Contacts of the helix formed by residues 228 - 242 (chain B) in PDB entry 6HYI
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 228 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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227B LYS* 1.3 76.7 - - - +
229B GLU* 1.3 66.3 + - - +
230B ASP* 3.5 9.4 + - - +
231B GLU* 2.9 38.9 + - - +
232B MET* 2.9 22.6 + - - +
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Residues in contact with GLU 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227B LYS 4.0 0.4 + - - -
228B SER* 1.3 72.9 - - - +
230B ASP* 1.3 61.2 + - - +
232B MET* 3.3 8.7 + - + +
233B ASN* 2.9 50.9 + - - +
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Residues in contact with ASP 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228B SER* 3.2 8.1 + - - +
229B GLU* 1.3 80.6 - - - +
231B GLU* 1.3 57.4 + - + +
233B ASN* 3.3 15.2 + - - +
234B LEU* 3.0 28.4 + - - +
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Residues in contact with GLU 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226B GLU 4.2 4.1 - - - +
227B LYS* 3.5 19.2 - - + -
228B SER* 2.9 40.5 + - - +
230B ASP* 1.3 74.6 - - + +
232B MET* 1.3 65.6 + - - +
234B LEU* 3.2 8.8 + - + +
235B ILE* 2.9 34.8 + - + +
262B ARG* 3.3 29.5 + - - +
333B TRP* 4.0 14.8 - - + -
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Residues in contact with MET 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224B TYR* 5.2 5.2 - - - +
227B LYS* 3.5 37.2 - - + +
228B SER 2.9 11.5 + - - +
229B GLU* 3.6 11.0 - - + +
231B GLU* 1.3 75.6 - - - +
233B ASN* 1.3 60.8 + - - +
235B ILE* 4.7 2.0 - - - +
236B THR* 2.8 46.6 + - - +
254B LYS* 3.7 36.1 - - + +
257B ALA* 3.4 33.7 - - + -
258B GLY* 4.2 7.9 - - - -
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Residues in contact with ASN 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229B GLU* 2.9 41.6 + - - +
230B ASP* 3.6 15.0 + - - +
231B GLU 3.2 0.2 - - - -
232B MET* 1.3 78.7 - - - +
234B LEU* 1.3 62.0 + - - +
236B THR* 3.9 4.2 - - - -
237B LYS* 3.0 25.5 + - - +
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Residues in contact with LEU 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230B ASP 3.0 16.9 + - - +
231B GLU* 3.6 9.2 - - + +
233B ASN* 1.3 77.7 - - - +
235B ILE* 1.3 65.9 + - + +
237B LYS* 3.3 5.9 + - - +
238B LEU* 3.2 35.0 + - + +
286B GLN* 3.6 39.3 - - + +
333B TRP* 3.7 17.5 - - + +
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Residues in contact with ILE 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227B LYS* 3.5 36.3 - - + -
231B GLU 2.9 21.0 + - - +
232B MET* 4.1 2.7 - - - +
234B LEU* 1.3 75.1 - - + +
236B THR* 1.3 67.0 + - - +
238B LEU* 3.0 9.5 + - + +
239B LEU* 2.9 30.2 + - + +
257B ALA* 3.6 26.2 - - + +
260B MET* 3.8 24.5 - - + -
333B TRP* 3.6 45.8 - - + +
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Residues in contact with THR 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232B MET* 2.8 40.7 + - - +
233B ASN* 3.9 5.2 - - - -
235B ILE* 1.3 76.6 - - - +
237B LYS* 1.3 57.8 + - - +
239B LEU* 3.1 3.7 + - - +
240B THR* 2.8 44.8 + - + +
250B THR* 6.6 0.4 - - + -
253B ILE* 3.8 24.9 + - + +
254B LYS* 5.1 1.9 - - - +
257B ALA* 4.2 4.0 - - - +
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Residues in contact with LYS 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233B ASN 3.0 17.4 + - - +
234B LEU* 3.6 6.7 - - - +
235B ILE 3.2 0.2 - - - -
236B THR* 1.3 76.1 - - - +
238B LEU* 1.3 63.6 + - + +
240B THR* 3.3 6.9 + - - +
241B HIS* 3.1 52.3 + - + +
501B ASP 5.7 3.6 - - - -
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Residues in contact with LEU 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234B LEU* 3.2 34.7 + - + +
235B ILE* 3.0 11.2 + - + +
237B LYS* 1.3 76.6 - - + +
239B LEU* 1.3 64.2 + - + +
241B HIS* 3.4 3.8 + - - +
242B ASN* 3.2 24.4 + - - +
284B ILE* 4.1 19.1 - - + -
285B ILE 3.8 17.3 - - - +
286B GLN* 4.1 17.5 - - + +
304B GLU* 6.0 0.4 - - + -
305B GLY* 4.0 18.5 - - - +
333B TRP* 3.9 20.2 - - + -
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Residues in contact with LEU 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235B ILE* 2.9 19.9 + - + +
236B THR 3.7 4.7 - - - +
238B LEU* 1.3 79.4 - - + +
240B THR* 1.3 62.2 + - - +
241B HIS 3.2 1.2 + - - -
242B ASN 3.3 18.0 + - - +
245B PHE* 3.5 47.9 - - + +
253B ILE* 3.8 41.5 - - + +
256B VAL* 4.0 11.7 - - + -
257B ALA* 3.9 25.1 - - + +
260B MET* 4.0 20.0 - - + -
284B ILE* 4.4 7.0 - - + -
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Residues in contact with THR 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236B THR* 2.8 37.7 + - + +
237B LYS* 3.3 11.6 + - - -
239B LEU* 1.3 76.7 - - - +
241B HIS* 1.3 69.0 + - - +
242B ASN 3.5 0.2 - - - -
253B ILE* 4.3 19.1 - - + -
461B ARG* 2.8 46.8 + - - +
462B HIS* 3.3 7.1 + - - -
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Residues in contact with HIS 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237B LYS* 3.1 49.0 + - + +
238B LEU* 3.8 3.6 - - - +
239B LEU 3.1 0.6 - - - -
240B THR* 1.3 92.8 + - - +
242B ASN* 1.3 57.7 + - - +
305B GLY 5.5 1.3 - - - -
461B ARG* 3.1 37.5 + - + +
462B HIS* 3.7 9.3 - - - -
465B MET* 3.9 18.4 - - - +
500B VAL* 4.1 13.7 - - + +
501B ASP 3.7 22.8 + - - -
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Residues in contact with ASN 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238B LEU 3.2 16.1 + - - +
239B LEU 3.3 7.5 + - - +
241B HIS* 1.3 78.1 - - - +
243B VAL* 1.3 66.0 + - - +
244B LEU* 2.9 43.3 + - - +
245B PHE* 3.1 28.4 + - + -
246B SER 4.0 2.4 + - - -
284B ILE* 4.2 5.7 - - + +
305B GLY 3.0 24.5 + - - +
306B THR 3.7 0.6 - - - -
307B ALA* 3.6 19.8 - - - +
462B HIS* 4.0 4.1 + - - -
465B MET* 3.4 21.7 - - - +
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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