Contacts of the helix formed by residues 227 - 238 (chain A) in PDB entry 3QLD
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 ASP 227 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223A LEU* 5.2 1.4 - - - +
224A PRO 4.5 2.9 + - - +
225A GLU 3.9 1.0 - - - -
226A ASP* 1.3 85.4 - - + +
228A TRP* 1.3 63.2 + - - +
229A PHE* 2.7 35.8 + - - +
230A ASP* 2.7 41.0 + - - +
231A LEU* 3.2 19.8 + - - +
252B ARG* 4.1 9.8 - - + +
255B LYS* 4.3 29.8 + - + +
256B LEU 6.2 0.2 - - - +
259B ARG* 4.1 10.9 + - - +
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Residues in contact with TRP 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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227A ASP* 1.3 73.7 + - - +
229A PHE* 1.3 59.1 + - + +
231A LEU* 3.3 15.1 + - + +
232A ALA* 3.0 27.0 + - - +
244A LEU* 4.4 13.5 - - + -
247A SER* 3.6 18.6 - - - -
253A GLU* 3.6 31.9 - - + -
256A LEU* 3.6 27.0 - - + +
257A THR* 3.5 30.7 - - - -
260A LEU* 3.6 28.1 - - + +
262A ALA* 4.5 8.0 - - + +
252B ARG* 3.5 45.9 + - + +
253B GLU* 4.5 6.2 + - + +
256B LEU* 4.0 28.6 - - + +
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Residues in contact with PHE 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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227A ASP* 2.7 14.5 + - - +
228A TRP* 1.3 72.5 - - - +
230A ASP* 1.3 58.7 + - - +
232A ALA* 3.6 11.7 - - + +
233A LYS* 2.9 35.1 + - - +
260A LEU* 3.6 23.6 - - + -
229B PHE* 4.7 2.9 - + - -
256B LEU* 3.8 29.2 - - + -
259B ARG* 3.6 57.4 - - + +
260B LEU* 4.1 23.8 - - + -
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Residues in contact with ASP 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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202A PRO* 3.3 37.1 - - + +
223A LEU* 3.7 8.9 - - + +
226A ASP* 5.6 2.6 - - - +
227A ASP* 2.7 43.6 + - - +
229A PHE* 1.3 72.3 - - - +
231A LEU* 1.3 59.0 + - - +
233A LYS* 3.5 11.6 + - - +
234A LEU* 2.9 29.6 + - - +
259B ARG* 4.5 6.9 + - - -
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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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222A PRO* 4.1 27.6 - - + -
223A LEU* 3.8 19.0 - - + +
227A ASP 3.2 10.6 + - - +
228A TRP* 3.5 19.1 - - + +
229A PHE 3.2 0.4 - - - -
230A ASP* 1.3 77.3 - - - +
232A ALA* 1.3 60.4 + - - +
234A LEU* 3.2 5.3 + - + +
235A GLN* 2.8 30.7 + - - +
242A VAL* 4.4 7.4 - - + -
244A LEU* 3.8 28.9 - - + -
247A SER* 5.6 2.7 - - - +
262A ALA* 3.4 31.9 - - + +
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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 TRP 3.0 16.9 + - - +
229A PHE* 3.3 20.4 + - + +
231A LEU* 1.3 75.5 - - - +
233A LYS* 1.3 58.3 + - - +
235A GLN* 4.0 1.2 - - - +
236A ALA* 3.0 29.5 + - - +
260A LEU* 3.5 31.3 - - + +
261A GLY 4.1 2.8 - - - +
262A ALA* 4.0 12.5 - - - +
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Residues in contact with LYS 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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202A PRO* 6.5 1.1 - - + -
229A PHE* 2.9 18.9 + - - +
230A ASP* 3.7 11.5 + - - +
232A ALA* 1.3 75.3 - - - +
234A LEU* 1.3 65.4 + - - +
236A ALA* 3.5 7.3 + - - +
237A SER* 3.3 21.0 + - - -
259B ARG* 3.7 25.0 - - - +
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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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202A PRO* 6.3 2.9 - - + -
205A ALA* 3.9 30.1 - - + -
208A LEU* 3.9 20.0 - - + -
222A PRO* 3.7 35.7 - - + -
223A LEU* 3.9 20.4 - - + -
230A ASP 2.9 17.6 + - - +
231A LEU* 3.2 6.5 + - + +
233A LYS* 1.3 78.7 - - - +
235A GLN* 1.3 62.4 + - - +
237A SER* 2.7 24.1 + - - +
238A LEU* 3.2 29.5 + - + +
242A VAL* 5.0 0.9 - - + -
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Residues in contact with GLN 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 2.8 13.0 + - - +
234A LEU* 1.3 70.6 - - - +
236A ALA* 1.4 63.1 + - - +
238A LEU* 3.1 16.4 + - - +
240A THR 3.0 24.7 + - - -
242A VAL* 2.7 40.8 + - + +
261A GLY 3.3 25.6 - - - +
262A ALA 3.6 18.4 - - - +
263A ALA* 4.1 1.6 - - - +
264A ARG* 3.4 46.6 + - + +
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Residues in contact with ALA 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 ALA 3.0 18.9 + - - +
233A LYS* 3.8 8.5 - - - +
234A LEU 3.2 0.4 - - - -
235A GLN* 1.4 75.7 - - - +
237A SER* 1.3 51.7 + - - +
239A ARG* 2.7 25.5 + - - -
261A GLY 4.7 1.7 + - - +
264A ARG* 5.8 0.9 - - - +
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Residues in contact with SER 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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205A ALA* 4.7 8.7 + - - +
209A ARG* 3.5 24.6 - - - +
233A LYS* 3.3 11.1 + - - -
234A LEU* 2.7 34.0 + - - +
236A ALA* 1.3 77.3 - - - +
238A LEU* 1.3 59.6 + - - +
239A ARG* 3.4 13.5 + - - +
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Residues in contact with LEU 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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205A ALA 4.9 0.2 - - - +
208A LEU* 3.6 20.0 - - + +
209A ARG* 3.6 36.8 - - + +
212A ASP* 3.9 7.4 - - - +
219A ILE* 4.7 14.8 - - + -
222A PRO* 5.9 0.9 - - + -
234A LEU* 3.4 38.1 - - + +
235A GLN* 3.1 13.7 + - - +
236A ALA 3.4 0.2 - - - -
237A SER* 1.3 84.0 - - - +
239A ARG* 1.3 68.4 + - - +
240A THR 3.7 14.4 - - - +
242A VAL* 4.2 19.1 - - + -
264A ARG* 3.1 19.1 + - - -
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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