Contacts of the helix formed by residues 228 - 239 (chain A) in PDB entry 3F3Z
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 THR 228 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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226A ALA 3.2 1.5 - - - -
227A PRO* 1.3 85.5 - - + +
229A ASP* 1.3 66.2 + - - +
230A SEP 2.6 36.5 + - - +
231A GLU* 3.1 24.1 + - - +
232A VAL* 3.1 23.8 + - - +
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Residues in contact with ASP 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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189A PRO* 3.6 34.7 - - + +
190A TYR* 4.6 13.5 - - - -
228A THR* 1.3 72.1 - - - +
230A SEP 1.3 65.3 + - - +
232A VAL* 3.3 5.2 + - - +
233A MET* 3.0 36.3 + - + +
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Residues in contact with SEP 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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228A THR* 2.6 32.9 + - - +
229A ASP* 1.3 77.4 + - - +
231A GLU* 1.3 64.3 + - - +
233A MET* 3.3 15.3 + - - +
234A LEU* 3.0 36.8 + - - +
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Residues in contact with GLU 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A ALA* 3.4 17.4 - - + +
227A PRO* 3.5 25.8 - - - +
228A THR* 3.1 28.4 + - - +
230A SEP 1.3 82.8 + - - +
232A VAL* 1.3 66.4 + - - +
234A LEU* 3.4 15.4 + - + +
235A LYS* 3.1 30.8 + - - +
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Residues in contact with VAL 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A PRO* 3.6 29.4 - - + +
190A TYR* 3.8 24.9 - - + -
224A PHE* 3.7 18.5 - - - +
226A ALA* 3.6 31.4 - - - +
228A THR 3.1 15.0 + - - +
229A ASP* 3.5 10.5 - - - +
231A GLU* 1.3 77.8 - - - +
233A MET* 1.3 57.3 + - - +
235A LYS* 3.2 10.1 + - - +
236A ILE* 3.0 31.8 + - + +
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Residues in contact with MET 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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189A PRO* 4.1 33.4 - - + +
192A VAL* 4.4 2.2 - - + -
197A LEU* 3.4 38.1 - - + +
229A ASP* 3.0 35.4 + - + +
230A SEP 3.8 11.0 - - - +
232A VAL* 1.3 72.6 - - - +
234A LEU* 1.3 60.2 + - - +
236A ILE* 3.2 3.7 + - - -
237A ARG* 2.9 34.7 + - - +
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Residues in contact with LEU 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 SEP 3.0 21.8 + - - +
231A GLU* 3.6 18.4 - - + +
233A MET* 1.3 76.2 - - - +
235A LYS* 1.3 61.3 + - + +
237A ARG* 3.5 36.2 + - - +
238A GLU* 3.4 25.2 + - - +
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Residues in contact with LYS 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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224A PHE* 3.6 21.5 - - + -
225A SER 2.8 39.3 + - - +
226A ALA* 4.3 9.6 - - + +
231A GLU* 3.1 17.8 + - - +
232A VAL* 3.2 8.9 + - - +
234A LEU* 1.3 74.2 - - + +
236A ILE* 1.3 60.0 + - - +
238A GLU* 3.4 9.5 + - - +
239A GLY 3.0 21.7 + - - -
240A THR 4.2 3.6 + - - +
297A GOL 5.8 2.2 + - - -
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Residues in contact with ILE 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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189A PRO 3.0 29.2 - - - +
190A TYR 4.2 8.3 - - - +
192A VAL* 3.3 30.1 - - + +
194A PRO* 3.4 30.0 - - + +
197A LEU* 3.8 10.8 - - + -
208A TRP* 4.2 6.2 - - + +
224A PHE* 3.6 28.3 - - + -
232A VAL* 3.0 28.6 + - + +
233A MET* 3.2 7.8 + - - +
235A LYS* 1.3 72.8 - - - +
237A ARG* 1.3 68.7 + - - +
239A GLY* 3.0 15.2 + - - -
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Residues in contact with ARG 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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194A PRO* 4.5 9.5 - - - +
197A LEU* 3.8 27.1 - - + -
198A GLU* 5.7 5.9 - - + +
233A MET 2.9 20.2 + - - +
234A LEU* 3.6 33.2 + - - +
236A ILE* 1.3 76.5 - - - +
238A GLU* 1.3 61.5 + - + +
265A LYS* 3.0 26.2 + - - -
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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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234A LEU 3.4 14.7 + - - +
235A LYS* 3.5 9.6 - - - +
236A ILE 3.2 0.2 - - - -
237A ARG* 1.3 81.3 + - + +
239A GLY* 1.3 56.8 + - - +
240A THR* 3.4 17.5 + - - +
265A LYS* 3.1 22.9 + - - +
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Residues in contact with GLY 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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208A TRP* 4.6 10.8 - - - -
224A PHE* 3.6 12.5 - - - -
235A LYS 3.0 6.9 + - - -
236A ILE 3.0 16.6 + - - -
238A GLU* 1.3 76.0 - - - +
240A THR* 1.3 62.1 + - - +
241A PHE* 3.5 18.5 - - - -
263A LEU 5.1 1.4 - - - +
265A LYS* 4.6 10.7 - - - +
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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