Contacts of the helix formed by residues 239 - 254 (chain D) in PDB entry 6S6A
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 GLN 239 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60D SER* 5.7 1.2 + - - -
109D PHE* 5.8 5.7 - - - -
237D ILE* 3.1 16.4 - - + +
238D PRO* 1.3 107.2 - - + +
240D LEU* 1.3 58.2 + - - +
241D PRO* 4.0 0.9 - - - -
242D THR* 3.5 20.8 + - + +
243D LEU* 3.4 18.3 - - + +
366D VAL* 4.2 26.4 - - + +
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Residues in contact with LEU 240 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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234D GLN* 3.2 40.4 - - + +
237D ILE* 3.2 27.1 - - + +
238D PRO 3.2 0.6 + - - -
239D GLN* 1.3 73.0 - - - +
241D PRO* 1.4 67.7 - - + +
242D THR 2.6 6.1 + - - -
243D LEU* 2.6 34.5 + - + -
244D GLU* 3.3 31.3 + - - +
270D ILE 4.8 2.2 - - - +
271D ALA* 4.4 18.2 - - + -
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Residues in contact with PRO 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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237D ILE 4.8 0.2 - - - +
238D PRO 4.0 9.9 - - - +
239D GLN* 4.2 0.4 - - - -
240D LEU* 1.4 96.1 - - + +
242D THR* 1.3 58.8 + - - +
244D GLU* 3.6 12.2 - - + +
245D ASN* 3.2 28.4 + - - +
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Residues in contact with THR 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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239D GLN* 3.5 25.3 + - - +
240D LEU 2.6 3.8 + - - -
241D PRO* 1.3 71.4 - - - +
243D LEU* 1.3 61.6 + - - +
245D ASN* 3.2 6.0 + - - +
246D LEU* 3.0 45.9 + - + +
366D VAL* 4.3 15.0 - - + -
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Residues in contact with LEU 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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109D PHE* 6.5 0.7 - - + -
237D ILE* 4.1 14.1 - - + -
239D GLN* 3.4 21.5 - - + +
240D LEU* 2.6 14.7 + - + +
242D THR* 1.3 67.9 - - - +
244D GLU* 1.3 64.0 + - - +
245D ASN 3.3 0.2 + - - -
246D LEU* 3.4 9.4 + - + +
247D LEU* 3.0 27.4 + - + +
261D LEU* 4.4 10.1 - - + -
270D ILE* 3.9 28.5 - - + -
271D ALA* 3.7 18.8 - - + -
359D PHE* 5.2 0.3 - - - -
363D ILE* 4.7 21.3 - - + -
366D VAL* 4.1 28.9 - - + -
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Residues in contact with GLU 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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234D GLN* 5.2 3.9 + - - -
240D LEU* 3.3 24.9 + - - +
241D PRO* 3.6 21.3 - - + +
243D LEU* 1.3 78.1 - - - +
245D ASN* 1.3 59.7 + - - +
247D LEU* 3.5 9.0 + - - +
248D ASN* 2.7 28.8 + - - -
271D ALA* 4.3 1.6 - - - +
272D THR* 2.9 33.9 + - - +
273D ASP* 4.4 1.6 - - - -
274D SER* 3.3 27.4 + - - +
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Residues in contact with ASN 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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241D PRO 3.2 15.1 + - - +
242D THR* 3.2 8.7 + - - +
244D GLU* 1.3 79.2 - - - +
246D LEU* 1.3 58.3 + - - +
247D LEU 3.0 1.6 - - - -
248D ASN* 2.6 36.9 + - - +
249D ILE* 2.9 13.7 + - - +
274D SER* 4.9 1.2 + - - -
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Residues in contact with LEU 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 THR* 3.0 25.2 + - + +
243D LEU* 3.5 13.7 - - - +
245D ASN* 1.3 72.7 - - - +
247D LEU* 1.3 54.7 + - - +
249D ILE* 3.4 24.7 - - + +
250D PHE 3.2 14.2 + - - -
359D PHE* 3.1 40.8 - - + +
362D ALA* 3.4 46.4 - - + +
363D ILE* 4.9 6.7 - - + -
366D VAL* 4.2 15.0 - - + -
