Contacts of the helix formed by residues 233 - 246 (chain D) in PDB entry 6APL
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 233 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117D LEU* 4.9 4.3 - - - -
202D ASN* 6.5 1.1 - - + -
231D PRO 3.5 1.2 - - - -
232D SER* 1.3 83.1 - - - +
234D ILE* 1.3 83.8 + - - +
235D ARG* 3.1 33.4 + - + +
236D ASP* 2.9 25.6 + - - +
237D TYR* 3.5 12.2 - - - -
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Residues in contact with ILE 234 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117D LEU* 3.6 34.7 - - + +
118D SER* 5.4 2.9 - - - +
121D VAL* 5.8 4.0 - - + -
122D ILE* 5.7 1.6 - - + -
233D ASP* 1.3 84.4 + - - +
235D ARG* 1.3 86.4 + - + +
237D TYR* 2.9 15.4 + - + +
238D VAL* 2.9 37.1 + - + +
251D GLU* 6.0 1.1 - - + +
252D GLY* 4.6 18.2 - - - -
253D LEU 5.2 0.7 - - - +
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Residues in contact with ARG 235 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201D VAL* 3.8 16.2 - - + +
202D ASN* 3.3 43.0 + - - +
205D LYS* 4.3 10.1 - - - +
233D ASP* 3.1 23.5 - - + +
234D ILE* 1.3 89.0 - - + +
236D ASP* 1.3 57.2 + - - +
238D VAL* 3.9 5.3 - - - +
239D MSE 2.8 33.3 + - - +
252D GLY* 5.9 0.2 - - - -
253D LEU* 4.1 34.4 - - + +
254D ASP* 2.8 47.6 + - - +
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Residues in contact with ASP 236 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199D PHE 4.8 1.0 - - - +
200D THR* 3.6 1.7 - - - -
201D VAL* 2.7 40.6 + - - +
229D PHE* 3.7 13.2 - - + -
230D ILE 3.0 25.5 - - - +
231D PRO* 4.3 5.6 - - + -
232D SER* 2.9 24.6 + - - -
233D ASP* 2.9 23.6 + - - +
235D ARG* 1.3 73.4 - - - +
237D TYR* 1.3 59.5 + - - +
240D LEU* 2.8 31.5 + - - +
274D LEU* 5.9 1.8 - - + -
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Residues in contact with TYR 237 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92D LEU* 5.3 0.2 - - - +
113D GLY 5.5 1.9 + - - -
114D TRP* 3.3 33.2 - + - +
117D LEU* 3.9 18.2 - - + -
121D VAL* 4.4 11.0 - - + -
122D ILE* 4.1 20.9 - - + -
125D THR* 3.2 37.8 - - + +
126D LEU* 4.8 2.5 - - + -
231D PRO* 3.3 33.1 + - + +
233D ASP 3.5 17.3 - - - -
234D ILE* 2.9 12.8 + - - +
236D ASP* 1.3 78.0 - - + +
238D VAL* 1.3 56.9 + - - +
240D LEU* 3.2 7.1 + - + +
241D ARG 2.8 26.7 + - - -
274D LEU* 4.3 25.8 - - + -
277D PRO* 4.4 4.3 - - - +
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Residues in contact with VAL 238 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121D VAL* 3.8 23.3 - - + -
234D ILE* 2.9 31.9 + - + +
235D ARG* 3.9 5.8 - - - +
237D TYR* 1.3 73.9 - - - +
239D MSE 1.3 57.4 + - - +
241D ARG* 3.4 12.6 + - - +
242D SER* 2.8 37.7 + - - +
249D VAL* 3.6 28.3 - - + -
250D PRO* 4.5 4.5 - - + -
251D GLU* 4.1 28.9 - - + +
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Residues in contact with MSE 239 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201D VAL* 3.6 29.6 - - + -
204D MSE 6.4 0.2 - - - -
205D LYS* 4.9 1.1 - - + -
229D PHE* 3.6 19.1 - - + -
235D ARG 2.8 21.7 + - - +
236D ASP 3.9 0.4 - - - +
238D VAL* 1.3 73.8 - - - +
240D LEU* 1.3 57.9 + - - +
242D SER* 3.7 3.6 - - - -
243D ALA* 2.8 32.6 + - - +
249D VAL* 4.6 14.8 - - + +
