Contacts of the helix formed by residues 217 - 233 (chain B) in PDB entry 1B3U
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
---------------------------
Residue Dist Surf HB Arom Phob DC
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215B GLU 4.2 3.9 - - - +
216B GLN* 1.3 66.9 - - - +
218B SER* 1.3 58.6 + - - +
219B VAL 2.9 10.8 + - - -
220B ARG* 3.1 31.6 + - - +
221B LEU* 2.9 28.7 + - - +
254B LYS* 5.5 2.3 - - - -
255B SER* 3.9 22.1 - - - +
257B ARG* 4.2 20.2 + - + +
258B VAL* 5.6 1.8 - - + +
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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
----------------------------------------------------------
182B ARG* 3.2 44.7 + - - -
216B GLN* 4.4 8.8 - - - +
217B ASP* 1.3 76.0 - - - +
219B VAL* 1.3 57.7 + - - +
221B LEU* 4.0 16.8 - - - +
222B LEU* 3.4 17.2 - - - +
257B ARG* 4.2 18.2 - - - +
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Residues in contact with VAL 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B PRO* 4.2 10.3 - - + +
181B ARG* 4.4 16.8 - - + +
182B ARG* 3.6 24.5 - - + +
185B ALA* 4.8 4.1 - - + +
211B LEU* 4.0 28.3 - - + +
214B ASP* 3.6 33.9 - - + +
216B GLN* 3.1 17.6 + - + +
217B ASP 2.9 0.8 - - - -
218B SER* 1.3 78.9 - - - +
220B ARG* 1.3 67.5 + - - +
221B LEU 3.1 1.1 - - - -
222B LEU* 3.0 19.9 + - - +
223B ALA* 3.7 3.3 + - - +
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Residues in contact with ARG 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B LEU 3.7 8.5 - - - -
212B ALA* 3.1 25.9 - - - +
213B SER* 3.7 4.7 - - - +
214B ASP 2.7 58.3 + - - +
215B GLU* 3.4 16.8 + - - +
216B GLN 3.3 2.0 + - - +
217B ASP* 3.1 31.6 + - - +
219B VAL* 1.3 76.8 - - - +
221B LEU* 1.3 63.5 + - - +
223B ALA* 3.0 20.1 + - - +
224B VAL* 4.2 2.1 + - - +
253B ASP* 2.9 41.5 + - - +
254B LYS* 4.2 19.8 - - - +
255B SER* 3.7 7.1 - - - -
258B VAL* 4.7 12.0 - - + +
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Residues in contact with LEU 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B ASP 2.9 14.1 + - - +
218B SER* 4.0 10.1 - - - +
220B ARG* 1.3 78.8 - - - +
222B LEU* 1.3 82.7 + - + +
223B ALA 3.3 0.9 + - - -
224B VAL* 3.6 18.0 + - - +
225B GLU 4.8 0.3 + - - -
257B ARG* 3.8 45.5 - - + +
258B VAL* 4.3 18.1 - - + +
261B MET* 3.8 38.3 - - + +
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Residues in contact with LEU 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B ARG* 3.4 50.7 - - + +
185B ALA* 4.0 18.4 - - + +
186B SER* 4.9 9.3 - - - +
218B SER 3.4 17.3 - - - +
219B VAL 3.0 8.3 + - - +
221B LEU* 1.3 91.7 - - + +
223B ALA* 1.3 62.4 + - - +
224B VAL 3.3 0.8 + - - -
225B GLU* 3.6 16.1 + - - +
226B ALA* 3.6 9.9 + - - +
261B MET* 6.2 0.9 - - + -
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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
----------------------------------------------------------
185B ALA* 5.3 3.3 - - - +
208B PHE* 3.5 14.9 - - + +
211B LEU* 4.6 6.5 - - + -
212B ALA* 3.8 35.4 - - + +
219B VAL 3.7 2.9 + - - +
220B ARG 3.0 17.4 + - - +
222B LEU* 1.3 76.7 - - - +
224B VAL* 1.3 58.5 + - - +
226B ALA* 3.0 11.5 + - - +
227B CYS 2.8 24.4 + - - -
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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
----------------------------------------------------------
220B ARG 4.7 1.6 - - - +
221B LEU 3.7 15.3 - - - +
222B LEU 3.3 0.4 - - - -
223B ALA* 1.3 77.4 - - + +
225B GLU* 1.3 63.5 + - - +
227B CYS* 3.0 24.0 + - + +
228B VAL* 3.2 8.7 + - - +
247B LEU* 5.4 2.9 - - + -
250B ALA* 4.5 8.1 - - + -
258B VAL* 4.1 20.2 - - + +
261B MET* 3.8 37.5 - - + +
262B VAL* 3.9 21.3 - - + -
265B LYS* 4.6 11.7 - - + -
269B LEU* 4.6 11.0 - - + -
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Residues in contact with GLU 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B SER* 5.3 9.0 - - - +
189B GLY 5.6 1.2 + - - -
221B LEU 4.8 0.2 + - - -
222B LEU* 3.6 11.6 + - - +
