Contacts of the helix formed by residues 229 - 241 (chain D) in PDB entry 1K9A
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 229 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208D ASP* 5.7 3.8 - - - +
222D LYS* 5.6 4.0 - - - -
227D ASP* 2.5 23.5 + - + +
228D ALA* 1.3 75.5 - - - +
230D ALA* 1.3 75.0 + - - +
231D GLN* 2.6 4.3 + - - +
232D ALA* 2.7 21.5 + - - +
233D PHE* 3.1 32.5 + - + -
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Residues in contact with ALA 230 (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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79D LEU* 5.1 2.5 - - + -
224D ILE* 3.5 19.5 - - + +
225D LYS 3.0 28.9 - - - +
226D ASN* 4.3 6.7 - - - +
227D ASP* 2.6 15.9 + - - +
228D ALA 4.8 0.2 - - - +
229D THR* 1.3 76.1 - - - +
231D GLN* 1.3 63.6 + - - +
233D PHE* 3.0 9.3 + - - +
234D LEU* 2.9 28.4 + - + +
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Residues in contact with GLN 231 (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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75D THR* 3.3 36.2 + - + +
76D LYS 5.4 0.6 - - - -
77D LEU* 3.7 16.6 + - + +
78D SER* 5.4 4.6 - - - +
228D ALA 4.2 6.8 + - - +
229D THR 2.6 6.5 + - - +
230D ALA* 1.3 76.8 - - - +
232D ALA* 1.3 56.6 + - - +
234D LEU* 3.3 11.1 + - - +
235D ALA* 2.9 27.7 + - - +
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Residues in contact with ALA 232 (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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75D THR* 6.4 0.2 - - - -
229D THR* 2.7 21.2 + - - +
231D GLN* 1.3 73.1 - - - +
233D PHE* 1.3 64.6 + - + +
235D ALA* 3.3 8.1 + - - +
236D GLU* 2.8 27.3 + - - +
334D GLY* 3.7 14.2 - - - -
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Residues in contact with PHE 233 (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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222D LYS* 3.3 46.4 - - + -
224D ILE* 3.5 24.4 - - + +
229D THR* 3.1 33.4 - - + -
230D ALA* 3.0 4.5 + - - +
232D ALA* 1.3 79.2 - - + +
234D LEU* 1.3 61.4 + - - +
236D GLU* 3.4 28.3 + - - +
237D ALA* 3.0 26.7 + - - +
264D ILE* 5.0 4.3 - - + +
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Residues in contact with LEU 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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77D LEU* 3.5 50.1 - - + +
78D SER* 4.1 7.9 - - - +
79D LEU* 4.3 18.6 - - + +
179D ALA* 4.1 11.7 - - + -
183D PHE* 4.7 6.5 - - + -
224D ILE* 4.5 13.9 - - + -
230D ALA* 2.9 20.3 + - + +
231D GLN* 3.6 11.7 - - - +
233D PHE* 1.3 74.4 - - - +
235D ALA* 1.3 66.3 + - - +
237D ALA* 3.2 6.9 + - - +
238D SER 2.9 18.4 + - - -
262D LEU* 4.0 27.6 - - + -
264D ILE* 5.0 1.8 - - + -
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Residues in contact with ALA 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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74D GLY* 3.6 20.0 + - - +
75D THR* 3.9 27.6 - - + -
231D GLN 2.9 18.1 + - - +
232D ALA* 3.4 7.4 - - - +
234D LEU* 1.3 77.4 - - - +
236D GLU* 1.3 62.6 + - - +
238D SER* 3.0 13.9 + - - -
239D VAL* 3.0 18.8 + - + +
333D PHE 4.7 0.7 - - - -
334D GLY 4.0 11.9 - - - +
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Residues in contact with GLU 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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232D ALA 2.8 17.3 + - - +
233D PHE* 3.5 31.5 - - - +
234D LEU 3.2 0.2 - - - -
235D ALA* 1.3 76.0 - - - +
237D ALA* 1.3 63.6 + - - +
239D VAL* 3.3 4.7 + - - +
240D MET* 3.0 46.3 + - - +
264D ILE* 5.8 4.3 - - - +
331D SER* 5.1 0.3 - - - -
332D ASP* 3.0 18.9 + - - -
333D PHE* 3.0 41.5 + - + +
334D GLY* 3.8 8.9 - - - +
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Residues in contact with ALA 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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183D PHE* 3.8 18.2 - - + -
233D PHE 3.0 14.0 + - - +
234D LEU* 3.2 9.2 + - - +
236D GLU* 1.3 76.2 + - - +
238D SER* 1.3 63.4 + - - +
240D MET* 3.1 15.2 + - - +
241D THR* 3.1 26.8 + - - +
251D LEU* 3.6 7.1 - - + +
254D VAL* 5.2 0.2 - - + -
264D ILE* 4.3 27.6 - - + -
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Residues in contact with SER 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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71D VAL 2.5 29.2 + - - +
72D LYS* 3.9 2.3 + - - -
74D GLY* 3.2 31.4 + - - -
77D LEU* 3.9 9.4 - - - -
183D PHE* 4.1 5.6 - - - -
234D LEU 2.9 12.3 + - - -
235D ALA 3.0 11.2 + - - -
237D ALA* 1.3 76.9 - - - +
239D VAL* 1.3 61.9 + - - +
241D THR* 2.5 28.3 + - - -
242D GLN* 3.3 7.1 + - - -
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Residues in contact with VAL 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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74D GLY* 6.1 2.0 - - - -
235D ALA* 3.0 13.6 + - + +
236D GLU 3.6 6.3 - - - +
238D SER* 1.3 77.5 - - - +
240D MET* 1.3 58.3 + - - +
242D GLN* 2.8 31.4 + - - +
243D LEU* 3.3 33.5 - - + +
310D PHE* 4.5 10.3 - - + -
333D PHE* 3.8 15.5 - - + +
334D GLY 5.5 0.2 - - - +
336D THR* 3.5 46.9 - - + +
337D LYS* 5.6 0.2 - - - -
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Residues in contact with MET 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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188D TRP* 4.8 3.1 - - - -
236D GLU* 3.0 37.7 + - - +
237D ALA* 3.1 13.2 + - - +
239D VAL* 1.3 72.5 - - - +
241D THR* 1.3 61.5 + - - +
242D GLN 2.9 6.6 + - - -
243D LEU* 3.3 25.1 + - + +
249D VAL* 3.1 42.8 - - + +
251D LEU* 3.7 33.5 + - + +
264D ILE* 5.8 0.9 - - - -
266D THR* 4.2 15.7 - - + -
331D SER* 5.4 2.2 - - - -
333D PHE* 3.5 31.6 - - + -
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Residues in contact with THR 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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69D GLU 4.5 0.3 - - - -
70D GLY* 3.7 10.9 + - - -
71D VAL* 2.8 26.7 + - + -
183D PHE* 3.8 19.1 - - + -
188D TRP* 3.7 46.2 - - + +
237D ALA 3.2 14.8 - - - +
238D SER 2.5 18.4 + - - +
240D MET* 1.3 76.0 - - - +
242D GLN* 1.3 56.7 + - - +
243D LEU 3.6 0.9 - - - -
251D LEU* 3.5 17.3 - - + -
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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