Contacts of the helix formed by residues 226 - 243 (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 ASN 226 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225J HIS* 1.3 77.7 - - - +
227J ALA* 1.3 60.9 - - - +
228J VAL* 3.2 8.5 + - + +
229J ASN* 3.5 17.1 + - - +
230J ALA* 3.0 27.6 + - - +
60L ARG* 5.5 0.2 - - - -
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Residues in contact with ALA 227 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226J ASN* 1.3 73.6 - - - +
228J VAL* 1.3 60.3 + - + +
230J ALA* 4.1 0.7 - - - +
231J THR* 2.7 33.1 + - - -
57L TYR* 3.8 20.2 - - + +
60L ARG* 4.1 30.7 - - + +
61L VAL* 4.5 12.6 - - + +
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Residues in contact with VAL 228 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226J ASN* 3.2 6.2 - - + -
227J ALA* 1.3 75.7 - - + +
229J ASN* 1.3 67.9 + - - +
231J THR* 3.8 2.6 - - - -
232J LEU* 3.1 33.8 + - + +
42L VAL* 4.7 3.6 - - + -
46L VAL* 3.4 43.1 - - + -
48L PHE* 3.9 4.5 - - + -
57L TYR* 3.8 28.9 - - + +
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Residues in contact with ASN 229 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225J HIS* 4.1 22.6 + - + +
226J ASN* 3.5 19.4 + - - +
228J VAL* 1.3 82.9 - - - +
230J ALA* 1.3 54.5 + - - +
232J LEU* 2.8 15.3 + - - +
233J ILE* 2.6 44.3 + - + +
270J ALA* 4.6 14.7 + - + +
272J ASN* 3.0 32.5 - - - +
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Residues in contact with ALA 230 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225J HIS* 4.0 12.7 - - + +
226J ASN 3.0 19.4 + - - +
229J ASN* 1.3 74.7 - - - +
231J THR* 1.3 57.4 + - - +
233J ILE* 3.5 12.6 + - - +
234J ASP* 3.0 34.3 + - - +
60L ARG* 3.5 34.3 - - - +
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Residues in contact with THR 231 (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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227J ALA 2.7 22.2 + - - -
228J VAL 3.8 3.6 - - - -
229J ASN 3.2 0.4 - - - -
230J ALA* 1.3 74.3 - - - +
232J LEU* 1.3 55.1 + - - +
234J ASP* 3.4 5.2 + - - +
235J SER* 2.8 32.2 + - - -
48L PHE* 3.6 23.8 - - + -
53L SER* 3.0 35.8 + - - +
56L ARG* 4.3 3.5 + - + -
57L TYR* 3.5 20.5 + - + +
60L ARG* 3.5 15.7 + - - +
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Residues in contact with LEU 232 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228J VAL* 3.1 21.4 + - + +
229J ASN* 2.8 15.6 + - - +
231J THR* 1.3 72.1 - - - +
233J ILE* 1.3 60.5 + - + +
235J SER* 3.4 10.8 + - - +
236J TRP* 3.0 49.3 + - + +
269J LEU 4.5 13.0 - - - +
270J ALA* 5.4 7.2 - - - +
47L ILE 5.8 1.3 - - - +
48L PHE* 4.2 16.8 - - + -
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Residues in contact with ILE 233 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225J HIS* 3.5 38.4 - - + +
229J ASN* 2.6 27.5 + - + +
230J ALA* 3.5 7.4 - - - +
232J LEU* 1.3 70.4 - - + +
234J ASP* 1.3 67.7 + - - +
236J TRP* 3.1 16.0 + - + +
237J VAL* 3.2 13.7 + - - +
270J ALA* 4.3 13.7 - - + -
275J THR* 3.7 24.9 - - + +
276J VAL* 3.4 32.8 - - + -
277J ALA* 3.7 15.5 - - + +
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Residues in contact with ASP 234 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215J ARG* 3.2 51.0 + - - +
230J ALA 3.0 17.5 + - - +
231J THR 3.6 5.2 - - - +
233J ILE* 1.3 79.6 - - - +
235J SER* 1.3 61.1 + - - +
237J VAL* 3.3 2.3 + - - -
238J ASP* 3.2 14.1 + - - +
276J VAL* 5.4 0.5 - - - +
56L ARG* 3.0 40.8 + - - +
60L ARG* 3.3 20.0 + - - -
68L TYR* 3.7 3.8 + - - -
75L HIS* 5.3 0.7 - - - -
79L ASP* 4.2 0.9 - - - +
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Residues in contact with SER 235 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231J THR 2.8 15.7 + - - -
232J LEU* 3.4 16.2 - - - -
234J ASP* 1.3 75.5 - - - +
236J TRP* 1.3 60.0 + - - +
238J ASP* 3.4 10.9 + - - +
239J ILE* 3.2 35.1 + - - +
48L PHE* 5.0 5.1 - - - -
