Contacts of the helix formed by residues 229 - 248 (chain B) in PDB entry 1H5R
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 229 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16B ARG* 4.4 24.7 - - - +
17B LEU* 3.7 8.1 - - - -
145B ARG* 6.1 4.3 - - - +
226B ASP* 5.3 4.3 - - - +
228B GLY* 1.3 82.9 - - - +
230B HIS* 1.3 64.8 + - - +
231B GLN* 3.6 7.3 + - - +
232B SER* 3.0 28.0 + - - +
233B LEU* 3.0 24.6 + - - +
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Residues in contact with HIS 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A TYR* 3.5 43.3 - - + +
33A ASP* 3.8 20.2 - - + +
279A ASN* 4.4 4.3 - - - -
280A ASN* 5.5 6.3 + - - -
281A TYR* 6.1 0.9 - - + -
16B ARG* 4.4 12.8 + - - +
17B LEU* 3.2 49.5 + - + +
18B TYR 4.1 8.5 - - - -
20B VAL* 3.6 14.9 - - + +
229B THR* 1.3 75.2 - - - +
231B GLN* 1.3 65.3 + - - +
233B LEU* 3.3 12.8 + - + +
234B ILE* 3.2 25.8 + - - +
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Residues in contact with GLN 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A TYR* 3.9 16.6 + - + +
241A ALA* 4.2 18.4 - - - +
245A GLU* 5.6 4.8 - - + +
229B THR* 3.2 7.5 + - - +
230B HIS* 1.3 80.9 - - - +
232B SER* 1.3 56.6 + - - +
234B ILE* 3.3 10.9 + - - +
235B GLU* 3.0 52.7 + - - +
245C GLU* 5.7 0.4 + - - -
231D GLN* 4.7 14.8 - - - +
235D GLU* 5.4 6.0 + - - +
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Residues in contact with SER 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B ASP* 2.8 53.3 + - - +
228B GLY 3.2 2.4 + - - -
229B THR* 3.0 34.8 + - - -
231B GLN* 1.3 75.6 - - - +
233B LEU* 1.3 59.5 + - - +
235B GLU* 3.1 17.7 + - - +
236B ALA* 2.8 24.3 + - - +
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Residues in contact with LEU 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A PRO* 6.4 0.9 - - + -
17B LEU* 3.8 31.6 - - + -
20B VAL* 6.0 0.2 - - + -
29B LEU* 4.1 15.9 - - + -
30B PRO 5.7 1.3 - - - +
31B ILE* 4.0 10.6 - - + +
36B MET* 3.5 31.2 - - + -
227B THR* 3.6 23.6 - - + +
229B THR 3.0 19.8 + - - +
230B HIS* 3.6 15.7 - - + +
231B GLN 3.3 0.2 - - - -
232B SER* 1.3 73.7 + - - +
234B ILE* 1.3 66.5 + - + +
236B ALA* 3.1 5.4 + - - +
237B SER* 2.9 26.7 + - - -
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Residues in contact with ILE 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A TYR* 3.6 26.9 - - + +
234A ILE* 4.4 7.2 - - + +
237A SER* 3.4 44.2 - - - +
238A ASN* 2.5 37.5 - - - +
241A ALA* 4.1 6.7 - - + -
230B HIS 3.2 10.5 + - - +
231B GLN* 3.3 13.4 + - - +
233B LEU* 1.3 78.0 - - + +
235B GLU* 1.3 64.5 + - + +
237B SER* 3.1 7.9 + - - -
238B ASN* 2.9 26.2 + - - +
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Residues in contact with GLU 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B GLN* 3.0 41.0 + - - +
232B SER* 3.6 23.8 - - - +
233B LEU 3.1 0.4 - - - -
234B ILE* 1.3 77.4 - - + +
236B ALA* 1.3 64.1 + - - +
238B ASN* 3.3 11.2 + - - +
239B PHE* 2.9 24.3 + - - +
238C ASN* 5.0 7.2 - - - +
241C ALA* 5.7 0.3 - - - +
242C THR* 3.4 35.8 + - + +
245C GLU* 3.2 24.0 - - - +
231D GLN* 5.3 1.6 + - - +
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Residues in contact with ALA 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B ILE* 4.1 20.6 - - + -
