Contacts of the helix formed by residues 222 - 241 (chain B) in PDB entry 3HB8
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 GLY 222 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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214B GLN* 5.1 0.4 - - - -
218B ASP* 3.4 9.3 + - - -
221B LEU* 1.3 76.3 - - - +
223B VAL* 1.3 63.6 + - - +
224B PRO* 3.3 6.4 - - - +
225B PHE* 3.2 9.3 + - - +
226B ASN* 2.7 37.4 + - - +
314B EDO 3.6 15.2 + - - -
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Residues in contact with VAL 223 (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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33B TYR* 4.1 15.7 - - + -
36B GLN* 5.4 2.2 - - - +
65B TYR* 5.6 0.2 - - - +
214B GLN* 4.4 1.1 - - - +
217B GLY* 3.9 17.5 - - - -
218B ASP 3.0 19.0 + - - +
219B MET* 3.5 29.2 - - + -
222B GLY* 1.3 70.7 - - - +
224B PRO* 1.3 64.2 - - + +
226B ASN* 3.0 8.8 + - - +
227B ILE* 2.8 46.5 + - + +
250B HIS* 3.5 26.0 - - + +
252B LEU* 4.2 6.3 - - + -
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Residues in contact with PRO 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B TYR* 3.2 29.2 - - + +
72B PRO 5.3 1.0 - - - +
73B LEU* 5.4 0.2 - - - +
74B LEU* 3.3 28.5 + - + +
77B LYS* 3.5 23.6 - - - +
79B VAL* 4.3 10.4 - - + +
219B MET 3.4 10.5 - - - +
220B GLY 3.6 8.7 - - - +
222B GLY 3.5 9.4 - - - +
223B VAL* 1.3 96.6 - - + +
225B PHE* 1.3 58.9 + - - +
227B ILE* 3.6 7.9 + - + +
228B ALA* 3.4 18.5 + - - +
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Residues in contact with PHE 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B LYS* 5.2 0.2 - - - +
79B VAL* 4.0 13.9 - - + +
80B PHE* 3.8 29.4 - + + -
83B GLY 3.9 6.3 - - - -
84B VAL* 3.6 33.2 - - + +
87B GLU* 3.2 28.3 - - - -
108B ILE* 4.1 6.5 - - + -
221B LEU 5.6 0.2 - - - -
222B GLY* 3.2 13.2 + - - +
224B PRO* 1.3 76.2 - - - +
226B ASN* 1.3 72.6 + - - +
228B ALA* 3.1 5.9 + - - +
229B SER* 2.8 42.0 + - - -
314B EDO 3.7 40.8 - - - +
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Residues in contact with ASN 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B HIS* 2.9 36.2 + - + -
212B LEU* 4.8 3.1 - - + -
214B GLN* 2.9 34.6 + - - +
222B GLY* 2.7 26.5 + - - +
223B VAL* 3.4 5.1 + - - +
225B PHE* 1.3 82.7 - - - +
227B ILE* 1.3 67.6 + - - +
228B ALA 2.7 3.2 + - - -
229B SER* 2.9 18.2 + - - -
230B TYR* 3.1 17.5 + - - +
248B PHE* 5.2 1.6 - - - -
250B HIS* 4.8 2.7 - - - +
314B EDO 5.2 5.7 + - - -
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Residues in contact with ILE 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B TYR* 5.3 3.1 - - + -
65B TYR* 3.6 45.3 - - + +
72B PRO* 4.3 18.4 - - + +
74B LEU* 5.3 7.6 - - + -
223B VAL* 2.8 40.2 + - + +
224B PRO* 3.6 10.8 - - + +
226B ASN* 1.3 72.2 - - - +
228B ALA* 1.3 57.5 + - - +
231B ALA* 3.2 26.9 + - - +
248B PHE* 3.8 13.3 - - + -
250B HIS* 3.1 43.5 - - + +
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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
----------------------------------------------------------
71B PHE* 3.8 15.8 - - + -
72B PRO 4.4 4.4 + - - +
73B LEU* 4.0 25.1 - - + -
79B VAL* 4.7 0.2 - - + -
81B TRP* 5.0 1.1 - - + -
84B VAL* 3.7 17.0 - - + -
224B PRO 3.4 9.7 + - - +
225B PHE* 3.1 9.8 + - - +
226B ASN 2.7 1.0 + - - -
227B ILE* 1.3 78.4 - - - +
229B SER* 1.3 66.9 + - - +
231B ALA* 3.1 1.0 + - - +
232B LEU* 2.9 25.5 + - - +
