Contacts of the helix formed by residues 271 - 284 (chain J) in PDB entry 5XTE
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 GLU 271 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128J PHE* 4.8 2.5 - - - -
131J TYR* 3.5 56.1 + - + +
252J ASP* 6.4 2.9 - - + -
269J LYS* 3.9 5.0 + - - +
270J PRO* 1.3 78.5 - - - +
272J TRP* 1.3 68.6 + - + +
273J TYR* 3.1 38.2 + - + +
274J PHE* 3.0 43.3 + - - +
275J LEU 3.4 4.3 + - - -
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Residues in contact with TRP 272 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88J SER* 3.6 38.6 + - - -
91J PHE* 4.4 4.7 - - + -
92J ILE* 3.4 28.9 - - + -
95J PHE* 4.2 13.5 - + - -
250J LEU* 3.2 42.7 + - + +
269J LYS* 5.5 4.2 - - - +
270J PRO 3.7 0.6 + - - -
271J GLU* 1.3 75.0 - - + +
273J TYR* 1.3 94.5 + + + +
275J LEU* 2.9 34.7 + - + +
276J PHE* 4.0 5.7 + - - -
336J THR* 4.7 16.0 + - + +
403J PEE 3.7 31.9 - - + -
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Residues in contact with TYR 273 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87J ALA* 4.7 2.1 - - + +
88J SER* 3.8 17.7 - - - -
91J PHE* 3.4 55.9 - + + -
95J PHE* 3.6 11.6 - - + -
124J MET* 4.6 4.7 - - - +
127J ALA* 3.8 5.4 + - + +
131J TYR* 5.0 1.4 - - - -
271J GLU* 3.3 28.2 + - + +
272J TRP* 1.3 117.1 - + + +
274J PHE* 1.3 88.2 + + - +
276J PHE* 3.3 22.6 - - - -
401J HEM 3.6 26.5 - - - +
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Residues in contact with PHE 274 (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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91J PHE* 4.8 0.2 - + - -
124J MET* 3.1 60.1 - - + -
127J ALA* 3.9 7.6 - - + -
128J PHE* 3.4 30.7 - + + -
270J PRO* 4.7 10.1 - - + -
271J GLU* 3.0 37.6 + - - +
273J TYR* 1.3 94.8 - + - +
275J LEU* 1.3 59.1 + - - +
276J PHE* 3.3 3.6 - - - -
277J ALA* 2.9 33.1 + - + +
278J TYR* 3.6 3.0 + - - +
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Residues in contact with LEU 275 (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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269J LYS* 4.4 13.0 - - + +
270J PRO* 3.2 31.6 - - + +
271J GLU 3.4 3.3 + - - +
272J TRP* 2.9 25.7 + - + +
274J PHE* 1.3 76.0 - - - +
276J PHE* 1.3 65.7 + - - +
277J ALA 3.1 0.2 - - - -
278J TYR* 2.9 25.2 + - + +
279J THR* 3.5 4.7 + - - +
336J THR* 3.0 44.9 - - + +
339J GLY* 3.3 30.3 - - - +
340J GLY* 4.1 6.7 - - - +
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Residues in contact with PHE 276 (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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95J PHE* 3.9 17.5 - + - -
124J MET* 5.5 4.9 - - + -
272J TRP 4.0 3.0 + - - -
273J TYR 3.3 26.7 - - - -
274J PHE* 4.0 2.5 - - - -
275J LEU* 1.3 79.0 - - - +
277J ALA* 1.3 82.6 + - + +
279J THR* 2.5 30.0 + - - -
280J ILE* 3.7 4.8 + - + +
297J SER* 4.3 13.7 - - - -
298J ILE* 4.4 7.4 - - + -
332J LEU* 4.6 16.4 - - + +
335J LEU* 3.9 37.7 - - + +
336J THR* 3.9 15.7 + - - +
358J TYR* 5.5 3.1 - + - -
403J PEE 3.8 31.2 - - + -
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Residues in contact with ALA 277 (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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274J PHE* 2.9 14.1 + - + +
276J PHE* 1.3 97.6 - - + +
278J TYR* 1.3 62.6 + - - +
280J ILE* 2.9 23.9 + - + +
281J LEU* 3.3 16.6 + - - +
294J LEU* 3.7 23.3 - - + +
297J SER* 4.9 6.1 - - - +
298J ILE* 5.4 4.3 - - + -
