Contacts of the helix formed by residues 236 - 247 (chain B) in PDB entry 1HJV
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 236 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208B PHE* 3.6 18.3 - - - -
221B PRO* 3.6 11.9 - - + +
223B PHE* 3.6 28.1 - - - +
224B ARG* 3.6 21.4 + - - +
232B ASP 4.8 1.0 + - - -
233B ARG 3.2 26.3 + - - -
234B PHE 3.0 3.4 + - - +
235B SER* 1.3 78.6 - - - +
237B THR* 1.3 68.8 + - - +
238B ASP* 3.5 10.9 + - - +
239B TYR* 2.9 30.7 + - - +
240B ALA 3.3 12.6 + - - -
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Residues in contact with THR 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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205B THR* 3.6 38.2 + - - +
208B PHE* 3.8 2.2 - - - -
220B SER* 4.3 0.7 + - - -
221B PRO 2.8 22.7 + - - -
222B LEU* 3.9 12.8 - - + +
236B ASN* 1.3 70.5 - - - +
238B ASP* 1.3 56.6 + - - +
240B ALA* 3.0 5.0 + - - +
241B VAL* 2.8 40.1 + - + +
256B MET* 3.4 37.9 - - + -
337B LYS* 4.3 9.4 + - - -
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Residues in contact with ASP 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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222B LEU* 2.8 24.2 + - - +
223B PHE* 3.5 20.8 - - + +
224B ARG 5.5 0.3 + - - -
236B ASN* 3.5 5.1 - - - +
237B THR* 1.3 72.2 - - - +
239B TYR* 1.3 64.8 + - - +
242B GLY* 2.8 21.8 + - - -
340B TYR* 2.7 34.9 + - + +
344B ARG* 3.6 3.6 + - - -
225C GLY 4.0 1.0 - - - +
226C GLN* 3.2 19.8 - - - +
227C GLU* 2.8 34.4 + - - +
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Residues in contact with TYR 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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1385A SO4 2.7 34.6 + - - -
182B LYS* 3.4 24.5 - - + -
233B ARG* 3.7 28.0 - - + +
234B PHE* 3.4 34.3 - + + -
236B ASN* 2.9 24.6 + - - +
238B ASP* 1.3 76.7 - - - +
240B ALA* 1.3 58.0 + - - +
242B GLY 3.5 0.5 - - - -
243B TYR* 2.5 70.6 + + + +
246B ARG* 4.3 0.9 - - - -
227C GLU* 2.8 41.5 - - + +
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Residues in contact with ALA 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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180B ALA* 3.4 26.2 - - + +
185B ILE* 5.2 3.6 - - + +
203B ILE* 3.8 11.2 - - + +
205B THR* 3.8 20.4 - - + -
208B PHE* 4.5 0.9 - - + -
234B PHE 5.1 0.4 - - - +
236B ASN 3.3 8.1 + - - +
237B THR 3.0 7.5 + - - +
239B TYR* 1.3 86.1 - - + +
241B VAL* 1.3 63.8 + - - +
243B TYR* 3.7 3.7 - - - +
244B MET* 3.0 26.7 + - - +
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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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203B ILE* 4.7 8.1 - - + -
205B THR* 4.6 4.0 - - + -
237B THR* 2.8 32.6 + - + +
238B ASP 3.8 2.9 - - - +
240B ALA* 1.3 72.6 - - - +
242B GLY* 1.3 59.2 + - - +
244B MET* 3.5 1.9 + - - +
245B LEU* 3.0 33.7 + - + +
254B LEU* 4.2 6.4 - - + +
256B MET* 3.6 32.3 - - + -
340B TYR* 3.8 19.3 - - + +
344B ARG* 4.2 9.0 - - + +
346B LEU* 3.6 26.9 - - + -
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Residues in contact with GLY 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 ASP 2.8 17.0 + - - -
239B TYR 3.5 0.7 - - - -
241B VAL* 1.3 75.9 - - - +
243B TYR* 1.3 55.6 - - - +
245B LEU* 3.8 3.5 - - - +
246B ARG* 3.0 40.7 + - - +
344B ARG* 3.2 28.2 - - - +
227C GLU* 5.9 0.4 - - - -
228C ASP* 4.0 6.1 - - - +
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Residues in contact with TYR 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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243A TYR* 5.2 2.7 - + - -
246A ARG* 3.5 21.6 + - - -
1385A SO4 4.2 9.4 - - - -
182B LYS* 3.2 30.6 + - + -
185B ILE* 4.2 21.8 - - + -
186B ASP* 2.6 25.9 + - - -
239B TYR* 2.5 49.6 + + + +
240B ALA* 3.2 5.1 + - - +
242B GLY* 1.3 74.0 - - - +
244B MET* 1.3 58.7 + - - +
246B ARG* 3.3 29.0 - - - +
247B LEU* 2.9 65.2 + - + +
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Residues in contact with MET 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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178B LEU* 4.2 15.5 - - + -
179B SER 3.5 12.3 - - - +
185B ILE* 3.3 36.8 - - + -
189B TYR* 4.7 0.4 - - + -
191B ILE* 3.7 40.4 - - + -
201B ILE* 4.7 2.0 - - - -
203B ILE* 3.3 24.9 - - + -
240B ALA 3.0 13.6 + - - +
241B VAL 4.0 2.7 - - - +
243B TYR* 1.3 75.8 - - - +
245B LEU* 1.3 67.5 + - - +
247B LEU* 2.9 19.1 + - + +
248B GLY 3.2 0.9 + - - -
249B ALA* 3.2 20.1 + - + +
254B LEU* 4.2 21.1 - - + -
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Residues in contact with LEU 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* 3.0 19.0 + - + +
242B GLY* 3.8 4.0 - - - +
244B MET* 1.3 75.7 - - - +
246B ARG* 1.3 64.3 + - - +
248B GLY* 3.0 13.2 + - - -
249B ALA* 3.6 26.7 + - - +
251B ALA* 3.6 29.4 - - + +
254B LEU* 4.3 8.7 - - + +
344B ARG* 3.4 46.4 - - - +
346B LEU* 4.2 11.0 - - + -
228C ASP* 5.7 0.4 - - - +
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Residues in contact with ARG 246 (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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182A LYS* 4.3 13.0 - - - +
186A ASP* 3.5 19.8 + - + +
243A TYR* 3.2 28.7 - - + +
247A LEU* 3.7 13.7 - - - +
1385A SO4 4.0 12.3 + - - -
239B TYR* 4.3 1.8 - - - -
242B GLY 3.0 32.7 + - - +
243B TYR* 3.3 35.2 - - + +
245B LEU* 1.3 79.2 - - - +
247B LEU* 1.3 56.3 + - + +
248B GLY* 3.1 4.7 + - - -
227C GLU* 2.6 42.6 + - - +
228C ASP* 3.7 21.5 + - - +
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Residues in contact with LEU 247 (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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243A TYR* 5.1 4.0 - - + -
246A ARG* 4.0 32.9 - - + +
247A LEU* 3.7 31.2 - - + +
185B ILE* 4.2 15.3 - - + -
186B ASP* 5.1 0.9 - - - +
191B ILE* 4.3 16.2 - - + -
192B ALA* 3.9 21.1 + - - +
243B TYR* 2.9 64.2 + - + +
244B MET* 2.9 10.5 + - - +
246B ARG* 1.3 74.7 - - + +
248B GLY* 1.3 58.3 + - - +
249B ALA 3.8 0.4 - - - -
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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