Contacts of the helix formed by residues 227 - 245 (chain B) in PDB entry 1HYH
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 LEU 227 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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206B TRP* 3.6 41.3 - - + +
216B ILE* 3.7 30.3 - - + +
217B VAL* 4.0 28.7 - - + -
219B LEU 6.1 0.9 - - - +
225B ILE* 3.6 13.9 + - + +
226B ASP* 1.3 72.4 - - - +
228B ALA* 1.3 51.6 + - - +
230B ILE* 3.4 16.8 + - + +
231B GLU* 2.5 37.9 + - - +
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Residues in contact with ALA 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B ASP* 3.2 1.6 - - - +
227B LEU* 1.3 74.1 - - - +
229B ALA* 1.3 58.3 + - - +
231B GLU* 3.4 12.5 - - - +
232B GLU* 2.7 36.8 + - - +
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Residues in contact with ALA 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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226B ASP* 3.2 16.5 + - - +
228B ALA* 1.3 78.1 - - - +
230B ILE* 1.3 58.2 + - + +
232B GLU* 3.2 12.6 + - - +
233B GLU* 2.9 28.5 + - - +
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Residues in contact with ILE 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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175B MET* 5.7 0.4 - - + -
178B ALA* 3.7 16.5 - - + +
179B VAL* 3.7 31.9 - - + +
182B ALA* 4.2 24.7 - - + -
183B PHE* 4.9 8.1 - - + -
206B TRP* 3.9 8.1 - - + -
216B ILE* 5.3 0.7 - - + -
225B ILE* 4.7 11.9 - - + -
226B ASP 3.5 14.8 - - - +
227B LEU* 3.5 24.5 - - + +
229B ALA* 1.3 72.8 - - + +
231B GLU* 1.4 66.0 + - - +
233B GLU* 3.2 7.5 + - - +
234B ALA* 3.0 24.1 + - + +
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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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203B PHE* 4.7 5.5 - - - +
204B VAL* 3.7 29.3 + - + +
206B TRP* 3.2 34.4 + - + +
227B LEU 2.5 21.3 + - - +
228B ALA* 3.2 13.2 + - - +
230B ILE* 1.4 73.5 - - - +
232B GLU* 1.3 58.0 + - - +
234B ALA* 3.5 5.6 - - - +
235B ARG* 2.8 39.2 + - + +
310B LYS* 5.9 0.7 + - - -
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Residues in contact with GLU 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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228B ALA 2.7 19.9 + - - +
229B ALA* 3.4 9.8 - - - +
231B GLU* 1.3 71.6 - - - +
233B GLU* 1.3 58.7 + - - +
235B ARG* 4.3 5.2 - - - +
236B LYS* 2.7 70.1 + - + +
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Residues in contact with GLU 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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177B ARG* 3.0 36.5 + - - +
178B ALA* 3.9 19.1 - - + -
181B GLU* 5.3 4.3 - - - +
229B ALA 2.9 12.5 + - - +
230B ILE* 3.2 10.5 + - - +
232B GLU* 1.3 76.3 - - - +
234B ALA* 1.3 55.0 + - - +
236B LYS* 5.2 1.3 - - - -
237B GLY* 2.7 38.2 + - - -
240B THR* 5.7 0.7 + - - -
64D ILE* 5.1 6.9 - - - +
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Residues in contact with ALA 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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171B ASP* 5.2 2.3 - - - +
174B ARG* 3.8 33.1 - - + +
175B MET* 3.8 35.2 - - + +
177B ARG* 4.9 0.7 - - - +
178B ALA* 4.3 1.5 - - + +
194B ASN* 5.5 2.5 - - - +
202B GLN* 5.6 1.5 + - - -
204B VAL* 5.2 6.1 - - + -
206B TRP* 6.5 0.2 - - + -
230B ILE 3.0 17.4 + - - +
231B GLU* 3.5 6.7 - - - +
233B GLU* 1.3 80.4 - - - +
235B ARG* 1.3 61.9 + - - +
237B GLY 3.7 3.6 + - - -
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Residues in contact with ARG 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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174B ARG* 5.7 1.2 + - - -
200B ASN 6.0 2.5 - - - -
202B GLN* 4.6 25.8 - - - +
231B GLU* 2.8 28.0 + - + +
232B GLU* 3.9 5.2 - - - +
234B ALA* 1.3 76.7 - - - +
236B LYS* 1.3 73.9 + - + +
238B GLY* 4.3 3.6 + - - -
239B PHE* 3.6 14.5 - - + -
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Residues in contact with LYS 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 GLU* 2.7 58.7 + - + +
233B GLU* 4.5 1.1 - - - +
235B ARG* 1.3 81.5 - - + +