113B ILE* 4.4 4.3 - - + -
225B LEU* 4.0 33.4 - - + +
226B ASP 4.2 6.5 - - - +
227B THR* 4.8 0.9 - - + -
232B SER 2.8 16.0 + - - +
233B LEU* 3.6 5.2 - - - +
235B GLU* 1.3 76.7 - - - +
237B SER* 1.3 63.0 + - - +
239B PHE* 3.2 3.1 + - - +
240B ILE* 3.0 29.1 + - - +
242C THR* 5.7 0.4 - - - -
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Residues in contact with SER 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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234A ILE* 3.7 21.9 - - - +
30B PRO 3.5 6.8 + - - -
31B ILE* 3.3 12.1 - - - +
32B TYR* 2.9 33.7 + - - +
233B LEU 2.9 14.3 + - - -
234B ILE* 3.4 10.3 - - - -
235B GLU 3.1 0.2 - - - -
236B ALA* 1.3 77.7 - - - +
238B ASN* 1.3 57.1 + - - +
240B ILE 3.4 0.9 + - - -
241B ALA* 2.9 29.6 + - - +
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Residues in contact with ASN 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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231A GLN* 5.5 1.2 + - - -
234A ILE* 2.6 33.4 - - - +
238A ASN* 3.1 27.8 + - - +
234B ILE* 2.9 20.2 + - - +
235B GLU* 3.3 12.5 + - - +
237B SER* 1.3 76.0 - - - +
239B PHE* 1.3 63.5 + - - +
241B ALA* 3.4 6.5 + - - +
242B THR* 3.0 30.8 + - - +
238C ASN* 4.3 24.0 + - + +
242C THR* 5.9 0.7 - - - +
238D ASN* 5.8 1.4 - - - +
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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
----------------------------------------------------------
115B TYR* 3.9 10.1 - + + -
223B ALA* 3.6 28.9 - - + -
225B LEU* 3.7 24.0 - - + -
235B GLU 2.9 17.3 + - - +
236B ALA* 3.4 5.8 - - - +
237B SER 3.2 0.2 - - - -
238B ASN* 1.3 77.3 - - - +
240B ILE* 1.3 65.9 + - + +
242B THR* 3.3 7.3 + - - -
243B ILE* 3.1 49.6 + - + +
115C TYR* 5.0 0.7 - + - -
239C PHE* 3.2 41.5 - + - +
242C THR* 3.9 21.1 - - + -
243C ILE* 3.4 27.1 - - + -
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Residues in contact with ILE 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B ILE* 3.9 16.6 - - + -
32B TYR* 4.3 9.0 - - + -
39B TYR* 3.5 26.0 - - + +
113B ILE* 4.7 4.0 - - + -
115B TYR* 5.2 3.4 - - + -
225B LEU* 4.0 18.6 - - + -
236B ALA 3.0 20.7 + - - +
237B SER 3.9 2.9 - - - +
239B PHE* 1.3 83.9 - - + +
241B ALA* 1.3 62.9 + - - +
243B ILE* 3.2 7.7 + - + +
244B GLU* 2.9 46.7 + - + +
251B VAL* 3.8 32.1 - - + -
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Residues in contact with ALA 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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231A GLN* 3.7 15.0 - - - +
234A ILE* 4.2 3.8 - - + -
32B TYR* 3.6 38.7 - - + -
237B SER 2.9 17.6 + - - +
238B ASN* 3.7 6.5 - - - +
240B ILE* 1.3 77.2 - - - +
242B THR* 1.3 58.1 + - - +
245B GLU* 2.8 38.0 + - + +
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Residues in contact with THR 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B ASN* 3.0 19.1 + - - +
239B PHE* 3.6 4.9 - - - -
240B ILE 3.2 0.2 - - - -
241B ALA* 1.3 74.4 - - - +
243B ILE* 1.3 68.1 + - - +
245B GLU* 4.5 2.4 - - - +
246B ARG* 3.2 24.4 + - + +
225C LEU* 4.8 9.9 - - + -
235C GLU* 3.8 47.9 + - + +
