Contacts of the helix formed by residues 217 - 233 (chain B) in PDB entry 6HBU
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 ASP 217 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80A GLY 3.8 2.5 - - - +
81A PRO* 3.3 26.2 - - - +
82A THR* 3.9 4.2 - - - +
243A HIS* 3.4 26.7 + - + +
244A GLN* 3.1 18.0 + - - +
295A LEU* 3.5 22.9 - - + +
299A ASN* 3.4 14.6 + - - -
216B LEU* 1.3 72.7 - - - +
218B SER* 1.3 64.7 + - - +
219B SER* 3.9 6.2 + - - -
220B THR* 2.9 26.7 + - - -
221B ALA* 3.2 12.6 + - - +
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Residues in contact with SER 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A GLN* 3.8 27.3 + - - +
245A PRO* 5.0 1.2 - - - +
291A ALA 4.2 7.9 + - - -
292A ASP* 2.8 33.2 + - - -
295A LEU* 4.4 12.0 - - - +
296A ASP* 5.5 0.4 - - - -
217B ASP* 1.3 78.2 - - - +
219B SER* 1.3 59.3 + - - +
221B ALA* 4.3 1.9 - - - +
222B ASN 3.7 9.2 + - - -
246B ARG* 3.3 35.2 + - - +
249B ILE* 5.1 0.9 - - - +
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Residues in contact with SER 219 (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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295A LEU* 3.3 19.8 + - - +
296A ASP* 3.3 26.4 + - - -
299A ASN* 3.5 15.6 + - - +
305A VAL* 3.6 24.3 - - - +
217B ASP* 3.3 3.0 + - - -
218B SER* 1.3 78.5 - - - +
220B THR* 1.3 64.8 + - - +
221B ALA 3.3 0.9 - - - -
222B ASN* 3.6 3.4 + - - +
223B ALA* 3.2 20.4 + - - +
246B ARG* 4.5 3.1 + - - +
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Residues in contact with THR 220 (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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81A PRO* 5.4 0.5 - - - +
82A THR* 4.2 9.4 + - - -
299A ASN* 3.4 13.4 + - - +
304A ALA* 4.9 8.4 - - + +
305A VAL* 5.1 2.1 - - - +
168B LEU 4.6 2.2 - - - +
193B ARG* 3.6 42.4 + - - +
216B LEU* 4.3 13.0 - - + -
217B ASP* 2.9 20.0 + - - -
219B SER* 1.3 74.5 - - - +
221B ALA* 1.3 59.3 + - - +
223B ALA* 3.0 5.9 + - - -
224B VAL* 2.8 32.3 + - + +
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Residues in contact with ALA 221 (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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244A GLN* 3.4 17.5 - - - +
213B THR* 3.7 24.5 - - + -
216B LEU* 4.2 9.3 - - + +
217B ASP 3.2 20.6 + - - +
218B SER 4.5 1.6 - - - +
220B THR* 1.3 79.3 - - - +
222B ASN* 1.3 60.6 + - - +
224B VAL* 3.8 0.4 - - - +
225B LEU* 3.1 30.0 + - - +
249B ILE* 3.9 13.2 - - + +
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Residues in contact with ASN 222 (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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218B SER 3.7 7.7 + - - +
219B SER 3.6 6.2 + - - +
220B THR 3.3 0.2 - - - -
221B ALA* 1.3 78.4 - - - +
223B ALA* 1.3 58.4 + - - +
225B LEU 3.5 0.4 + - - +
226B LEU* 2.9 49.1 + - + +
246B ARG* 2.7 38.6 + - - +
248B SER* 3.3 26.7 + - - -
249B ILE* 4.0 16.2 - - + +
252B LEU* 4.4 3.4 - - - +
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Residues in contact with ALA 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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304A ALA* 3.6 39.9 - - + +
305A VAL* 4.1 8.3 - - + +
308A ASN* 2.9 31.5 + - + +
167B GLU 4.9 1.2 - - - +
219B SER 3.2 12.7 + - - +
220B THR* 3.0 9.3 + - - +
222B ASN* 1.3 79.3 - - - +
224B VAL* 1.3 62.7 + - - +
226B LEU* 4.0 2.5 - - - -
227B LEU* 3.3 9.9 + - - +
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Residues in contact with VAL 224 (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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167B GLU 6.1 0.7 - - - +
168B LEU* 4.3 21.8 - - + +
193B ARG* 4.7 4.7 - - + -
196B ILE* 4.4 23.8 - - + -
212B PRO* 4.9 5.6 - - + -
213B THR* 5.0 0.9 - - + -
216B LEU* 3.8 20.9 - - + -
220B THR* 2.8 25.8 + - + +
221B ALA* 3.8 7.6 - - - +
222B ASN 3.2 0.2 - - - -
223B ALA* 1.3 77.9 - - - +
225B LEU* 1.3 64.7 + - + +
227B LEU* 3.1 11.7 + - + +
228B LEU* 3.0 41.0 + - + +
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Residues in contact with LEU 225 (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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75B LEU* 4.4 10.8 - - + +
