Contacts of the helix formed by residues 226 - 236 (chain A) in PDB entry 6D6U
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 TYR 226 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144A PRO* 3.4 30.4 - - + +
145A LEU* 3.9 11.7 - - + +
221A PHE* 5.6 1.6 - - + -
222A ILE* 2.9 40.9 + - + +
225A THR* 1.3 88.3 + - - +
227A MET* 1.3 67.3 + - - +
228A PRO 3.2 1.6 - - - -
229A SER* 3.2 15.9 + - - -
230A ILE* 3.3 25.4 + - + +
268A LEU* 5.9 0.4 - - + -
280A ALA* 6.1 0.2 - - - +
281A ILE* 3.6 34.1 - - + +
284A TYR* 4.5 23.5 - + + -
285A LEU* 6.0 3.1 - - + -
335A TYR* 4.2 15.0 + + - -
336A TRP* 3.6 32.1 - + + -
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Residues in contact with MET 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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222A ILE* 3.6 25.1 + - + +
223A LEU* 3.6 38.6 - - + +
226A TYR* 1.3 76.8 - - - +
228A PRO* 1.3 66.5 - - + +
230A ILE* 3.6 18.0 - - + +
231A LEU* 2.9 36.1 + - + +
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Residues in contact with PRO 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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223A LEU 4.1 9.4 - - - +
224A GLN 4.7 2.2 - - - +
225A THR 3.2 22.2 - - - +
227A MET* 1.3 90.5 - - + +
229A SER* 1.3 57.5 + - - +
231A LEU* 3.2 8.6 + - + +
232A ILE* 3.0 35.0 + - + +
264A ILE* 4.0 26.9 - - + -
298E LEU* 4.6 22.2 - - + -
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Residues in contact with SER 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 THR 4.6 2.5 + - - -
226A TYR* 3.2 9.8 + - - -
228A PRO* 1.3 77.6 - - - +
230A ILE* 1.3 57.2 + - - +
232A ILE* 3.3 1.7 + - - +
233A THR* 2.9 34.9 + - - -
261A MET* 3.6 31.7 - - - +
264A ILE* 4.1 12.4 - - - +
284A TYR* 4.9 3.1 - - - -
285A LEU* 3.4 28.5 - - - +
288A CYS* 4.4 11.7 - - - -
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Residues in contact with ILE 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 TYR* 3.4 30.3 - - + +
227A MET* 3.3 18.6 + - + +
228A PRO 3.2 0.6 - - - -
229A SER* 1.3 77.8 - - - +
231A LEU* 1.3 59.7 + - + +
233A THR* 3.3 6.6 + - - -
234A ILE* 2.9 46.9 + - + +
284A TYR* 3.3 27.6 - - + +
288A CYS* 5.5 0.9 - - - -
328A PHE* 4.8 11.9 - - + -
332A ASN* 5.9 0.4 - - - +
336A TRP* 5.9 5.4 - - + +
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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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227A MET* 2.9 29.9 + - + +
228A PRO* 3.7 7.4 - - + +
230A ILE* 1.3 76.9 - - + +
232A ILE* 1.3 62.3 + - + +
234A ILE* 3.4 14.6 + - + +
235A LEU* 2.9 30.0 + - - +
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Residues in contact with ILE 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 PRO 3.0 19.6 + - - +
229A SER 3.7 3.8 - - - +
231A LEU* 1.3 80.2 - - + +
233A THR* 1.3 63.1 + - - +
235A LEU* 3.2 18.0 + - + +
236A SER* 3.0 22.2 + - - -
257A THR* 3.7 27.4 - - + +
260A THR* 3.6 29.2 - - + -
261A MET* 3.6 30.1 - - + -
264A ILE* 4.1 7.4 - - + -
292A VAL* 4.9 0.9 - - + -
305E ILE* 5.9 0.7 - - + -
401E Y01 5.6 6.5 - - + -
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Residues in contact with THR 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 SER 2.9 18.4 + - - -
230A ILE* 3.7 4.9 - - - -
232A ILE* 1.3 77.4 - - - +
234A ILE* 1.3 62.3 + - - +
236A SER* 2.4 29.7 + - - +
237A TRP* 3.6 17.2 - - + +
261A MET* 4.9 0.7 - - - -
288A CYS* 3.8 21.5 - - - +
291A PHE* 4.6 15.7 - - + -
292A VAL* 4.0 11.2 - - + +
328A PHE* 3.7 35.4 - - + -
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Residues in contact with ILE 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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230A ILE* 2.9 38.5 + - + +
231A LEU* 3.9 14.8 - - + +
233A THR* 1.3 76.1 - - - +
235A LEU* 1.3 63.6 + - - +
237A TRP* 2.9 44.3 + - + +
238A VAL* 3.8 7.7 + - + +
328A PHE* 5.0 11.4 - - + -
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Residues in contact with LEU 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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231A LEU 2.9 18.1 + - - +
232A ILE* 3.2 16.6 + - + +
234A ILE* 1.3 78.2 - - - +
236A SER* 1.3 62.2 + - - +
237A TRP 3.0 1.4 + - - -
238A VAL* 3.1 28.8 + - + +
239A SER* 4.2 3.3 + - - -
253A LEU* 4.6 11.5 - - + +
256A THR* 5.9 0.7 - - + -
257A THR* 4.2 17.7 - - + +
406A Y01 3.4 36.3 - - + -
401E Y01 3.7 38.1 - - + -
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Residues in contact with SER 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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232A ILE 3.0 12.1 + - - -
233A THR* 2.4 30.8 + - - +
235A LEU* 1.3 76.0 - - - +
237A TRP* 1.3 67.2 + - - +
238A VAL 3.4 0.2 - - - -
239A SER* 3.5 21.9 + - - -
240A PHE* 4.4 6.8 - - - -
253A LEU* 5.9 0.9 - - - -
257A THR* 4.2 19.5 - - - +
291A PHE 5.8 0.2 - - - -
292A VAL* 3.9 22.6 - - - +
295A ALA* 5.1 12.3 - - - +
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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