223B ALA 3.3 0.2 - - - -
224B VAL* 1.3 79.5 - - - +
226B ALA* 1.3 67.8 + - - +
228B VAL* 3.2 19.6 + - + +
229B ASN* 3.2 34.4 + - - +
261B MET* 5.7 5.7 - - + +
265B LYS* 3.8 27.8 - - + +
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Residues in contact with ALA 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B ALA* 4.3 16.6 - - + +
188B LEU* 4.4 22.9 - - + -
189B GLY 4.9 4.0 - - - +
208B PHE* 4.3 5.4 - - + -
222B LEU 3.6 6.1 + - - +
223B ALA* 3.0 16.6 + - - +
225B GLU* 1.3 86.1 + - - +
227B CYS* 1.3 57.6 + - - +
229B ASN* 3.5 5.9 + - - +
230B ILE* 3.0 36.9 + - + +
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Residues in contact with CYS 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B PHE* 3.6 20.6 - - + -
223B ALA 2.8 12.1 + - - +
224B VAL* 3.0 17.2 + - - +
226B ALA* 1.3 75.6 - - - +
228B VAL* 1.3 64.0 + - - +
230B ILE* 3.4 3.1 + - - +
231B ALA* 3.0 24.3 + - - +
243B VAL* 3.6 29.1 - - - +
247B LEU* 4.1 30.3 - - + -
269B LEU* 4.3 6.5 - - + -
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Residues in contact with VAL 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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224B VAL 3.2 8.9 + - - +
225B GLU* 3.2 14.6 + - + +
227B CYS* 1.3 79.2 - - - +
229B ASN* 1.3 73.1 + - - +
231B ALA* 3.4 3.2 + - - +
232B GLN* 3.1 38.3 + - - +
265B LYS* 4.5 10.1 - - + -
268B GLU* 4.0 35.7 - - + +
269B LEU* 3.5 31.4 - - + -
272B ALA* 3.8 4.5 - - + +
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Residues in contact with ASN 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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189B GLY* 3.7 30.4 - - - +
190B GLU 4.7 1.0 + - - -
193B LYS* 5.7 10.1 - - + +
225B GLU* 3.2 35.0 + - - +
226B ALA 3.8 6.1 - - - +
227B CYS 3.3 0.4 - - - -
228B VAL* 1.3 86.8 - - - +
230B ILE* 1.3 63.2 + - - +
232B GLN* 3.1 30.5 + - - +
233B LEU* 3.5 18.0 - - + +
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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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188B LEU* 4.6 7.2 - - + -
189B GLY* 5.4 2.9 - - - -
192B ALA* 4.9 9.2 - - + -
200B VAL* 4.9 9.0 - - + -
204B ILE* 3.8 19.5 - - + -
205B ILE* 4.1 15.3 - - + -
208B PHE* 3.5 40.8 - - + -
226B ALA* 3.0 20.1 + - + +
227B CYS* 4.0 4.3 - - - +
229B ASN* 1.3 76.9 - - + +
231B ALA* 1.3 63.1 + - - +
233B LEU* 3.1 21.5 + - - +
234B LEU* 3.4 17.1 + - + +
243B VAL* 4.1 20.2 - - + -
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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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227B CYS* 3.0 19.5 + - - +
228B VAL* 3.7 4.5 - - - +
229B ASN 3.2 0.2 - - - -
230B ILE* 1.3 77.8 - - - +
232B GLN* 1.3 60.6 + - - +
233B LEU 3.0 1.3 + - - -
234B LEU 3.4 16.3 + - - +
239B LEU* 3.9 27.1 - - + +
243B VAL* 4.7 11.6 - - + +
269B LEU* 6.4 0.9 - - + -
272B ALA* 4.0 26.2 - - + +
273B VAL* 4.7 4.9 - - + +
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Residues in contact with GLN 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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193B LYS* 6.0 1.6 - - - +
228B VAL* 3.1 28.6 - - - +
229B ASN* 3.1 27.4 + - - +
231B ALA* 1.3 74.8 - - - +
233B LEU* 1.3 64.4 + - + +
234B LEU 3.7 1.9 - - - +
268B GLU* 5.3 1.6 + - - +
271B LYS* 6.2 1.6 - - - +
272B ALA* 3.7 20.6 - - + +
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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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189B GLY 5.1 0.2 - - - +
192B ALA* 4.0 39.5 - - + +
193B LYS* 4.0 30.1 - - + +
197B LEU* 3.8 16.5 - - + +
200B VAL* 5.0 14.4 - - + -
229B ASN* 3.5 16.8 - - + +
230B ILE* 3.5 10.3 - - - +
231B ALA 3.0 0.8 - - - -
232B GLN* 1.3 86.4 - - + +
234B LEU* 1.3 64.4 + - + +
235B PRO* 4.3 0.7 - - - +
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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