212B PRO* 4.9 4.9 - - + -
213B THR* 3.6 30.7 - - + -
221B ALA 3.1 15.3 + - - +
222B ASN 4.4 0.9 - - - +
224B VAL* 1.3 80.1 - - + +
226B LEU* 1.3 61.3 + - - +
228B LEU* 3.7 16.4 - - + +
229B LYS* 2.8 28.9 + - - +
240B PHE* 3.6 31.9 - - + -
242B ILE* 4.4 7.0 - - + -
249B ILE* 3.7 26.0 - - + +
252B LEU* 3.7 15.2 - - + +
253B PHE* 3.9 7.4 - - + -
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Residues in contact with LEU 226 (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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308A ASN* 4.2 21.9 - - + +
309A ARG* 3.7 42.4 - - + +
222B ASN* 2.9 41.8 + - - +
223B ALA* 4.8 1.6 - - - -
225B LEU* 1.3 74.6 - - - +
227B LEU* 1.3 60.3 + - - +
229B LYS* 3.8 5.2 - - + +
230B ARG* 3.1 27.9 + - - +
252B LEU* 3.9 27.4 - - + -
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Residues in contact with LEU 227 (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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308A ASN* 3.9 17.4 - - - +
167B GLU* 3.6 28.7 - - + +
168B LEU* 3.9 30.5 - - + -
200B LEU* 4.2 19.5 - - + -
223B ALA 3.3 14.9 + - - +
224B VAL* 3.1 13.8 + - + +
226B LEU* 1.3 77.6 - - - +
228B LEU* 1.3 59.4 + - + +
230B ARG* 3.5 33.1 + - - +
231B MET* 3.1 37.6 + - + +
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Residues in contact with LEU 228 (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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75B LEU* 4.0 15.7 - - + -
196B ILE* 5.9 0.7 - - + -
200B LEU* 4.6 15.0 - - + -
207B LEU* 4.1 24.5 - - + -
209B LEU* 4.1 30.3 - - + -
212B PRO* 5.1 3.4 - - + -
224B VAL* 3.0 28.9 + - + +
225B LEU* 3.8 22.2 - - + +
226B LEU 3.3 0.2 - - - -
227B LEU* 1.3 76.2 - - + +
229B LYS* 1.3 56.2 + - - +
231B MET* 3.1 13.1 + - - -
232B SER* 2.7 36.2 + - - -
238B ILE* 3.3 13.6 - - + +
240B PHE* 5.1 3.4 - - + -
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Residues in contact with LYS 229 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75B LEU* 4.0 10.2 - - + +
225B LEU 2.8 18.8 + - - +
226B LEU* 4.1 10.1 - - + +
228B LEU* 1.3 74.6 - - - +
230B ARG* 1.3 62.6 + - - +
232B SER* 2.9 21.9 + - - +
233B LYS* 3.3 38.6 - - - +
252B LEU* 3.2 44.1 + - + +
254B ASP* 3.1 34.1 + - - -
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Residues in contact with ARG 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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307A LEU 5.6 3.0 + - - -
308A ASN* 4.5 8.9 + - - +
163B ARG* 6.0 0.4 - - - +
167B GLU* 3.2 28.5 + - - -
226B LEU 3.1 19.0 + - - +
227B LEU* 3.5 27.9 + - - +
228B LEU 3.3 0.2 - - - -
229B LYS* 1.3 77.0 - - - +
231B MET* 1.3 66.7 + - - +
233B LYS* 3.8 20.0 + - - +
234B GLN* 3.8 32.3 + - - +
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Residues in contact with MET 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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200B LEU* 3.8 38.4 - - + +
203B ASP* 5.9 8.1 - - + -
204B PRO 5.9 0.2 - - - +
207B LEU* 4.2 24.7 - - - -
227B LEU* 3.1 28.4 + - + +
228B LEU* 3.1 18.5 + - + +
230B ARG* 1.3 83.2 - - - +
232B SER* 1.3 61.9 + - - +
233B LYS 3.3 0.7 - - - -
234B GLN* 3.3 21.8 + - - +
236B ARG* 3.4 34.0 - - + +
238B ILE* 4.4 6.1 - - + -
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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
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73B PRO 4.9 1.6 - - - +
74B GLY* 3.3 38.3 + - - -
75B LEU* 4.4 2.8 - - - +
228B LEU 2.7 18.0 + - - -
229B LYS* 2.9 29.2 + - - +
231B MET* 1.3 71.4 - - - +
233B LYS* 1.3 60.1 + - - +
234B GLN 3.2 2.7 - - - -
235B GLY* 3.4 12.0 + - - -
236B ARG 3.5 15.2 - - - +
238B ILE* 3.8 8.7 - - - +
254B ASP* 4.7 1.6 + - - -
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Residues in contact with LYS 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 LYS* 3.3 44.9 + - - +
230B ARG* 4.1 13.1 - - - +
231B MET 3.3 1.0 - - - -
232B SER* 1.3 78.0 + - - +
234B GLN* 1.3 61.8 + - - +
235B GLY 3.3 1.5 + - - -
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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