50L ASP* 4.7 6.8 + - - +
53L SER* 2.9 28.5 + - - -
56L ARG* 4.7 0.6 - - - +
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Residues in contact with TRP 236 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232J LEU* 3.0 38.0 + - + +
233J ILE* 3.1 10.1 + - - +
235J SER* 1.3 72.3 - - - +
237J VAL* 1.3 63.2 + - - +
239J ILE* 3.5 34.3 - - + +
240J ALA* 3.2 22.9 + - - +
255J VAL 4.8 0.4 - - - -
258J SER* 3.9 24.2 - - - -
259J MET* 3.6 42.0 - - + -
262J ALA* 4.0 9.4 - - + +
269J LEU* 3.7 49.8 + - + +
270J ALA* 5.9 0.4 - - - -
277J ALA* 3.6 20.2 - - + +
281J LEU* 3.7 18.5 - - + +
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Residues in contact with VAL 237 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211J GLY* 3.6 31.2 - - - +
215J ARG* 3.5 26.7 - - + +
233J ILE 3.2 15.1 + - - +
234J ASP 3.5 7.4 - - - +
235J SER 3.3 0.2 - - - -
236J TRP* 1.3 73.2 - - - +
238J ASP* 1.3 65.5 + - - +
240J ALA* 3.1 7.3 + - - +
241J ILE* 3.0 31.6 + - + +
276J VAL* 4.4 18.2 - - + -
277J ALA* 4.1 20.9 - - - +
280J VAL* 4.4 11.7 - - + -
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Residues in contact with ASP 238 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215J ARG* 3.6 12.4 + - - +
234J ASP 3.2 8.5 + - - +
235J SER* 3.4 9.5 + - - +
237J VAL* 1.3 77.4 - - - +
239J ILE* 1.3 62.2 + - + +
241J ILE* 3.5 2.2 + - - -
242J PHE* 3.1 53.8 + - + +
243J GLN* 4.2 1.4 + - - +
50L ASP* 3.8 22.3 - - - +
52L ASN* 4.5 10.0 + - - +
56L ARG* 3.3 30.9 + - - -
83L GLU* 5.1 5.4 - - - +
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Residues in contact with ILE 239 (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 SER* 3.2 24.1 + - - +
236J TRP* 3.5 39.5 - - + +
237J VAL 3.2 0.2 - - - -
238J ASP* 1.3 75.1 - - + +
240J ALA* 1.3 60.4 + - - +
243J GLN* 3.0 55.3 + - - +
244J LEU 3.1 8.0 + - - -
255J VAL* 4.0 31.4 - - + -
258J SER* 5.7 3.6 - - - +
281J LEU* 5.6 0.9 - - + -
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Residues in contact with ALA 240 (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 3.2 9.9 + - - +
237J VAL* 3.1 8.4 + - - +
239J ILE* 1.3 79.5 - - - +
241J ILE* 1.3 62.6 + - - +
244J LEU* 3.4 13.8 - - - +
245J LYS 3.1 22.3 + - - -
280J VAL* 4.2 5.4 - - + -
281J LEU* 3.7 37.2 - - + +
284J VAL* 3.5 19.1 - - + +
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Residues in contact with ILE 241 (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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210J GLU* 3.4 42.2 - - + +
211J GLY* 3.8 23.6 - - - +
237J VAL* 3.0 21.1 + - + +
238J ASP* 4.0 3.4 - - - +
239J ILE 3.4 0.2 - - - -
240J ALA* 1.3 73.3 - - - +
242J PHE* 1.3 88.3 + - + +
245J LYS* 3.1 28.5 - - + +
246J GLU* 4.4 3.3 + - - +
280J VAL* 3.7 22.9 - - + -
284J VAL* 4.5 5.8 - - + -
83L GLU* 4.9 5.6 - - - +
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Residues in contact with PHE 242 (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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194J LYS* 5.6 3.1 - - - -
238J ASP* 3.1 40.7 + - + +
241J ILE* 1.3 93.1 - - + +
243J GLN* 1.3 70.1 + - + +
244J LEU 3.5 0.4 - - - -
246J GLU* 3.4 29.2 + - - +
83L GLU* 3.4 44.6 - - + -
86L ALA* 6.0 3.1 - - + -
87L THR* 3.8 24.0 - - + -
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Residues in contact with GLN 243 (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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238J ASP 5.4 0.6 - - - -
239J ILE* 3.0 41.8 + - - +
242J PHE* 1.3 79.4 - - + +
244J LEU* 1.3 61.7 + - - +
247J GLY* 3.4 12.0 - - - -
251J GLU* 3.2 34.0 - - + +
255J VAL* 4.8 11.2 - - + +
50L ASP* 6.2 1.6 - - - -
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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
------------------------------------------------------------
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