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Residues in contact with SER 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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84B VAL* 3.2 17.9 - - - +
87B GLU* 4.1 6.6 + - - -
88B LEU* 3.6 14.7 - - - +
91B PHE* 5.9 4.0 - - - -
196B HIS* 5.8 0.9 - - - -
225B PHE* 2.8 42.4 + - - -
226B ASN* 2.9 13.2 + - - -
228B ALA* 1.3 73.2 - - - +
230B TYR* 1.3 66.5 + - - -
232B LEU* 3.3 5.2 - - - +
233B LEU* 3.1 19.5 + - - +
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Residues in contact with TYR 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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91B PHE* 6.1 1.7 - + - -
135B TYR* 4.7 4.7 - - - -
139B TRP* 3.7 22.7 + + - -
181B ALA* 6.0 0.3 - - - +
196B HIS* 3.5 46.5 + + - +
198B LEU 6.1 0.2 - - - -
199B CYS* 4.2 21.0 - - + -
210B CYS* 4.6 8.0 - - - -
212B LEU* 3.7 33.9 - - + +
226B ASN 3.1 9.3 + - - +
229B SER* 1.3 83.3 - - - +
231B ALA* 1.3 67.0 + - - +
232B LEU 3.1 1.6 - - - -
233B LEU* 3.0 31.0 + - + +
234B THR* 2.9 26.1 + - - -
248B PHE* 3.5 26.7 - + + -
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Residues in contact with ALA 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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67B LEU* 3.9 12.6 - - + -
71B PHE* 3.9 14.4 - - + -
72B PRO* 3.7 24.7 - - + -
227B ILE 3.2 21.8 + - - +
228B ALA 3.1 4.3 + - - +
230B TYR* 1.3 75.1 - - - +
232B LEU* 1.3 62.6 + - - +
234B THR* 3.2 9.7 + - - -
235B TYR* 3.1 25.3 + - - -
248B PHE* 4.6 9.5 - - + -
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Residues in contact with LEU 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B PHE* 3.8 11.5 - - + -
81B TRP* 3.7 30.7 - - + -
84B VAL* 4.5 3.4 - - + -
85B LEU* 3.8 31.2 - - + +
88B LEU* 3.5 23.1 - - + -
228B ALA 2.9 12.1 + - - +
229B SER 3.3 8.1 - - - +
231B ALA* 1.3 74.8 - - - +
233B LEU* 1.3 65.9 + - - +
235B TYR* 3.1 4.3 + - - +
236B MET* 2.9 31.8 + - + +
279B LEU* 3.8 21.1 - - + -
296B PHE* 4.0 20.0 - - + -
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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
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88B LEU* 3.7 19.0 - - + +
92B ILE* 4.9 1.8 - - + -
139B TRP* 3.8 27.8 - - + -
161B LEU* 4.6 7.0 - - + -
179B MET* 3.8 18.2 - - + -
201B PHE* 4.1 12.6 - - + -
210B CYS* 6.2 0.2 - - - -
229B SER 3.1 13.3 + - - +
230B TYR* 3.0 29.5 + - + +
232B LEU* 1.3 74.7 - - - +
234B THR* 1.3 63.1 + - - +
236B MET* 3.3 21.2 + - + +
237B ILE* 3.1 41.0 + - + +
288B ILE* 5.0 0.9 - - + -
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Residues in contact with THR 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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67B LEU* 3.5 27.5 - - + +
201B PHE* 4.7 5.6 - - - -
208B LEU* 3.5 34.8 - - + +
210B CYS* 3.2 30.5 - - + +
230B TYR 2.9 14.5 + - - -
231B ALA* 3.3 10.4 - - - -
233B LEU* 1.3 74.0 - - - +
235B TYR* 1.3 59.8 + - - +
237B ILE* 3.3 1.6 + - - -
238B ALA* 2.8 30.7 + - - +
245B PRO* 4.8 5.4 - - + -
248B PHE* 4.8 2.4 - - - -
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Residues in contact with TYR 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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67B LEU* 2.7 38.7 + - + -
69B ASP* 4.5 1.7 + - - -
70B GLU 2.8 21.0 + - - -
71B PHE* 4.0 20.6 - + - +
