Contacts of the helix formed by residues 245 - 257 (chain J) in PDB entry 3EXG
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 245 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196J GLY 3.4 15.7 - - - +
197J LYS* 3.1 21.8 - - - +
198J ALA* 3.0 36.9 + - + +
238J MET* 5.4 3.6 + - - +
240J THR* 4.4 4.2 + - - -
243J PRO 3.6 1.8 + - - -
244J MET* 1.3 70.5 - - - +
246J MET* 1.3 58.8 + - - +
247J GLU* 3.3 9.4 + - - +
248J THR* 2.9 36.9 + - - -
249J ILE* 3.5 25.3 + - - +
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Residues in contact with MET 246 (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 MET* 2.9 13.5 + - - +
245J ASP* 1.3 71.7 - - - +
247J GLU* 1.3 66.5 + - - +
249J ILE* 3.5 24.2 + - + +
250J GLU* 2.8 48.9 + - + +
275J ILE* 3.9 12.8 - - + +
278J ARG* 3.2 64.6 - - + +
279J ILE* 3.7 37.2 - - + +
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Residues in contact with GLU 247 (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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245J ASP* 3.3 8.4 + - - +
246J MET* 1.3 79.2 - - - +
248J THR* 1.3 59.8 + - - +
250J GLU* 2.8 15.4 + - - +
251J ALA* 2.8 28.9 + - - +
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Residues in contact with THR 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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197J LYS* 4.7 4.3 - - - +
198J ALA* 4.4 14.4 + - + +
200J ILE* 4.2 29.3 - - + +
236J ILE* 4.3 14.8 - - + -
245J ASP* 2.9 29.7 + - - -
247J GLU* 1.3 78.8 - - - +
249J ILE* 1.3 62.7 + - - +
251J ALA* 3.4 9.2 - - + +
252J SER* 3.2 21.0 + - - -
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Residues in contact with ILE 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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198J ALA* 5.7 1.1 - - + -
208J THR* 5.2 1.1 - - + -
210J VAL* 3.6 46.4 - - + -
236J ILE* 4.2 16.6 - - + -
238J MET* 4.8 7.4 - - + -
244J MET* 5.5 2.7 - - + -
245J ASP 3.5 18.1 + - - +
246J MET* 3.5 28.0 + - + +
247J GLU 3.2 0.4 - - - -
248J THR* 1.3 76.9 - - - +
250J GLU* 1.3 56.5 + - - +
252J SER* 3.4 2.6 + - - -
253J VAL* 3.0 30.2 + - + +
259J LEU* 4.5 11.7 - - + -
275J ILE* 4.2 23.6 - - + -
279J ILE* 4.7 0.9 - - + -
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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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246J MET* 2.8 34.0 - - + +
247J GLU* 2.8 19.1 + - - +
249J ILE* 1.3 70.7 - - - +
251J ALA* 1.3 67.4 + - - +
252J SER 3.1 1.1 - - - -
253J VAL* 4.1 0.3 - - - +
254J MET* 3.2 30.6 + - + +
278J ARG 4.2 4.0 - - - +
279J ILE* 3.9 21.5 - - + +
282J GLY* 3.6 10.9 - - - -
283J PRO* 3.3 36.6 - - + +
284J ALA* 4.2 13.4 + - + -
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Residues in contact with ALA 251 (chain J).
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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200J ILE* 6.5 0.4 - - + -
247J GLU 2.8 15.0 + - - +
248J THR* 3.4 14.6 - - + +
250J GLU* 1.3 74.3 - - - +
252J SER* 1.3 63.6 + - - +
254J MET* 3.4 15.5 + - - +
255J LYS* 3.4 18.2 + - - +
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Residues in contact with SER 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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200J ILE* 5.8 1.3 - - - -
208J THR* 2.9 23.3 + - - +
234J GLU* 2.8 32.1 + - - +
236J ILE* 3.7 14.6 - - - -
248J THR* 3.2 13.7 + - - -
249J ILE 3.7 4.7 - - - -
250J GLU 3.1 0.8 - - - -
251J ALA* 1.3 80.5 - - - +
253J VAL* 1.3 61.6 + - - +
255J LYS* 3.5 4.9 + - - +
256J THR* 2.9 26.0 + - - +
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Residues in contact with VAL 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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208J THR* 3.5 17.7 - - - +
249J ILE* 3.0 22.0 + - + +
250J GLU 4.1 2.7 - - - +
251J ALA 3.2 0.6 - - - -
252J SER* 1.3 74.1 - - - +
254J MET* 1.3 57.7 + - - +
255J LYS 2.9 4.5 - - - -
256J THR* 2.7 5.8 + - - -
257J ASN* 2.7 36.7 + - - +
258J HIS 4.3 0.7 - - - +
259J LEU* 4.0 31.9 - - + -
279J ILE* 4.8 4.0 - - + -
284J ALA* 4.2 20.4 - - + +
287J PHE* 4.5 1.7 - - + +
288J LEU* 3.3 32.1 - - + -
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Residues in contact with MET 254 (chain J).
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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250J GLU* 3.2 20.1 + - + +
251J ALA* 3.7 12.6 - - - +
253J VAL* 1.3 74.6 - - - +
255J LYS* 1.3 59.3 + - - +
257J ASN* 4.5 4.4 + - - -
283J PRO* 5.2 11.2 - - - +
284J ALA* 4.0 14.4 - - + -
287J PHE* 3.5 62.1 - - + -
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Residues in contact with LYS 255 (chain J).
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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203J GLN* 4.4 8.3 + - - +
204J GLY 3.2 17.9 + - - +
205J THR* 3.9 25.5 - - + +
234J GLU* 2.6 36.0 + - - -
251J ALA 3.4 10.3 + - - +
252J SER* 3.7 6.7 - - - +
253J VAL 2.9 0.6 - - - -
254J MET* 1.3 82.1 - - - +
256J THR* 1.3 66.9 + - + +
257J ASN* 4.2 6.1 - - - +
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Residues in contact with THR 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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204J GLY 4.3 5.2 - - - +
205J THR 3.5 27.0 - - - +
206J HIS* 3.5 23.6 - - - +
207J ILE 3.8 7.9 - - - +
208J THR* 2.9 23.1 + - - +
234J GLU* 4.8 0.9 - - + -
252J SER* 2.9 19.5 + - - +
253J VAL 2.7 10.1 + - - -
255J LYS* 1.3 81.9 - - + +
257J ASN* 1.3 74.5 + - - +
258J HIS* 3.1 16.7 + - - -
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Residues in contact with ASN 257 (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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253J VAL* 2.7 17.1 + - - -
254J MET 4.5 6.3 + - - -
255J LYS 4.2 5.4 - - - +
256J THR* 1.3 75.3 - - - +
258J HIS* 1.3 76.2 + - + +
287J PHE* 2.6 41.3 + - - +
288J LEU* 3.6 6.9 - - - +
289J ASP* 2.8 44.8 + - + +
290J ALA 3.9 0.9 + - - -
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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