236C ALA* 5.7 0.2 - - - -
238C ASN* 6.0 0.5 - - - +
239C PHE* 4.1 22.5 - - + +
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Residues in contact with ILE 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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115B TYR* 3.7 35.2 - - + +
239B PHE* 3.1 46.2 + - + +
240B ILE* 3.5 8.7 - - + +
242B THR* 1.3 76.8 - - - +
244B GLU* 1.3 64.3 + - + +
246B ARG* 3.2 4.7 + - - +
247B GLN* 3.0 50.4 + - - +
251B VAL* 3.7 23.3 - - + -
138C TYR* 5.5 0.4 - - - +
220C ARG 4.8 0.2 - - - +
223C ALA* 5.3 2.9 - - + -
239C PHE* 3.8 14.4 - - + -
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Residues in contact with GLU 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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32B TYR* 3.5 9.0 - - + -
33B ASP* 2.4 29.0 - - - +
34B LYS* 2.8 21.3 + - - -
240B ILE* 2.9 33.4 + - + +
241B ALA 4.0 2.0 - - - +
243B ILE* 1.3 74.3 - - - +
245B GLU* 1.3 68.8 + - - +
247B GLN* 4.6 0.4 - - - +
248B GLY* 2.8 30.7 + - - -
249B LEU 3.3 19.7 + - - +
250B LYS* 3.3 12.4 + - - +
251B VAL* 2.8 32.4 + - + +
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Residues in contact with GLU 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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231A GLN* 5.3 4.3 - - + +
32B TYR* 2.8 33.4 + - + +
241B ALA* 2.8 26.8 + - + +
242B THR* 4.5 2.2 - - - +
244B GLU* 1.3 76.2 - - - +
246B ARG* 1.3 52.8 + - - +
248B GLY* 5.9 0.5 - - - -
141C ASN* 1.6 41.9 + - - +
235C GLU* 6.1 1.6 - - - +
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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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242B THR* 3.2 20.9 + - + +
243B ILE* 3.2 4.8 + - - +
244B GLU 3.1 0.6 - - - -
245B GLU* 1.3 77.6 - - - +
247B GLN* 1.3 58.8 + - + +
138C TYR* 3.9 17.3 - - - +
140C VAL* 3.4 14.3 - - - +
141C ASN* 3.2 24.8 + - - +
142C ASP* 4.4 3.5 + - - +
145C ARG* 4.0 4.4 - - - +
146C TYR* 2.8 37.2 + - - -
224C TRP* 2.6 66.9 + - - +
225C LEU* 4.1 1.2 + - - -
226C ASP* 3.7 39.2 - - + +
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Residues in contact with GLN 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B ILE* 3.0 36.8 + - - +
246B ARG* 1.3 80.7 - - + +
248B GLY* 1.3 57.4 + - - +
249B LEU* 3.1 28.0 - - + +
250B LYS 5.3 1.4 - - - +
251B VAL* 5.4 1.6 - - - +
138C TYR* 3.0 32.0 + - + +
139C HIS* 2.8 46.8 + - + +
140C VAL 3.3 5.2 - - - -
141C ASN 3.7 2.0 - - - -
220C ARG* 3.0 45.8 + - - +
222C TYR 3.7 1.2 + - - -
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Residues in contact with GLY 248 (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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244B GLU 2.8 17.4 + - - -
245B GLU* 5.9 0.4 - - - -
246B ARG 3.5 1.8 - - - -
247B GLN* 1.3 73.1 - - - +
249B LEU* 1.3 66.7 + - - +
284B TYR* 3.8 12.2 - - - -
139C HIS* 4.4 4.5 - - - -
141C ASN* 3.6 23.2 - - - +
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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
------------------------------------------------------------
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