Contacts of the helix formed by residues 228 - 240 (chain A) in PDB entry 6TT8
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 HIS 228 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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187A PRO* 3.4 34.3 - - + +
225A ASP* 2.7 39.4 + - - +
227A GLU* 1.3 101.4 + - + +
229A TYR* 1.3 58.4 + - - +
230A ALA 3.3 2.0 - - - -
231A ALA* 3.1 13.2 + - + +
232A SER* 2.9 30.5 + - - +
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Residues in contact with TYR 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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187A PRO 3.5 6.9 + - - -
188A GLY* 3.3 29.8 - - - -
189A HIS* 3.5 13.2 - - - +
209A LEU* 2.8 33.3 + - + -
211A LYS* 2.7 33.1 + - - -
218A LEU* 4.7 2.9 - - + -
221A LEU* 3.8 21.1 - - + -
224A ALA* 4.5 0.2 - - + -
225A ASP 3.0 19.1 + - - +
226A THR* 4.6 2.2 - - - -
227A GLU 3.4 0.6 - - - -
228A HIS* 1.3 77.4 - - - +
230A ALA* 1.3 64.0 + - - +
232A SER* 3.3 0.7 + - - -
233A ALA* 3.0 25.7 + - + +
262A THR* 4.1 12.8 - - + -
266A ALA* 3.8 19.7 - - + -
269A LEU* 3.9 17.5 - - + -
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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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226A THR 5.7 0.2 + - - -
227A GLU 4.5 8.4 + - - +
228A HIS* 3.3 0.6 - - - +
229A TYR* 1.3 76.9 - - - +
231A ALA* 1.3 59.8 + - - +
233A ALA* 4.2 1.7 + - - +
234A ARG* 2.9 34.4 + - - +
263A ALA* 4.5 2.0 - - - +
266A ALA* 3.7 27.6 + - - +
267A ASP* 3.5 26.2 - - - +
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Residues in contact with ALA 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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185A PRO 5.0 0.2 - - - -
227A GLU 5.1 1.1 + - - +
228A HIS* 3.1 17.2 + - + +
230A ALA* 1.3 78.5 - - - +
232A SER* 1.3 60.8 + - - +
233A ALA 3.3 0.2 - - - -
234A ARG* 3.1 9.8 + - - +
235A ALA* 2.8 27.8 + - - +
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Residues in contact with SER 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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185A PRO* 3.2 37.5 + - - +
186A GLY* 3.4 15.3 - - - -
187A PRO* 2.7 31.2 + - - +
209A LEU* 4.1 11.3 - - - +
228A HIS* 2.9 10.5 + - - +
229A TYR* 3.8 3.8 - - - -
231A ALA* 1.3 76.3 - - - +
233A ALA* 1.3 61.6 + - - +
235A ALA* 3.2 8.5 + - - -
236A PHE* 3.2 10.7 + - - +
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Residues in contact with ALA 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A LEU* 4.6 1.9 - - - +
210A ILE* 3.8 25.2 - - + +
229A TYR* 3.0 20.1 + - + +
230A ALA 4.4 0.7 - - - +
232A SER* 1.3 77.5 - - - +
234A ARG* 1.3 61.0 + - - +
236A PHE* 3.6 4.3 + - - +
237A GLY 3.5 6.2 + - - -
259A ILE* 3.3 21.8 - - - +
262A THR* 4.1 8.7 - - + -
263A ALA* 4.0 29.8 - - + +
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Residues in contact with ARG 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 ALA* 2.9 29.8 + - - +
231A ALA* 3.1 10.4 + - - +
233A ALA* 1.3 75.6 - - - +
235A ALA* 1.3 60.9 + - - +
236A PHE 3.2 0.7 - - - -
237A GLY* 3.2 2.6 + - - +
238A ALA* 2.9 30.0 + - - +
259A ILE* 4.9 4.3 - - + -
263A ALA* 3.8 27.6 + - + +
264A ARG* 4.7 7.3 - - - +
267A ASP* 2.7 37.8 + - - -
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Residues in contact with ALA 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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183A PHE* 3.4 13.1 - - + -
185A PRO* 3.7 24.5 - - + +
231A ALA 2.8 13.9 + - - +
232A SER 3.2 9.4 + - - +
234A ARG* 1.3 77.6 - - - +
236A PHE* 1.3 57.3 + - - +
238A ALA* 3.3 6.7 + - - +
239A ALA* 2.9 28.9 + - - +
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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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183A PHE* 4.0 9.4 - - - -
185A PRO* 4.4 9.0 - - + -
195A THR* 3.5 26.2 - - + -
204A ALA* 3.7 22.7 - - + -
205A PHE 3.7 15.3 - - - -
206A GLY* 3.9 13.0 - - - -
209A LEU* 4.7 0.4 - - + -
210A ILE* 3.6 32.1 - - + -
232A SER 3.2 8.7 + - - +
233A ALA 3.7 7.0 - - - +
234A ARG 3.2 0.2 - - - -
235A ALA* 1.3 79.5 - - - +
237A GLY* 1.3 63.9 + - - +
239A ALA* 3.2 2.8 + - - +
240A PHE* 3.1 42.5 + + + +
246A ILE* 3.9 14.4 - - + -
259A ILE* 3.8 24.0 - - + -
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Residues in contact with GLY 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 ALA 3.5 4.9 + - - -
234A ARG* 3.2 6.9 + - - -
236A PHE* 1.3 80.6 - - - +
238A ALA* 1.3 60.6 + - - +
240A PHE 3.3 12.3 - - - -
241A PRO* 3.4 2.8 - - - +
256A ARG* 3.0 24.5 + - - -
259A ILE* 3.9 31.2 - - - -
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Residues in contact with ALA 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 ARG 2.9 16.6 + - - +
235A ALA* 3.8 7.2 - - - +
237A GLY* 1.3 73.9 - - - +
239A ALA* 1.3 65.0 + - - +
241A PRO* 3.6 14.2 - - - +
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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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168A TRP* 4.1 19.2 - - + -
183A PHE* 3.6 37.0 - - + -
235A ALA 2.9 17.7 + - - +
236A PHE 3.2 6.0 + - - +
238A ALA* 1.3 79.1 - - - +
240A PHE* 1.3 73.4 + - + +
241A PRO* 3.3 7.7 - - - +
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Residues in contact with PHE 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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168A TRP* 4.0 23.6 - + - -
181A LYS* 3.4 36.6 - - + -
183A PHE* 4.0 18.6 - - + -
195A THR* 4.5 1.6 - - - -
196A VAL 4.4 1.8 - - - -
197A GLY* 3.5 25.1 - - - -
203A ILE 5.8 0.4 - - - -
204A ALA* 4.2 8.3 - - + -
236A PHE* 3.1 38.7 + + + +
237A GLY* 3.3 6.2 - - - +
239A ALA* 1.3 85.0 - - + +
241A PRO* 1.3 53.3 - - - -
242A LYS 3.3 2.9 - - - +
243A ALA* 3.6 22.4 + - + +
246A ILE* 5.3 0.7 - - + +
256A ARG* 2.7 26.2 + - - -
259A ILE* 5.2 0.9 - - - +
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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