Contacts of the helix formed by residues 247 - 256 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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204J LYS* 3.6 14.7 + - - +
245J THR* 3.3 1.3 - - - +
246J THR* 1.3 77.8 - - - +
248J VAL* 1.3 58.8 + - - +
249J THR* 3.5 14.0 + - - -
250J GLU* 3.4 52.7 + - - +
251J LEU* 3.1 29.0 + - - +
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Residues in contact with VAL 248 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204J LYS* 3.2 24.4 - - + +
206J PRO* 4.2 19.5 - - + -
223J ALA 3.5 25.1 - - - +
224J LEU* 3.9 18.2 - - + +
225J GLY 3.5 24.9 - - - +
226J VAL* 4.0 4.7 - - + -
246J THR 4.3 4.9 - - - +
247J ASP* 1.3 69.2 - - - +
249J THR* 1.3 60.7 + - - +
251J LEU* 3.6 7.3 - - - +
252J ARG* 2.9 37.5 + - - +
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Residues in contact with THR 249 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204J LYS* 5.2 0.2 - - - +
247J ASP* 3.5 12.5 + - - -
248J VAL* 1.3 76.2 - - - +
250J GLU* 1.3 57.6 + - + +
252J ARG* 3.2 14.5 + - + +
253J GLU* 3.0 30.9 + - + +
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Residues in contact with GLU 250 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244J GLY 5.4 0.2 - - - +
245J THR* 3.4 31.0 - - + +
247J ASP* 3.4 31.1 + - - +
249J THR* 1.3 77.1 - - - +
251J LEU* 1.3 60.2 + - - +
253J GLU* 3.4 18.1 - - - +
254J LYS* 3.3 21.1 + - - +
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Residues in contact with LEU 251 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206J PRO* 3.7 22.4 - - + -
226J VAL* 4.3 8.2 - - + +
237J ILE* 3.6 26.2 - - + -
240J ALA* 3.6 24.7 - - + -
241J ILE* 3.4 24.0 - - + -
245J THR* 3.4 26.2 - - + +
247J ASP 3.1 21.2 + - - +
248J VAL* 3.6 8.7 - - - +
249J THR 3.3 0.2 - - - -
250J GLU* 1.3 73.5 - - - +
252J ARG* 1.3 59.6 + - - +
254J LYS* 3.4 2.4 + - + +
255J PHE* 3.0 37.7 + - + +
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Residues in contact with ARG 252 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219J VAL 3.4 10.7 + - - -
220J SER* 3.3 28.7 + - - +
222J PHE 2.6 31.3 + - - -
223J ALA* 4.4 4.5 - - - +
225J GLY 2.8 25.3 + - - +
226J VAL* 4.8 3.8 - - + -
248J VAL* 2.9 26.2 + - + +
249J THR* 3.2 13.4 + - + +
251J LEU* 1.3 73.9 - - - +
253J GLU* 1.3 60.1 + - - +
256J HIS* 2.7 70.5 + - + +
257J LYS* 5.8 0.7 - - - +
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Residues in contact with GLU 253 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249J THR* 3.0 13.6 + - - +
250J GLU* 3.4 21.7 - - - +
252J ARG* 1.3 78.5 - - - +
254J LYS* 1.3 59.3 + - - +
255J PHE 3.7 0.2 + - - -
256J HIS 4.8 1.6 + - - -
257J LYS* 5.5 6.9 - - - +
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Residues in contact with LYS 254 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240J ALA* 5.4 9.1 - - + +
250J GLU 3.3 12.4 + - - +
251J LEU* 3.4 2.0 + - + +
252J ARG 3.3 0.2 - - - -
253J GLU* 1.3 78.3 - - + +
255J PHE* 1.3 89.8 + - + +
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Residues in contact with PHE 255 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226J VAL* 4.5 9.2 - - + -
227J TYR 4.7 11.6 - - - +
233J ASP* 4.4 15.3 - - + -
236J LYS* 3.2 60.8 - - + -
237J ILE* 3.4 30.1 - - + -
240J ALA* 4.2 13.5 - - + -
251J LEU* 3.0 26.1 + - + +
254J LYS* 1.3 104.5 - - + +
256J HIS* 1.3 70.7 + - - +
258J HIS* 4.5 9.7 + - - -
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Residues in contact with HIS 256 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216J GLN* 3.3 37.0 + - + +
219J VAL* 4.6 2.4 - - + +
220J SER* 3.0 26.8 + - - -
226J VAL* 4.2 5.5 - - + +
227J TYR* 3.4 34.4 + - + -
252J ARG* 2.7 56.6 + - + +
253J GLU 4.7 1.9 + - - -
255J PHE* 1.3 84.2 - - - +
257J LYS* 1.3 80.6 + - + +
258J HIS* 4.6 2.4 + - - -
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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