Contacts of the helix formed by residues 266 - 279 (chain J) in PDB entry 5G04
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 SER 266 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208J LYS* 5.3 5.3 + - - -
232J ASP* 5.3 2.0 - - - -
235J VAL* 3.6 19.3 - - - +
239J GLU* 4.7 8.8 + - - +
264J HIS* 3.2 18.1 + - - -
265J ALA* 1.3 77.5 - - - +
267J CYS* 1.3 61.6 + - - +
269J PRO* 3.3 19.6 - - - +
270J VAL* 3.5 8.5 - - - +
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Residues in contact with CYS 267 (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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235J VAL* 3.4 26.9 - - + -
254J THR* 4.5 6.0 + - - +
257J VAL* 3.4 31.0 - - + -
258J MET* 3.4 31.2 - - - -
264J HIS* 3.2 27.6 + - + -
265J ALA 3.2 0.4 - - - -
266J SER* 1.3 76.6 - - - +
268J LEU* 1.3 56.6 + - - +
269J PRO 3.5 0.2 - - - -
270J VAL* 3.4 4.1 + - - +
271J HIS* 2.8 31.5 + - - +
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Residues in contact with LEU 268 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258J MET* 3.7 31.9 - - + -
263J PHE* 4.4 21.5 - - + +
264J HIS 3.2 18.8 - - - +
265J ALA* 3.4 10.1 + - + +
266J SER 3.3 0.4 - - - -
267J CYS* 1.3 74.8 - - - +
269J PRO* 1.4 68.7 - - + +
271J HIS* 4.2 3.1 - - - -
272J ILE* 2.7 40.4 + - + +
287J LEU* 4.6 7.0 - - + -
291J LEU* 3.8 26.0 - - + -
298J ASN* 5.6 1.8 - - - +
300J VAL* 3.7 27.1 - - + -
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Residues in contact with PRO 269 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1G MET* 4.6 13.2 + - + +
265J ALA 3.4 11.4 - - - +
266J SER* 3.3 19.5 - - - +
268J LEU* 1.4 91.0 - - + +
270J VAL* 1.3 58.1 + - + +
272J ILE* 4.0 7.8 - - + +
273J GLY* 3.0 24.9 + - - -
300J VAL* 4.9 10.1 - - + -
303J PHE* 4.7 11.6 - - + -
333J TYR* 4.6 13.0 - - - +
335J PRO* 5.7 7.9 - - + -
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Residues in contact with VAL 270 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235J VAL* 4.4 5.8 - - + -
238J ALA* 4.2 8.5 - - + +
239J GLU* 3.9 48.0 - - + +
242J TYR* 4.3 16.5 - - + -
243J TYR* 6.1 0.2 - - + -
250J CYS* 4.2 11.9 - - - -
254J THR* 4.4 8.7 - - - +
266J SER 3.5 21.8 - - - +
267J CYS* 3.5 8.3 - - - +
269J PRO* 1.3 74.3 - - + +
271J HIS* 1.3 60.5 + - - +
273J GLY* 3.3 2.0 + - - -
274J THR* 2.9 32.3 + - - +
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Residues in contact with HIS 271 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251J TYR* 4.4 10.1 - + - -
254J THR* 2.7 41.2 - - + +
255J SER* 4.6 8.1 - - - -
258J MET* 3.3 32.7 - - + +
267J CYS* 2.8 19.5 + - - +
268J LEU* 3.7 3.4 - - - +
270J VAL* 1.3 74.2 - - - +
272J ILE* 1.3 59.3 + - - +
274J THR* 3.1 9.9 - - + +
275J LEU* 3.0 55.4 + - + +
283J GLU* 4.0 13.7 + - + +
287J LEU* 3.4 17.9 - - + +
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Residues in contact with ILE 272 (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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268J LEU* 2.7 33.0 + - + +
269J PRO 4.0 2.7 - - - +
271J HIS* 1.3 71.8 - - - +
273J GLY* 1.3 67.1 + - - +
275J LEU* 3.2 6.9 + - - +
276J VAL* 3.0 27.1 + - + +
284J LEU* 4.3 17.2 - - + +
287J LEU* 4.6 10.8 - - + -
291J LEU* 4.8 2.9 - - + -
300J VAL* 4.1 12.8 - - + -
303J PHE* 3.6 32.8 - - + -