237B GLY* 1.3 53.8 + - - +
238B GLY 3.2 3.1 - - - -
239B PHE* 2.8 55.7 + - + +
240B THR* 3.4 9.7 + - - +
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Residues in contact with GLY 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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174B ARG* 4.5 6.3 - - - -
177B ARG* 4.1 15.3 - - - -
233B GLU* 2.7 26.8 + - - -
234B ALA 3.7 4.0 + - - -
235B ARG 3.4 2.0 - - - -
236B LYS* 1.3 70.6 - - - +
238B GLY* 1.3 59.1 + - - +
240B THR* 3.7 10.5 + - - -
241B VAL* 3.3 27.1 + - - +
64D ILE* 4.3 4.0 - - - +
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Residues in contact with GLY 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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174B ARG* 3.6 37.8 - - - +
235B ARG 4.3 4.3 + - - -
236B LYS 3.0 1.2 + - - -
237B GLY* 1.3 73.6 - - - +
239B PHE* 1.3 62.6 + - - +
241B VAL* 3.6 3.4 + - - +
242B LEU* 2.9 30.4 + - - +
248B THR* 3.9 4.0 - - - +
331B SO4 4.5 6.5 - - - -
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Residues in contact with PHE 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 ARG* 3.6 18.6 - - + -
236B LYS* 2.8 50.1 + - + +
238B GLY* 1.3 70.5 - - - -
240B THR* 1.3 56.0 + - - +
242B LEU* 3.1 14.9 + - + -
243B ASN* 2.5 53.2 + - - +
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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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233B GLU* 5.7 0.5 + - - -
236B LYS* 3.5 13.7 + - - +
237B GLY* 3.8 13.2 + - - -
239B PHE* 1.3 78.8 - - - +
241B VAL* 1.3 51.3 + - - +
243B ASN* 3.7 4.7 - - - +
244B GLY* 2.8 31.7 + - - -
60D LYS* 5.3 7.6 - - + -
61D ALA* 4.4 2.9 - - - +
64D ILE* 4.1 23.1 - - + -
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Residues in contact with VAL 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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174B ARG* 5.2 1.6 - - - +
237B GLY 3.3 15.9 + - - +
238B GLY* 3.8 7.6 - - - +
239B PHE 3.3 0.4 - - - -
240B THR* 1.3 73.7 - - - +
242B LEU* 1.3 63.6 + - - +
244B GLY 3.2 0.7 + - - -
245B LYS* 3.1 41.5 + - + +
247B TYR 3.7 7.4 - - - +
248B THR* 3.6 23.3 - - + -
61D ALA* 3.6 19.4 - - - +
64D ILE* 3.5 26.7 - - + -
65D ASP* 3.9 15.0 - - - +
68D ASP* 4.7 4.9 - - - +
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Residues in contact with LEU 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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100B ILE* 4.5 12.6 - - + -
103B GLN* 4.5 30.1 - - + +
104B GLN* 5.1 5.6 - - + -
238B GLY 2.9 20.2 + - - +
239B PHE* 3.6 17.7 - - + +
241B VAL* 1.3 78.3 - - - +
243B ASN* 1.3 63.2 + - - +
246B GLY* 2.7 58.7 + - - +
247B TYR* 3.6 14.6 - - - +
248B THR* 4.3 5.4 - - + +
331B SO4 4.6 13.2 - - - +
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Residues in contact with ASN 243 (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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239B PHE* 2.5 36.0 + - - +
240B THR* 4.0 4.5 - - - +
242B LEU* 1.3 83.2 + - - +
244B GLY* 1.3 60.4 + - - +
245B LYS 5.0 0.2 - - - -
246B GLY 4.5 1.2 + - - -
57D ALA* 5.5 0.3 - - - +
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Residues in contact with GLY 244 (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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240B THR 2.8 21.9 + - - -
241B VAL 3.2 1.8 + - - -
243B ASN* 1.3 74.5 - - - +
245B LYS* 1.3 60.7 + - - +
55D ASN* 5.3 1.4 + - - -
57D ALA* 3.7 28.7 - - - +
58D LYS* 3.6 19.4 + - - +
61D ALA* 3.8 5.4 - - - -
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Residues in contact with LYS 245 (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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241B VAL* 3.1 12.9 + - - +
243B ASN 5.0 0.2 - - - -
244B GLY* 1.3 77.1 - - - +
246B GLY* 1.3 59.3 + - - +
247B TYR* 3.3 62.9 + - + +
249B SER* 4.0 3.6 + - - -
250B TYR* 3.5 13.5 - - - -
58D LYS* 3.6 22.4 - - + -
61D ALA* 3.9 12.3 - - + -
62D ASP* 2.7 30.7 + - - +
65D ASP* 2.8 32.2 + - - +
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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