Contacts of the helix formed by residues 227 - 241 (chain A) in PDB entry 1FR8
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 227 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220A GLN* 3.0 7.5 + - - -
226A PHE* 1.3 73.4 - - - +
228A ARG* 1.3 69.0 + - - +
229A ALA* 3.9 2.6 + - - +
230A LYS* 3.0 36.7 + - - +
231A LEU* 3.2 21.9 + - - +
309A ASN 3.0 24.1 + - - +
311A TYR 3.2 17.7 + - - +
312A TRP* 3.0 36.1 - - + -
398A ILE* 3.3 19.1 - - + -
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Residues in contact with ARG 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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100A GDU 4.4 11.0 - - - -
187A PRO* 3.8 22.1 - - + +
226A PHE* 3.7 22.6 - - + -
227A ASN* 1.3 72.7 + - - +
229A ALA* 1.3 65.4 + - - +
231A LEU* 3.0 14.7 + - - +
232A LEU* 3.0 36.4 + - + +
250A PHE* 5.0 7.7 + - - +
251A SER 5.9 0.2 - - - -
252A ASP* 3.2 25.1 + - - +
290A PHE 5.1 3.2 + - - -
291A GLY* 4.9 2.8 - - - -
292A GLY 4.2 24.8 + - - +
294A SER* 5.3 4.0 + - - -
311A TYR 5.3 0.6 + - - -
313A GLY* 5.7 1.0 - - - +
317A GLU* 3.1 39.7 + - - +
318A ASP* 4.2 13.9 - - - +
321A ILE* 5.0 5.3 - - - +
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Residues in contact with ALA 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A ASN* 3.5 3.9 + - - +
228A ARG* 1.3 77.9 - - - +
230A LYS* 1.3 64.1 + - - +
232A LEU* 3.0 17.9 + - - +
233A ASN* 3.0 23.0 + - - +
307A PHE* 4.3 13.4 - - + +
308A PRO* 3.1 21.8 - - + +
311A TYR* 5.3 3.6 + - + +
317A GLU* 4.0 29.2 - - + +
321A ILE* 5.1 1.8 - - + -
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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
----------------------------------------------------------
227A ASN* 3.0 35.8 + - + +
229A ALA* 1.3 76.6 - - - +
231A LEU* 1.3 63.7 + - - +
233A ASN* 2.9 14.8 + - - +
234A VAL* 2.9 13.3 + - + +
308A PRO 3.9 0.8 + - - -
309A ASN* 3.3 39.6 - - + +
312A TRP* 4.7 5.0 - - + -
378A LEU* 3.9 14.1 - - + -
379A THR* 3.1 35.0 + - - +
398A ILE* 2.8 48.2 + - + +
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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
----------------------------------------------------------
187A PRO* 4.3 6.3 - - + -
188A PHE 4.4 0.4 - - - +
218A ILE* 3.3 48.6 - - + +
220A GLN* 3.3 38.8 - - + +
226A PHE* 3.4 30.5 - - + -
227A ASN 3.2 11.8 + - - +
228A ARG 3.0 7.1 + - - +
230A LYS* 1.3 76.0 - - - +
232A LEU* 1.3 57.0 + - - +
234A VAL* 3.2 6.9 + - - +
235A GLY 2.9 23.2 + - - -
396A VAL* 3.8 20.0 - - + -
398A ILE* 4.4 9.9 - - + -
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Residues in contact with LEU 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A ILE* 3.9 13.9 - - + +
187A PRO* 3.5 33.7 - - + -
228A ARG* 3.0 45.6 + - + +
229A ALA* 3.0 12.3 + - - +
231A LEU* 1.3 74.9 - - - +
233A ASN* 1.3 64.1 + - - +
235A GLY* 3.1 2.6 + - - -
236A PHE* 3.1 18.2 + - - +
250A PHE* 3.7 53.3 - - + -
307A PHE* 3.9 18.8 - - + -
321A ILE* 5.5 2.0 - - + -
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Residues in contact with ASN 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A ALA 3.0 10.2 + - - -
230A LYS 2.9 8.6 + - - +
232A LEU* 1.3 75.2 - - - +
234A VAL* 1.3 63.1 + - - +
236A PHE* 3.2 6.6 + - - +
237A LYS* 3.1 22.9 + - - +
301A PHE* 3.1 19.6 - - - -
306A GLY* 3.8 0.6 - - - -
307A PHE* 2.6 51.7 + - - +
308A PRO 4.0 2.4 + - - -
309A ASN* 2.8 25.1 + - - +
374A GLY 4.2 4.8 - - - -
375A LEU* 4.8 7.5 - - + +
378A LEU* 3.9 18.8 - - + +
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Residues in contact with VAL 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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218A ILE* 4.1 11.4 - - + -
