Contacts of the helix formed by residues 245 - 258 (chain J) in PDB entry 1XFB
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 245 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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243F LYS* 4.7 11.9 - - - +
244J TYR* 1.3 73.4 - - - +
246J PRO* 1.3 65.1 - - + +
247J GLU* 2.7 39.9 - - + +
248J GLU* 2.6 52.9 + - - +
249J ILE* 2.9 11.7 + - - +
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Residues in contact with PRO 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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241F PRO* 5.7 9.6 - - + +
243F LYS* 5.1 11.0 - - - +
244J TYR 3.8 4.2 - - - +
245J THR* 1.3 89.4 - - + +
247J GLU* 1.3 69.0 + - - +
249J ILE* 3.8 4.9 - - + +
250J ALA* 2.9 22.3 + - - +
282J PHE* 4.5 18.6 - - + +
283J ASN* 3.1 34.5 + - - +
286J ALA* 3.2 24.8 - - + +
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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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243F LYS* 4.3 8.1 + - - -
245J THR* 2.7 35.5 - - + +
246J PRO* 1.3 90.0 - - - +
248J GLU* 1.3 52.0 + - + +
250J ALA* 3.1 7.8 + - - +
251J MET* 2.8 38.3 + - - +
286J ALA* 4.1 15.5 - - - +
289J ARG* 5.0 9.9 + - - -
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Residues in contact with GLU 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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199J LEU* 3.7 12.1 - - + +
243J LYS 4.0 3.3 - - - +
244J TYR* 3.0 32.4 - - + +
245J THR* 2.6 45.4 + - - +
247J GLU* 1.3 77.5 - - + +
249J ILE* 1.3 59.9 + - - +
251J MET* 3.3 8.7 + - - +
252J ALA* 3.1 18.7 + - - +
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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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199J LEU* 4.4 10.1 - - + -
233J MET* 4.7 5.8 - - + -
234J VAL 3.5 20.4 - - - +
235J THR* 3.9 22.0 - - + -
236J PRO* 4.8 4.0 - - + -
244J TYR* 4.3 20.6 - - + +
245J THR 2.9 13.5 + - - +
246J PRO* 3.8 8.7 - - + +
248J GLU* 1.3 72.7 - - - +
250J ALA* 1.3 63.1 + - - +
252J ALA* 3.3 2.6 + - - +
253J THR* 2.9 39.1 + - - +
279J GLU* 5.9 2.2 - - - +
283J ASN* 3.8 36.6 - - + +
287J ILE* 5.5 1.1 - - + -
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Residues in contact with ALA 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 PRO 2.9 19.9 + - - +
247J GLU* 3.4 5.2 - - - +
249J ILE* 1.3 75.7 - - - +
251J MET* 1.3 59.2 + - - +
253J THR* 4.4 0.2 - - - -
254J VAL* 2.9 36.5 + - - +
283J ASN 4.6 0.2 - - - +
286J ALA* 3.5 8.3 - - + +
287J ILE* 3.4 46.4 - - + +
290J CYS* 4.5 5.6 - - + -
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Residues in contact with MET 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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247J GLU 2.8 18.5 + - - +
248J GLU* 3.5 10.3 - - - +
249J ILE 3.2 0.2 - - - -
250J ALA* 1.3 76.4 - - - +
252J ALA* 1.3 52.7 + - - +
254J VAL* 4.0 0.7 - - - +
255J THR* 2.7 40.7 + - - +
290J CYS* 3.9 6.0 - - - -
291J PRO* 3.8 33.7 - - + -
292J LEU* 3.6 28.9 - - + +
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Residues in contact with ALA 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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199J LEU* 3.9 15.0 - - + -
203J GLN* 3.4 24.2 - - - +
234J VAL* 3.3 24.7 - - + -
