Contacts of the helix formed by residues 275 - 286 (chain J) in PDB entry 6IY6
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 275 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218J PHE* 3.6 13.9 - - + -
225J HIS* 3.5 28.9 - - + +
233J ILE* 3.7 14.3 - - + +
270J ALA* 3.4 26.3 + - + +
273J GLU 3.4 13.9 - - - +
274J LEU* 1.3 74.3 - - - +
276J VAL* 1.3 65.9 + - - +
277J ALA* 3.8 15.5 - - - +
278J ASP* 2.8 34.5 + - - +
279J VAL* 3.4 7.1 + - - +
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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
----------------------------------------------------------
138J LEU* 4.7 3.6 - - + -
214J ALA* 3.6 32.8 - - + +
215J ARG* 3.8 14.8 - - + +
218J PHE* 3.6 34.7 - - + -
233J ILE* 3.4 23.8 - - + -
234J ASP* 5.4 0.7 - - - +
237J VAL* 4.4 10.5 - - + -
275J THR* 1.3 70.3 - - - +
277J ALA* 1.3 64.8 + - - +
279J VAL* 3.1 6.0 + - - +
280J VAL* 2.9 39.6 + - + +
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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
----------------------------------------------------------
233J ILE* 3.7 18.4 - - + +
236J TRP* 3.6 33.8 - - + +
237J VAL* 4.1 11.8 - - - -
269J LEU* 4.0 9.7 - - + +
270J ALA 5.5 0.2 - - - +
275J THR* 3.8 13.2 + - - +
276J VAL* 1.3 80.9 - - - +
278J ASP* 1.3 59.4 + - - +
280J VAL* 4.3 1.0 - - - +
281J LEU* 3.2 27.9 + - - +
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Residues in contact with ASP 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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268J TRP* 3.6 16.1 - - - +
269J LEU* 3.0 35.0 + - - +
274J LEU* 3.4 20.1 - - + -
275J THR* 2.8 40.5 + - - +
277J ALA* 1.3 72.8 - - - +
279J VAL* 1.3 65.0 - - - +
282J TRP* 3.0 29.8 + - - +
302J TRP* 3.3 24.4 + - + +
306J CYS* 4.8 1.1 - - - -
312J PHE* 5.0 1.3 - - - -
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Residues in contact with VAL 279 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134J SER 3.7 20.0 - - - +
137J VAL* 3.6 23.1 - - + -
138J LEU* 3.8 18.8 - - + -
141J LEU* 4.2 18.2 - - + -
218J PHE* 4.4 5.8 - - + -
274J LEU* 4.6 5.4 - - + -
275J THR 3.9 10.5 - - - +
276J VAL* 3.1 11.6 + - - +
278J ASP* 1.3 75.9 - - - +
280J VAL* 1.3 56.4 + - + +
282J TRP* 3.8 2.9 - - - +
283J SER* 2.6 36.3 + - - +
312J PHE* 3.7 24.9 - - + -
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Residues in contact with VAL 280 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134J SER* 4.0 18.1 - - - -
210J GLU 5.8 0.2 - - - +
211J GLY* 5.2 0.2 - - - -
214J ALA* 3.4 33.0 - - + -
237J VAL* 4.4 15.3 - - + -
240J ALA* 4.2 10.8 - - + -
241J ILE* 3.7 34.8 - - + -
276J VAL* 2.9 26.4 + - + +
277J ALA 4.3 2.2 - - - +
279J VAL* 1.3 77.1 - - + +
281J LEU* 1.3 57.3 + - - +
283J SER* 3.2 4.3 + - - -
284J VAL* 2.9 35.4 + - + +
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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
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236J TRP* 3.7 24.5 - - + +
239J ILE* 5.6 0.2 - - + -
240J ALA* 3.7 22.9 - - + +
244J LEU* 3.6 15.7 - - + -
255J VAL* 5.2 1.6 - - + -
259J MET* 3.6 29.4 - - + -
269J LEU* 3.6 23.8 - - + -
277J ALA 3.2 16.0 + - - +
278J ASP 4.0 1.8 - - - +
280J VAL* 1.3 75.3 - - - +
282J TRP* 1.3 65.3 + - - +
284J VAL* 3.1 4.3 + - - +
285J LEU* 3.0 42.9 + - + +
302J TRP* 4.2 3.4 - - + -
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Residues in contact with TRP 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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133J LEU* 4.2 13.9 - - + -
137J VAL* 4.1 17.0 - - + -
278J ASP 3.0 19.1 + - - +
279J VAL 3.8 0.9 - - - +
281J LEU* 1.3 74.8 - - - +
283J SER* 1.3 81.3 + - - +
285J LEU* 3.1 7.0 + - - +
286J GLN* 3.0 61.4 + - + +
302J TRP* 3.4 18.4 - + + -
303J MET* 3.6 33.9 + - + +
306J CYS* 3.6 20.8 - - + +
307J GLU* 4.4 13.9 + - + -
312J PHE* 3.4 48.5 - + + -
316J LEU* 3.8 23.1 - - + -
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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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133J LEU* 3.7 18.6 - - - +
134J SER* 3.4 36.7 + - - -
137J VAL* 3.9 7.3 - - - +
279J VAL 2.6 22.8 + - - -
280J VAL 3.3 6.3 - - - -
282J TRP* 1.3 89.2 - - - +
284J VAL* 1.3 61.6 + - - +
286J GLN 3.4 1.4 + - - -
287J GLN* 3.2 27.7 + - - +
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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
----------------------------------------------------------
134J SER* 5.9 0.7 - - - -
210J GLU* 5.2 2.5 - - - +
240J ALA* 3.5 35.4 - - + +
241J ILE* 4.5 9.9 - - + -
244J LEU* 3.9 14.4 - - + -
245J LYS* 3.8 29.6 - - + -
280J VAL* 2.9 25.9 + - + +
281J LEU* 3.1 8.7 + - - +
283J SER* 1.3 72.6 - - - +
285J LEU* 1.3 65.5 + - - +
287J GLN* 3.2 29.8 + - - +
288J ILE* 3.5 12.7 - - + +
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Residues in contact with LEU 285 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244J LEU* 3.9 22.0 - - + -
255J VAL* 6.1 0.2 - - + -
256J PHE* 3.6 33.0 - - + -
259J MET* 3.9 9.4 - - + -
281J LEU* 3.0 36.6 + - + +
282J TRP* 3.1 7.2 + - - +
284J VAL* 1.3 76.0 - - - +
286J GLN* 1.3 60.3 + - + +
287J GLN 3.2 0.2 - - - -
288J ILE* 3.3 30.4 + - + +
299J VAL* 4.9 0.2 - - + -
302J TRP* 3.8 23.3 - - + -
303J MET* 3.9 24.5 - - + +
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Residues in contact with GLN 286 (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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133J LEU* 3.9 14.0 - - + +
282J TRP* 3.0 66.7 + - + +
283J SER 3.8 6.3 - - - +
284J VAL 3.3 0.4 - - - -
285J LEU* 1.3 75.3 - - - +
287J GLN* 1.3 56.5 + - - +
288J ILE 3.6 3.5 + - - +
303J MET* 4.7 17.3 - - - +
307J GLU* 4.2 11.4 + - - +
316J LEU* 3.9 21.9 - - + +
319J LEU* 5.7 2.6 - - - +
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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