + -
222A ALA 2.9 18.8 + - - +
223A ILE 3.0 4.7 + - - +
225A GLU* 1.3 72.4 - - - +
227A ILE* 1.3 68.8 + - + +
229A ARG* 3.0 13.1 + - - +
230A LYS* 3.0 50.6 + - + +
240A TYR* 4.4 0.7 - - - -
261A ILE* 3.5 31.6 - - + +
263A MET* 3.8 38.6 - - + -
323A ASP* 3.9 24.3 + - - +
326A GLU* 3.9 17.5 - - + -
327A LEU* 3.7 22.2 - - + -
330A ILE* 4.0 22.2 - - + +
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Residues in contact with ILE 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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209A TYR* 4.5 10.5 - - + -
211A ILE* 4.3 20.6 - - + -
213A GLU* 3.6 26.2 - - - +
219A PHE* 3.6 32.3 - - + -
223A ILE* 2.9 34.4 + - + +
224A THR* 3.9 5.4 - - - +
226A TYR* 1.3 77.4 - - + +
228A GLN* 1.3 65.1 - - - +
230A LYS* 3.1 9.7 + - - +
231A LYS* 3.0 39.2 + - + +
263A MET* 5.0 2.5 - - + -
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Residues in contact with GLN 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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224A THR* 3.1 19.9 + - + +
225A GLU* 3.2 15.0 - - + +
226A TYR 3.1 0.2 - - - -
227A ILE* 1.3 79.0 - - - +
229A ARG* 1.3 58.4 + - + +
231A LYS* 3.1 9.6 + - - +
232A PHE* 2.8 65.2 + - + +
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Residues in contact with ARG 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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225A GLU* 3.0 26.5 + - + +
226A TYR* 3.0 7.6 + - + +
228A GLN* 1.3 76.8 - - + +
230A LYS* 1.3 70.8 + - + +
232A PHE 4.0 7.4 - - - -
233A PRO* 3.3 25.5 - - - +
234A PRO* 4.0 32.0 - - + +
326A GLU* 3.8 29.7 + - - +
329A GLU* 5.0 5.1 + - - +
330A ILE* 3.4 40.2 - - - +
333A LYS* 5.6 3.6 - - - +
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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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205A LYS* 4.9 1.2 - - - +
209A TYR* 4.0 24.0 - - + -
226A TYR* 3.0 47.6 + - + +
227A ILE* 3.4 11.0 - - - +
229A ARG* 1.3 87.5 + - + +
231A LYS* 1.3 57.5 + - - +
233A PRO* 4.0 1.3 - - - +
239A PRO* 3.3 8.5 - - - +
240A TYR* 3.1 75.1 + - + +
326A GLU* 2.8 35.7 + - - +
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Residues in contact with LYS 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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209A TYR* 3.3 26.2 - - + +
213A GLU* 2.8 25.3 + - - -
227A ILE* 3.0 24.3 + - + +
228A GLN* 3.8 9.2 - - - +
230A LYS* 1.3 79.5 - - - +
232A PHE* 1.3 75.0 + - + +
233A PRO* 3.5 7.4 - - - +
239A PRO* 3.6 17.6 - - - +
213B GLU* 3.4 32.7 + - - +
214B GLY* 4.5 6.3 - - - +
216B ALA* 3.8 18.4 - - + +
217B LYS* 4.0 11.3 + - - +
231B LYS* 4.1 5.5 - - - +
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Residues in contact with PHE 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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228A GLN* 2.8 49.5 + - + +
229A ARG* 3.7 4.2 - - - +
231A LYS* 1.3 86.8 - - + +
233A PRO* 1.3 66.8 - - - +
234A PRO* 3.3 8.0 - - - +
216B ALA* 4.4 9.9 - - + -
217B LYS* 3.7 51.1 - - + -
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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