Contacts of the helix formed by residues 247 - 256 (chain L) in PDB entry 2I2X
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 247 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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204L LYS* 2.9 26.4 + - - +
245L THR* 3.5 0.6 - - - +
246L THR* 1.3 79.9 - - - +
248L VAL* 1.3 68.6 + - - +
249L THR* 3.4 18.2 + - - -
250L GLU* 3.4 27.5 + - + +
251L LEU* 3.2 29.8 + - - +
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Residues in contact with VAL 248 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204L LYS* 3.8 23.4 - - + +
206L PRO* 4.6 12.1 - - + -
223L ALA 3.3 20.2 - - - +
224L LEU* 3.4 38.8 - - + +
225L GLY 3.6 3.4 - - - +
226L VAL* 3.8 7.0 - - + -
246L THR 4.7 1.6 - - - +
247L ASP* 1.3 73.7 + - - +
249L THR* 1.3 59.2 + - - +
250L GLU 3.0 4.5 - - - -
251L LEU* 3.1 6.1 + - - +
252L ARG* 2.8 52.9 + - - +
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Residues in contact with THR 249 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247L ASP* 3.4 9.6 + - - -
248L VAL* 1.3 77.2 - - - +
250L GLU* 1.3 59.2 - - - +
252L ARG* 4.3 13.6 + - + +
253L GLU* 3.5 21.7 + - + +
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Residues in contact with GLU 250 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244L GLY 4.8 2.5 - - - +
245L THR* 3.3 31.0 - - + +
246L THR 4.6 0.2 + - - -
247L ASP* 3.4 30.3 + - + +
248L VAL 3.0 0.2 - - - -
249L THR* 1.3 77.4 - - - +
251L LEU* 1.3 65.7 + - - +
253L GLU* 3.3 18.5 + - - +
254L LYS* 3.7 5.7 + - - +
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Residues in contact with LEU 251 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206L PRO* 3.5 33.4 - - + -
226L VAL* 4.4 13.2 - - + -
237L ILE* 4.6 6.7 - - + +
240L ALA* 3.5 29.6 - - + -
241L ILE* 3.8 5.6 - - + -
245L THR* 3.4 37.2 - - + +
247L ASP 3.2 17.6 + - - +
248L VAL* 3.1 7.0 + - - +
250L GLU* 1.3 76.8 - - - +
252L ARG* 1.3 56.7 + - - +
254L LYS* 2.8 25.6 + - - +
255L PHE* 3.2 29.4 - - + -
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Residues in contact with ARG 252 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220L SER* 3.0 30.7 + - - +
222L PHE 2.4 33.1 + - - -
223L ALA* 3.2 16.1 + - - +
225L GLY 2.8 21.2 + - - +
226L VAL* 4.3 7.1 - - + +
248L VAL* 2.8 30.4 + - + +
249L THR* 4.3 12.6 + - - +
251L LEU* 1.3 72.3 - - - +
253L GLU* 1.3 57.5 + - - +
254L LYS 3.0 2.4 + - - -
256L HIS* 2.7 76.0 + - + +
257L LYS* 5.8 0.5 - - - +
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Residues in contact with GLU 253 (chain L).
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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249L THR* 3.5 13.3 + - + +
250L GLU* 3.3 14.1 + - - +
251L LEU 3.1 0.8 - - - -
252L ARG* 1.3 77.6 - - - +
254L LYS* 1.3 56.8 + - - +
256L HIS 5.0 0.2 - - - -
257L LYS* 5.9 5.6 - - - +
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Residues in contact with LYS 254 (chain L).
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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240L ALA* 6.1 1.8 - - + -
250L GLU 3.7 4.9 + - - +
251L LEU* 2.8 11.5 + - - +
253L GLU* 1.3 79.1 - - - +
255L PHE* 1.3 83.2 + - + +
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Residues in contact with PHE 255 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226L VAL* 4.6 9.0 - - + -
227L TYR 4.6 11.4 - - - +
233L ASP* 5.4 6.7 - - + -
236L LYS* 3.8 42.0 - - + -
237L ILE* 3.5 38.1 - - + -
240L ALA* 4.1 19.3 - - + -
251L LEU* 3.2 27.3 + - + +
252L ARG 3.1 1.0 + - - -
253L GLU 3.7 0.2 - - - -
254L LYS* 1.3 104.0 - - + +
256L HIS* 1.3 70.4 + - - +
258L HIS* 4.5 12.0 + - - -
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Residues in contact with HIS 256 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216L GLN* 3.1 27.6 - - + +
219L VAL* 3.9 15.0 - - + +
220L SER* 3.2 22.7 + - - -
226L VAL* 4.0 4.2 - - - +
227L TYR* 3.5 33.1 + - + +
252L ARG* 2.7 62.1 + - + +
255L PHE* 1.3 82.2 - - - +
257L LYS* 1.3 80.0 + - + +
258L HIS* 3.5 7.2 + - - -
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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