230A LYS* 2.9 20.0 + - + +
231A LEU* 3.4 10.5 - - - +
233A ASN* 1.3 77.1 - - - +
235A GLY* 1.3 57.4 + - - +
237A LYS* 3.2 2.5 + - - +
238A GLU* 2.8 37.4 + - + +
378A LEU* 4.1 12.3 - - + -
380A TYR* 3.7 53.2 - - + -
396A VAL* 4.1 15.0 - - + -
398A ILE* 4.4 10.5 - - + -
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Residues in contact with GLY 235 (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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185A ILE* 3.7 27.0 - - - +
216A TYR* 5.4 0.8 - - - -
218A ILE* 3.8 16.8 - - - +
231A LEU 2.9 11.3 + - - -
232A LEU 3.1 4.6 + - - -
234A VAL* 1.3 76.8 - - - +
236A PHE* 1.3 55.4 + - - +
238A GLU* 4.6 1.1 - - - -
239A ALA* 2.8 35.7 + - - +
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Residues in contact with PHE 236 (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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185A ILE* 4.4 2.2 - - - +
232A LEU 3.1 10.9 + - - +
233A ASN 3.3 8.3 - - - +
235A GLY* 1.3 75.7 - - - +
237A LYS* 1.3 66.9 + - + +
240A LEU* 3.2 46.4 + - + +
248A PHE* 3.5 57.2 - + + -
250A PHE* 4.9 3.1 - + + -
298A LYS* 4.0 12.6 - - + -
301A PHE* 3.4 44.4 - + + -
302A LEU* 3.6 22.4 - - + -
375A LEU* 3.7 26.5 - - + -
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Residues in contact with LYS 237 (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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233A ASN 3.1 5.5 + - - +
234A VAL 3.7 6.1 - - - +
236A PHE* 1.3 86.5 - - + +
238A GLU* 1.3 63.0 + - - +
240A LEU* 3.6 12.1 + - + +
241A LYS* 3.5 17.8 + - - +
375A LEU* 3.6 47.4 + - + -
378A LEU* 3.6 30.7 + - + +
380A TYR* 3.7 19.9 - - + +
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Residues in contact with GLU 238 (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 TYR* 5.1 0.2 - - - -
234A VAL* 2.8 36.7 + - + +
235A GLY* 4.0 2.5 - - - +
237A LYS* 1.3 70.7 - - - +
239A ALA* 1.3 65.6 + - - +
241A LYS* 3.0 51.8 + - - +
242A ASP* 3.9 7.6 + - - +
380A TYR* 2.3 32.4 + - + +
382A VAL* 3.7 21.3 - - - +
385A VAL* 5.2 3.1 - - - +
394A ILE* 3.6 34.8 - - + +
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Residues in contact with ALA 239 (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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183A ALA* 4.0 9.4 - - + -
185A ILE* 4.3 0.7 - - + -
216A TYR* 3.9 29.1 - - + -
235A GLY 2.8 22.0 + - - +
236A PHE 4.0 3.1 - - - +
238A GLU* 1.3 74.0 - - - +
240A LEU* 1.3 59.1 + - - +
242A ASP* 2.7 23.0 + - - +
243A TYR 3.3 8.1 + - - -
245A TYR* 3.4 27.4 - - + -
248A PHE* 4.3 4.3 - - + -
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Residues in contact with LEU 240 (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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236A PHE* 3.2 56.1 + - + +
237A LYS* 3.8 7.6 - - + +
238A GLU 3.3 0.6 - - - -
239A ALA* 1.3 76.6 - - - +
241A LYS* 1.3 60.9 + - - +
242A ASP 3.0 1.1 + - - -
243A TYR 3.6 22.8 + - - +
244A ASP* 5.0 2.2 - - - -
245A TYR* 3.8 23.6 - - + +
248A PHE* 3.8 12.6 - - + -
298A LYS* 4.1 24.2 - - - +
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Residues in contact with LYS 241 (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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237A LYS* 3.5 12.1 + - - +
238A GLU* 3.0 49.3 + - - +
239A ALA 3.0 1.0 - - - -
240A LEU* 1.3 78.1 - - - +
242A ASP* 1.3 63.2 + - - +
380A TYR* 4.8 2.6 + - - -
382A VAL* 5.2 4.0 - - - +
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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
------------------------------------------------------------
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