248J GLU 3.1 16.0 + - - +
249J ILE 3.8 2.0 - - - +
251J MET* 1.3 73.4 - - - +
253J THR* 1.3 61.8 + - - +
255J THR* 3.3 2.3 + - - -
256J ALA* 2.9 32.6 + - - +
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Residues in contact with THR 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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232J ASN 5.2 0.7 - - - +
233J MET* 3.7 10.8 - - - +
234J VAL* 2.9 34.5 + - + +
249J ILE* 2.9 21.2 + - - +
250J ALA 3.8 2.9 - - - -
252J ALA* 1.3 77.2 - - - +
254J VAL* 1.3 64.2 + - + +
256J ALA* 3.4 2.1 + - - +
257J LEU* 3.1 25.8 + - + +
270J PHE* 3.3 40.2 - - + -
287J ILE* 3.8 13.7 - - + -
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Residues in contact with VAL 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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250J ALA 2.9 21.2 + - - +
251J MET 4.2 0.2 - - - +
253J THR* 1.3 74.6 - - + +
255J THR* 1.3 67.4 + - - +
257J LEU* 3.3 7.3 + - + +
258J ARG* 2.9 44.3 + - + +
287J ILE* 3.8 29.4 - - + +
290J CYS* 4.0 19.5 - - + -
292J LEU* 3.8 14.6 - - + -
294J ARG* 3.8 22.9 - - + -
296J TRP* 6.0 1.1 - - + +
298J LEU* 4.3 8.5 - - + -
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Residues in contact with THR 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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203J GLN* 3.7 7.2 - - - +
251J MET* 2.7 28.4 + - - +
252J ALA* 3.6 3.8 - - - -
254J VAL* 1.3 79.5 - - - +
256J ALA* 1.3 66.5 + - - +
258J ARG* 3.2 11.8 + - + +
259J ARG* 3.2 61.9 + - + +
292J LEU* 3.6 13.0 - - - +
225K GLU* 4.5 4.3 - - - +
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Residues in contact with ALA 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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203J GLN* 3.9 10.3 - - + +
206J THR* 4.1 13.5 - - + -
207J GLU* 3.7 28.3 - - + -
210J LEU* 5.2 1.1 - - - -
234J VAL* 4.0 11.4 - - + -
252J ALA 2.9 17.5 + - - +
253J THR 3.6 4.3 - - - +
255J THR* 1.3 77.1 - - - +
257J LEU* 1.3 63.9 + - + +
259J ARG* 3.1 14.4 + - - +
260J THR* 3.2 17.9 + - - +
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Residues in contact with LEU 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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206J THR* 5.9 0.9 - - + -
210J LEU* 3.8 18.2 - - + -
229J LEU* 4.0 10.8 - - + -
231J PRO* 4.3 6.3 - - + -
253J THR* 3.1 19.8 + - + +
254J VAL* 3.8 7.4 - - + +
256J ALA* 1.3 78.9 - - + +
258J ARG* 1.3 57.7 + - - +
259J ARG 3.2 0.5 + - - -
260J THR* 4.0 2.5 - - - -
261J VAL* 2.8 49.4 + - + +
268J VAL* 3.8 15.5 - - + -
270J PHE* 3.5 34.8 - - + -
296J TRP* 3.4 16.8 - - + +
298J LEU* 3.9 13.9 - - + -
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Residues in contact with ARG 258 (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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254J VAL* 2.9 42.9 + - + +
255J THR* 3.4 13.2 - - + +
257J LEU* 1.3 75.5 - - - +
259J ARG* 1.3 58.7 + - + +
260J THR 3.4 0.2 - - - -
292J LEU* 4.0 20.2 - - - +
293J PRO* 3.0 47.6 + - - +
295J PRO* 5.9 0.2 - - - +
296J TRP* 3.8 15.0 - - + -
225K GLU* 5.3 6.5 + - - +
262K PRO* 3.8 0.2 - - - +
263K PRO* 3.6 37.8 + - + +
264K ALA* 2.8 49.9 + - + +
295K PRO* 5.3 4.8 + - - +
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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