Contacts of the helix formed by residues 233 - 244 (chain K) in PDB entry 6D6Q
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 PRO 233 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174E GLU* 5.9 4.9 - - + -
231K HIS 3.7 3.3 - - - +
232K LEU* 1.3 97.1 - - + +
234K LEU* 1.3 67.3 + - - +
235K SER* 3.1 10.9 + - - +
236K LYS* 3.2 30.1 + - + +
237K LEU* 3.2 8.3 + - - +
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Residues in contact with LEU 234 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233K PRO* 1.3 73.8 - - - +
235K SER* 1.3 63.7 + - - +
237K LEU* 4.3 7.6 - - + +
238K GLN* 2.9 45.1 + - + +
348K ILE 4.4 4.4 + - - +
349K ILE* 3.7 52.3 - - + +
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Residues in contact with SER 235 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233K PRO* 3.1 10.7 - - - +
234K LEU* 1.3 78.1 - - - +
236K LYS* 1.3 64.7 + - - +
238K GLN* 3.0 22.5 + - - +
239K GLN* 2.9 31.4 + - - +
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Residues in contact with LYS 236 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232K LEU* 4.1 27.1 - - + +
233K PRO* 3.2 24.4 + - + +
235K SER* 1.3 81.7 - - - +
237K LEU* 1.3 58.8 + - - +
239K GLN* 3.3 17.8 + - + +
240K GLY* 2.8 27.7 + - - -
246K TYR* 5.2 3.2 - - - -
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Residues in contact with LEU 237 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232K LEU* 3.4 30.3 - - + +
233K PRO 3.2 11.0 + - - +
234K LEU* 3.7 11.4 - - - +
236K LYS* 1.3 77.4 - - - +
238K GLN* 1.3 63.7 + - - +
240K GLY* 3.0 2.4 + - - -
241K ILE* 3.0 30.8 + - + +
246K TYR* 4.8 8.7 - - + +
293K ALA* 3.6 26.9 - - + -
346K VAL* 4.1 14.8 - - + -
347K GLY* 3.6 11.4 - - - -
348K ILE 3.6 38.6 - - - +
349K ILE* 4.5 9.6 - - + -
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Residues in contact with GLN 238 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234K LEU* 2.9 31.8 + - + +
235K SER* 3.0 36.4 + - - +
237K LEU* 1.3 77.7 - - - +
239K GLN* 1.3 59.5 + - + +
241K ILE* 3.8 9.8 + - - +
242K LYS* 3.6 37.3 + - - +
349K ILE* 5.8 1.3 - - + +
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Residues in contact with GLN 239 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235K SER* 2.9 20.6 + - - +
236K LYS* 3.6 20.3 + - + +
238K GLN* 1.3 80.2 - - + +
240K GLY* 1.3 54.3 + - - +
242K LYS* 4.3 3.2 - - - +
243K SER* 2.6 54.6 + - - -
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Residues in contact with GLY 240 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236K LYS 2.8 16.1 + - - -
237K LEU 3.0 0.6 + - - -
239K GLN* 1.3 80.2 - - - +
241K ILE* 1.3 58.3 + - - +
243K SER* 3.1 7.9 - - - -
244K GLY 2.7 38.3 + - - +
245K THR* 5.4 0.4 - - - -
246K TYR* 4.2 20.9 - - - -
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Residues in contact with ILE 241 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237K LEU 3.0 23.3 + - - +
238K GLN* 4.1 8.1 - - - +
240K GLY* 1.3 79.6 - - - +
242K LYS* 1.3 69.0 + - + +
244K GLY* 3.2 11.3 + - - +
246K TYR* 3.2 31.4 - - + +
247K LEU* 4.1 8.3 - - + -
248K GLN* 3.9 22.0 - - + +
293K ALA* 4.8 3.8 - - + -
349K ILE* 3.6 31.0 - - + -
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Residues in contact with LYS 242 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238K GLN* 3.6 24.5 + - - +
239K GLN* 4.3 2.9 - - - +
240K GLY 3.4 0.2 - - - -
241K ILE* 1.3 85.3 - - + +
243K SER* 1.3 63.6 + - - +
244K GLY 3.3 0.2 + - - -
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Residues in contact with SER 243 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239K GLN* 2.6 42.6 + - - -
240K GLY* 3.1 10.2 - - - -
242K LYS* 1.3 77.9 - - - +
244K GLY* 1.3 59.8 + - - +
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Residues in contact with GLY 244 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240K GLY 2.7 19.0 + - - +
241K ILE 3.2 6.1 + - - +
242K LYS 3.3 2.4 + - - -
243K SER* 1.3 79.0 + - - +
245K THR* 1.3 67.4 + - - +
246K TYR 3.1 7.8 - - - +
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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