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Residues in contact with TYR 278 (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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145J VAL* 5.2 13.3 - - + +
146J ILE* 4.9 13.5 - - + -
268J ILE* 4.7 10.1 + - - +
269J LYS* 5.9 1.1 - - + -
270J PRO* 3.8 39.0 - - + -
274J PHE 3.6 1.9 + - - +
275J LEU* 2.9 18.9 + - + +
277J ALA* 1.3 79.5 - - - +
279J THR* 1.3 56.1 + - - +
281J LEU* 3.0 29.5 + - + +
282J ARG* 2.9 70.2 + - + +
339J GLY* 4.7 7.9 - - - -
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Residues in contact with THR 279 (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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275J LEU 4.1 0.9 - - - +
276J PHE 2.5 19.1 + - - +
278J TYR* 1.3 77.9 - - - +
280J ILE* 1.3 56.9 + - - +
282J ARG* 2.9 11.8 + - - +
283J SER* 2.7 41.5 + - - -
335J LEU* 3.0 50.6 - - - +
338J ILE* 4.0 14.1 - - + -
339J GLY* 3.4 24.2 - - - +
351J GLY* 5.6 2.0 - - - -
355J SER* 4.8 1.6 - - - -
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Residues in contact with ILE 280 (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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276J PHE* 4.1 4.0 - - + +
277J ALA* 2.9 20.7 + - - +
279J THR* 1.3 90.1 + - - +
281J LEU* 1.3 61.0 + - + +
283J SER* 3.8 6.1 - - - -
284J VAL* 3.2 25.1 - - + +
290J GLY* 4.2 3.7 - - - -
293J ALA* 3.5 36.1 - - + +
294J LEU* 4.4 0.9 - - - +
297J SER* 3.2 31.2 - - - +
335J LEU* 4.8 10.5 - - + -
355J SER* 4.1 16.2 - - - +
358J TYR* 4.6 17.0 - - + -
359J PHE* 4.5 11.2 - - + -
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Residues in contact with LEU 281 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146J ILE* 4.9 4.3 - - + -
149J LEU* 3.4 39.0 - - + -
277J ALA 3.3 17.0 - - - +
278J TYR* 3.0 29.0 + - + +
280J ILE* 1.3 77.8 - - - +
282J ARG* 1.3 65.7 + - + +
283J SER 3.2 1.0 + - - -
284J VAL* 3.2 21.1 + - - +
290J GLY* 3.9 17.9 - - - +
291J VAL* 6.1 0.2 - - + -
294J LEU* 3.6 38.1 - - + -
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Residues in contact with ARG 282 (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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278J TYR* 2.9 60.8 + - + +
279J THR* 2.9 9.4 + - - +
281J LEU* 1.3 73.1 - - - +
283J SER* 1.3 61.8 + - - +
284J VAL 4.4 2.3 - - - +
338J ILE* 2.9 45.5 + - - +
339J GLY* 4.0 11.7 + - - -
341J GLN 4.2 11.3 + - - -
343J VAL* 3.5 37.0 - - + +
347J PHE* 5.3 5.5 + - - +
348J THR* 5.4 12.0 - - + +
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Residues in contact with SER 283 (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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279J THR* 2.7 25.9 + - - -
280J ILE* 3.7 5.5 + - - -
282J ARG* 1.3 77.3 - - - +
284J VAL* 1.3 67.4 + - - +
285J PRO* 3.5 4.0 - - - +
348J THR* 5.0 6.7 - - - +
351J GLY* 4.1 24.5 - - - -
352J GLN* 2.3 39.5 + - - +
355J SER* 3.4 15.6 + - - -
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Residues in contact with VAL 284 (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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280J ILE* 3.2 24.2 - - + +
281J LEU 3.2 14.9 + - - +
282J ARG 4.4 2.7 - - - +
283J SER* 1.3 86.4 + - - +
285J PRO* 1.3 85.0 - - + +
286J ASN 3.9 5.2 + - - +
289J GLY* 3.8 8.5 - - - +
290J GLY* 3.8 20.0 - - - +
293J ALA* 4.4 13.0 - - + -
352J GLN* 4.7 2.7 - - - +
355J SER* 5.8 3.8 - - - -
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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