304J ALA* 3.6 28.5 - - + -
307J CYS* 3.8 25.1 - - + -
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Residues in contact with GLY 273 (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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1G MET 4.9 2.0 - - - -
2G LEU* 4.2 16.4 - - - +
242J TYR* 3.5 24.2 + - - -
269J PRO 3.0 19.7 + - - -
270J VAL 3.7 0.7 - - - -
272J ILE* 1.3 75.9 - - - +
274J THR* 1.3 61.2 + - - +
276J VAL* 3.1 13.5 + - - +
277J GLU* 3.2 14.0 + - - +
303J PHE* 5.9 1.1 - - - -
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Residues in contact with THR 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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242J TYR* 3.5 6.4 - - - -
247J PHE* 3.5 32.4 + - - -
250J CYS* 3.8 22.7 - - - -
251J TYR* 3.7 16.1 + - + +
254J THR* 4.0 11.4 - - + -
270J VAL 2.9 28.3 + - - +
271J HIS* 3.1 21.3 - - - +
273J GLY* 1.3 73.9 - - - +
275J LEU* 1.3 61.0 + - - +
277J GLU* 3.4 2.6 + - - +
278J LEU* 3.1 25.8 + - - +
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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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251J TYR* 3.3 36.6 - - + -
271J HIS* 3.0 37.0 + - + +
272J ILE* 3.2 4.9 + - - +
274J THR* 1.3 72.8 - - - +
276J VAL* 1.3 60.9 + - - +
278J LEU* 4.5 2.7 - - - +
279J ASN* 2.9 24.1 + - - -
280J LYS* 3.2 22.5 + - + +
283J GLU* 3.6 20.9 - - + +
284J LEU* 3.6 50.7 - - + +
287J LEU* 4.5 2.2 - - + -
311J MET* 3.6 3.3 - - - +
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Residues in contact with VAL 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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2G LEU* 3.8 37.2 - - + -
272J ILE* 3.0 23.2 + - + +
273J GLY 3.1 7.1 + - - +
275J LEU* 1.3 76.2 - - - +
277J GLU* 1.3 62.2 + - - +
279J ASN* 3.2 16.5 + - - +
284J LEU* 4.4 1.1 - - + -
307J CYS* 4.2 23.3 - - + +
310J LEU* 5.8 2.9 - - + -
311J MET* 3.5 34.8 - - + +
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Residues in contact with GLU 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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247J PHE* 3.1 71.4 - - + +
273J GLY 3.2 3.8 + - - +
274J THR 3.8 0.9 - - - +
275J LEU 3.3 0.2 - - - -
276J VAL* 1.3 81.8 - - - +
278J LEU* 1.3 66.4 + - - +
279J ASN* 3.2 3.5 + - - +
441J VAL 5.7 1.2 - - - +
442J ASP* 6.2 0.7 - - - +
443J LYS* 5.0 13.6 + - + +
149P GLU* 5.5 1.6 - - - +
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Residues in contact with LEU 278 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247J PHE* 3.7 17.9 - - + +
248J LYS* 4.0 23.6 - - + +
251J TYR* 3.5 43.3 - - + -
274J THR* 3.1 21.3 + - - +
275J LEU 4.2 0.2 - - - +
277J GLU* 1.3 87.8 - - - +
279J ASN* 1.3 68.9 + - - +
280J LYS* 3.3 28.8 + - + +
149P GLU* 4.5 13.1 - - - +
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Residues in contact with ASN 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 2.9 8.4 + - - -
276J VAL 3.2 8.8 + - - +
277J GLU 3.2 5.7 - - - +
278J LEU* 1.3 81.5 - - - +
280J LYS* 1.3 57.9 + - - +
281J ALA* 2.9 12.2 + - - +
311J MET* 3.8 28.0 - - - +
26M TYR* 5.0 3.0 + - - -
149P GLU* 5.2 12.2 + - - +
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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