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Residues in contact with LEU 247 (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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243D LEU* 3.0 13.3 + - + +
244D GLU 3.5 9.0 - - - +
245D ASN 2.8 3.0 + - - -
246D LEU* 1.3 70.8 - - - +
248D ASN* 1.3 60.1 + - - +
250D PHE 3.9 0.2 - - - -
251D ILE* 2.9 40.1 + - + +
259D ALA* 4.3 13.9 - - + +
261D LEU* 4.3 7.4 - - + -
271D ALA* 3.5 33.4 - - + -
272D THR* 3.6 16.2 - - - +
273D ASP* 3.6 17.7 - - + +
337D LEU* 3.4 25.4 - - + -
359D PHE* 3.4 27.6 - - + -
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Residues in contact with ASN 248 (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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244D GLU 2.7 25.7 + - - -
245D ASN* 2.6 20.2 + - - +
247D LEU* 1.3 69.2 - - - +
249D ILE* 1.3 57.0 + - - +
251D ILE* 4.3 6.7 - - - +
252D SER* 2.8 43.1 + - - +
273D ASP* 4.0 7.3 - - - +
274D SER* 3.0 39.7 + - - +
275D SER* 4.9 1.4 + - - -
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Residues in contact with ILE 249 (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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245D ASN 2.9 9.9 + - - +
246D LEU* 3.4 31.6 - - + +
248D ASN* 1.3 73.6 - - - +
250D PHE* 1.3 59.3 + - + +
252D SER* 4.7 0.4 - - - -
253D ASN* 2.6 50.7 + - - +
355D ASN* 6.5 0.2 - - + -
358D CYS* 6.5 1.1 - - + -
359D PHE* 5.2 5.6 - - + +
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Residues in contact with PHE 250 (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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246D LEU 3.2 2.4 + - - +
247D LEU 4.0 1.1 - - - +
248D ASN 3.2 0.8 - - - -
249D ILE* 1.3 81.8 - - + +
251D ILE* 1.3 67.3 + - + +
253D ASN* 3.6 2.8 - - - +
254D SER* 2.4 39.9 + - - -
256D ILE* 3.8 23.3 - - + -
337D LEU* 3.7 26.9 - - + -
339D CYS* 4.3 2.7 - - - -
352D ILE* 3.3 22.2 - - + -
355D ASN* 3.7 13.0 - - + -
356D PHE* 3.2 49.8 - + + -
359D PHE* 3.1 37.0 - + + -
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Residues in contact with ILE 251 (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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247D LEU* 2.9 29.2 + - + +
248D ASN* 4.3 7.0 - - - +
250D PHE* 1.3 86.8 - - + +
252D SER* 1.3 57.7 + - - +
254D SER 2.5 23.3 - - - +
256D ILE* 3.1 57.1 + - + +
257D GLU 4.6 2.0 - - - +
258D LYS 4.5 2.0 - - - +
259D ALA* 3.6 19.7 - - + -
273D ASP* 3.0 37.5 - - + +
275D SER* 5.7 0.9 - - - -
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Residues in contact with SER 252 (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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248D ASN* 2.8 24.5 + - - +
249D ILE* 4.7 0.4 - - - -
251D ILE* 1.3 77.1 - - - +
253D ASN* 1.3 64.2 + - - -
254D SER 2.9 7.7 + - - +
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Residues in contact with ASN 253 (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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249D ILE* 2.6 41.5 + - - +
250D PHE* 3.6 6.2 - - - +
252D SER* 1.3 75.4 - - - +
254D SER* 1.3 55.3 + - - +
351D LEU* 3.6 16.6 - - - +
355D ASN* 3.2 25.3 + - - +
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Residues in contact with SER 254 (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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250D PHE* 2.4 32.3 + - - -
251D ILE 2.5 30.3 - - - +
252D SER 3.0 5.4 - - - +
253D ASN* 1.3 75.1 - - - +
255D GLY* 1.3 52.5 + - - +
256D ILE* 2.7 31.2 + - - -
351D LEU* 4.3 6.1 - - - -
352D ILE* 4.1 16.3 - - - -
355D ASN* 3.2 21.0 + - - -
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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