Contacts of the helix formed by residues 223 - 234 (chain A) in PDB entry 1F0K
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 SER 223 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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193A GLN 5.3 2.6 + - - -
199A ASN* 3.9 11.7 + - - -
219A SER* 3.1 29.6 + - - -
220A GLY 3.2 3.8 + - - -
221A LYS 3.2 8.0 + - - -
222A GLY* 1.3 79.0 + - - +
224A GLN* 1.3 66.0 + - - +
225A GLN 3.4 2.9 - - - -
226A SER* 3.2 14.2 + - - +
227A VAL* 3.2 21.1 + - - +
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Residues in contact with GLN 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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219A SER* 3.0 14.0 + - - +
220A GLY 4.0 0.6 + - - -
222A GLY 3.7 1.4 - - - -
223A SER* 1.3 77.8 - - - +
225A GLN* 1.3 73.6 + - + +
228A GLU* 3.0 42.0 + - - +
241A VAL* 2.6 45.8 + - - +
242A THR* 3.9 1.3 - - - -
243A GLU* 3.6 34.5 - - + +
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Residues in contact with GLN 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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222A GLY 5.3 1.7 + - - +
223A SER 3.4 0.4 - - - -
224A GLN* 1.3 93.2 - - + +
226A SER* 1.3 57.2 + - - +
228A GLU* 3.7 5.2 - - + +
229A GLN* 3.1 30.4 + - - +
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Residues in contact with SER 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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200A GLN* 5.6 4.2 + - - -
222A GLY 5.6 1.7 + - - -
223A SER* 3.2 20.3 + - - -
224A GLN 3.4 0.4 - - - -
225A GLN* 1.3 78.6 - - - +
227A VAL* 1.3 65.9 + - - +
229A GLN* 3.5 11.9 + - - +
230A ALA* 3.0 24.9 + - - +
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Residues in contact with VAL 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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199A ASN* 3.6 38.1 - - + +
200A GLN* 5.9 0.7 - - - +
203A PRO* 4.7 0.9 - - + -
217A HIS* 4.0 15.5 - - + +
219A SER* 3.6 10.8 - - - -
223A SER* 3.2 17.1 + - - +
224A GLN 4.0 2.2 - - - +
226A SER* 1.3 84.2 + - - +
228A GLU* 1.3 65.1 + - - +
230A ALA* 3.1 7.2 + - - +
231A TYR* 3.0 48.6 + - + -
241A VAL* 3.9 14.8 - - + -
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Residues in contact with GLU 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 GLN* 3.0 31.1 + - - +
225A GLN* 3.7 9.0 - - + +
227A VAL* 1.3 77.1 - - - +
229A GLN* 1.3 61.7 + - - +
231A TYR* 3.4 5.9 + - - +
232A ALA* 3.2 20.8 + - - +
237A PRO* 4.5 3.3 - - - +
241A VAL* 3.3 31.7 + - - +
216B TRP* 5.8 0.3 - - - -
240B LYS* 3.0 32.6 + - - -
242B THR* 4.0 11.6 - - - +
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Residues in contact with GLN 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 GLN 3.1 19.1 + - - +
226A SER* 3.7 9.9 - - - +
228A GLU* 1.3 74.7 - - - +
230A ALA* 1.3 59.2 + - - +
232A ALA* 3.3 8.4 + - + +
233A GLU* 3.0 55.4 + - + +
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Residues in contact with ALA 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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199A ASN 4.9 3.4 - - - +
203A PRO* 3.8 24.3 - - + +
226A SER 3.0 15.7 + - - +
227A VAL* 3.1 12.5 + - - +
229A GLN* 1.3 77.4 - - - +
231A TYR* 1.3 57.5 + - - +
233A GLU* 3.4 10.3 + - - +
234A ALA* 3.0 27.5 + - - +
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Residues in contact with TYR 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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202A MET* 3.3 13.7 - - - +
203A PRO* 3.6 28.7 - - + -
206A ALA* 3.7 17.9 - - + -
215A ILE* 3.6 17.3 - - + +
217A HIS* 2.8 33.1 + - + -
227A VAL* 3.0 41.9 + - + -
228A GLU* 3.7 7.9 - - - +
229A GLN 3.3 0.2 - - - -
230A ALA* 1.3 74.0 - - - +
232A ALA* 1.3 63.3 + - - +
234A ALA* 3.1 10.4 + - - +
236A GLN* 2.9 37.6 + - + +
237A PRO* 4.7 4.0 - - + +
239A HIS* 3.6 30.1 - + + +
241A VAL* 3.7 15.7 - - + -
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Residues in contact with ALA 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 GLU 3.2 10.6 + - - +
229A GLN* 3.6 12.1 - - + +
230A ALA 3.3 0.2 - - - -
231A TYR* 1.3 79.3 - - - +
233A GLU* 1.3 58.5 + - + +
235A GLY* 2.9 19.8 + - - -
237A PRO* 3.9 25.8 - - + +
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Residues in contact with GLU 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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229A GLN* 3.0 46.2 + - + +
230A ALA* 3.8 8.0 - - - +
232A ALA* 1.3 73.2 - - + +
234A ALA* 1.3 60.1 + - - +
235A GLY 3.0 5.5 + - - -
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Residues in contact with ALA 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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203A PRO* 3.4 29.6 - - + +
204A GLN* 5.0 2.2 - - + -
207A ALA* 3.7 23.7 - - + +
230A ALA 3.0 16.7 + - - +
231A TYR* 3.5 7.9 - - + +
232A ALA 3.1 0.6 - - - -
233A GLU* 1.3 77.1 - - - +
235A GLY* 1.3 61.8 + - - +
236A GLN* 3.4 7.6 + - + +
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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