254D ASP* 3.8 29.4 - - + -
257D ASP* 4.1 10.5 - - - +
259D PRO* 4.6 11.0 - - - -
262D TYR* 4.1 28.5 - - + -
263D PHE* 4.1 13.2 - - + -
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Residues in contact with LEU 240 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125D THR* 5.3 8.3 - - - +
129D LEU* 4.1 11.4 - - + -
229D PHE* 3.6 24.6 - - + -
236D ASP 2.8 19.8 + - - +
237D TYR* 3.5 8.7 - - + +
239D MSE 1.3 77.2 - - - +
241D ARG* 1.3 63.0 + - - +
243D ALA* 3.4 0.9 + - - +
244D ILE* 3.1 41.4 + - + +
272D PHE* 3.5 32.1 - - + +
273D LYS 4.3 3.8 - - - +
274D LEU* 3.7 44.6 - - + -
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Residues in contact with ARG 241 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120D GLN* 4.3 5.7 + - - -
121D VAL* 3.7 30.3 - - - +
124D SER* 3.2 45.2 + - - +
125D THR* 3.5 20.6 - - + +
128D LEU* 4.2 10.3 - - + -
237D TYR 2.8 12.4 + - - +
238D VAL* 3.8 10.2 - - - +
240D LEU* 1.3 74.2 - - - +
242D SER* 1.3 64.5 + - - +
243D ALA 3.3 0.2 + - - -
244D ILE* 3.3 1.8 + - - +
245D LEU* 3.0 52.4 + - + +
247D VAL* 5.9 0.7 - - - -
250D PRO* 4.2 26.5 - - - +
251D GLU* 4.2 15.6 + - - -
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Residues in contact with SER 242 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238D VAL* 2.8 20.3 + - - +
239D MSE 3.9 4.9 - - - -
241D ARG* 1.3 78.7 - - - +
243D ALA* 1.3 56.6 + - - +
246D GLY* 2.8 24.3 + - - -
247D VAL* 3.1 39.6 + - - +
249D VAL* 3.3 29.2 - - - -
250D PRO* 3.8 9.4 - - - +
259D PRO* 3.4 6.8 - - - +
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Residues in contact with ALA 243 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229D PHE* 4.4 1.6 - - + -
239D MSE 2.8 21.8 + - - +
240D LEU 3.7 5.2 - - - +
241D ARG 3.2 0.2 - - - -
242D SER* 1.3 73.7 - - - +
244D ILE* 1.3 62.0 + - - +
246D GLY* 3.2 4.0 + - - -
259D PRO* 3.6 21.3 - - + +
260D HIS* 5.5 0.2 - - - -
263D PHE* 4.1 7.0 - - + -
267D ALA* 3.2 21.7 - - - +
272D PHE* 3.5 39.0 - - + -
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Residues in contact with ILE 244 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125D THR 5.5 0.7 - - - +
128D LEU* 3.7 31.4 - - + +
129D LEU* 3.7 31.2 - - + -
240D LEU* 3.1 31.8 + - + +
241D ARG* 5.4 0.2 - - - -
243D ALA* 1.3 76.0 - - - +
245D LEU* 1.3 62.2 + - + +
267D ALA 2.9 22.3 - - - +
268D SER* 3.8 18.8 - - - +
269D ALA* 4.2 10.1 - - + +
272D PHE* 3.7 27.8 - - + +
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Residues in contact with LEU 245 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128D LEU* 3.7 24.9 - - + -
241D ARG* 3.0 45.8 + - + +
244D ILE* 1.3 76.7 - - + +
246D GLY* 1.3 63.2 + - - +
247D VAL* 3.5 23.4 + - + +
267D ALA* 4.7 1.1 - - - +
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Residues in contact with GLY 246 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242D SER 2.8 8.8 + - - -
243D ALA 3.2 10.1 + - - -
244D ILE 3.3 0.4 + - - -
245D LEU* 1.3 79.4 - - - +
247D VAL* 1.3 58.6 + - - +
248D PRO* 4.3 3.5 - - - +
259D PRO* 4.6 2.2 - - - +
260D HIS* 3.4 37.3 + - - -
267D ALA* 4.0 5.2 - - - -
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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