231B ALA 3.1 18.7 + - - +
232B LEU 3.4 8.1 - - - +
234B THR* 1.3 77.8 - - - +
236B MET* 1.3 64.5 + - - +
238B ALA* 3.2 8.5 + - - +
239B HIS* 3.0 24.4 + - - +
245B PRO* 3.7 28.2 - - + +
278B LYS* 5.8 0.2 - - - -
279B LEU* 3.5 45.6 + - + -
281B ILE* 4.2 13.2 - - + +
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Residues in contact with MET 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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88B LEU* 3.7 27.4 - - + -
89B LEU* 4.9 7.4 - - - -
92B ILE* 3.1 36.1 - - + -
232B LEU* 2.9 31.7 + - + +
233B LEU* 3.7 10.5 - - + +
235B TYR* 1.3 76.2 - - - +
237B ILE* 1.3 62.5 + - - +
239B HIS* 3.3 7.1 + - - +
240B ILE* 3.2 26.7 + - - +
281B ILE* 4.9 2.0 - - - -
288B ILE* 3.8 10.5 - - + -
291B PHE* 3.9 23.4 - - + -
296B PHE* 4.0 29.2 - - + -
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Residues in contact with ILE 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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161B LEU* 4.4 9.0 - - + -
164B VAL* 4.7 1.8 - - + -
165B ILE* 3.4 32.5 - - + -
168B ILE* 3.7 18.6 - - + -
201B PHE* 3.6 33.9 - - + -
208B LEU* 3.7 16.2 - - + -
233B LEU* 3.1 34.5 + - + +
234B THR 3.8 2.5 - - - +
236B MET* 1.3 72.8 - - - +
238B ALA* 1.3 58.1 + - - +
240B ILE* 3.3 7.9 - - - +
241B THR* 2.7 37.9 + - + +
288B ILE* 4.4 7.0 - - + -
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Residues in contact with ALA 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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208B LEU* 3.5 14.5 - - + +
234B THR 2.8 17.8 + - - +
235B TYR* 3.3 10.1 - - - +
237B ILE* 1.3 77.2 - - - +
239B HIS* 1.3 56.8 + - - +
241B THR* 2.9 19.9 + - - -
242B GLY 2.9 16.6 + - - -
243B LEU 3.1 28.2 + - - +
244B LYS 4.5 0.7 - - - -
245B PRO* 4.3 16.8 - - + -
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Residues in contact with HIS 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 TYR 3.0 12.6 + - - +
236B MET* 3.3 9.4 + - - +
238B ALA* 1.3 76.6 - - - +
240B ILE* 1.3 62.9 + - + +
241B THR 3.5 0.7 + - - -
242B GLY* 3.7 8.1 + - - -
243B LEU 4.3 1.1 + - - -
281B ILE* 3.8 29.1 - - + +
283B ARG 3.5 15.7 + - - -
284B LYS* 3.7 25.3 + - + +
285B VAL* 3.0 49.7 + - + +
291B PHE* 4.4 3.6 - + + -
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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
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162B GLN* 5.8 0.4 - - - +
165B ILE* 3.7 34.5 - - + -
169B LYS* 3.4 21.1 + - - +
236B MET 3.2 10.5 + - - +
237B ILE* 3.3 14.1 - - - +
239B HIS* 1.3 78.8 - - + +
241B THR* 1.3 60.9 + - + +
242B GLY 3.5 0.7 - - - -
284B LYS* 6.1 0.7 - - - +
285B VAL 3.9 11.7 - - - +
286B GLU 3.3 28.6 - - - +
287B LYS* 4.1 2.9 - - - +
288B ILE* 4.0 31.9 - - + +
291B PHE* 3.9 20.0 - - + -
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Residues in contact with THR 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B ILE* 4.0 26.2 - - + +
168B ILE* 4.0 26.0 - - + +
169B LYS* 4.2 20.7 - - + +
208B LEU* 4.7 0.5 - - - +
237B ILE* 2.7 29.0 + - + +
238B ALA* 2.9 13.2 + - - -
240B ILE* 1.3 81.2 - - - +
242B GLY* 1.3 60.8 + - - +
243B LEU* 3.5 19.9 + - - +
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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
------------------------------------------------------------
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