Contacts of the helix formed by residues 215 - 234 (chain B) in PDB entry 4O46
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 SER 215 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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170B PRO* 3.7 26.0 - - - +
212B ASN* 3.0 25.8 + - - +
214B ASP* 1.3 79.5 - - - +
216B TYR* 1.4 62.1 + - - +
217B LYS* 3.3 3.1 - - - +
218B ASP* 3.3 15.3 + - - +
219B SER* 3.1 24.1 + - - -
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Residues in contact with TYR 216 (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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211B LEU* 4.1 30.0 - - + +
212B ASN 2.8 19.0 + - - +
213B GLU* 3.6 24.5 - - - -
214B ASP 3.8 0.4 - - - -
215B SER* 1.4 71.6 - - - +
217B LYS* 1.4 84.9 + - + +
219B SER* 3.3 2.8 + - - -
220B THR* 3.0 43.7 + - + +
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Residues in contact with LYS 217 (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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215B SER* 3.3 1.2 - - - -
216B TYR* 1.4 110.1 - - + +
218B ASP* 1.3 67.0 + - - +
220B THR* 3.1 17.7 + - - -
221B LEU* 3.2 15.8 + - - +
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Residues in contact with ASP 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B PRO* 4.1 16.4 - - + -
214B ASP 4.3 4.2 - - - +
215B SER* 3.3 23.3 + - - +
216B TYR 3.3 0.4 - - - -
217B LYS* 1.3 79.1 - - - +
219B SER* 1.4 60.8 + - - +
221B LEU* 3.6 9.3 + - - +
222B ILE* 3.3 31.3 + - + +
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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
----------------------------------------------------------
168B THR 2.7 28.1 + - - -
170B PRO* 3.4 13.9 - - - +
173B LEU* 3.6 14.4 - - - +
211B LEU* 3.5 24.3 - - - +
215B SER* 3.1 14.7 + - - -
216B TYR 3.6 2.7 - - - -
218B ASP* 1.4 74.8 - - - +
220B THR* 1.3 59.2 + - - +
222B ILE* 3.3 3.4 + - - +
223B MET* 3.0 31.9 + - - +
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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
----------------------------------------------------------
208B LEU* 5.5 2.5 - - + -
211B LEU* 4.6 19.1 - - + -
216B TYR* 3.0 30.1 + - + +
217B LYS* 3.1 16.5 + - - -
219B SER* 1.3 70.4 - - - +
221B LEU* 1.3 58.2 + - - +
223B MET* 3.3 16.9 + - - +
224B GLN* 3.0 37.0 + - - +
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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
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217B LYS 3.2 19.1 + - - +
218B ASP* 3.7 10.8 - - - +
219B SER 3.3 0.2 - - - -
220B THR* 1.3 76.9 + - - +
222B ILE* 1.4 63.0 + - + +
224B GLN* 3.3 22.0 + - + +
225B LEU* 3.3 30.9 + - + +
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Residues in contact with ILE 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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170B PRO* 3.3 36.6 - - + +
173B LEU* 3.6 34.5 - - + +
174B GLY* 3.8 7.4 - - - +
177B LEU* 3.9 22.7 - - + -
218B ASP* 3.3 20.4 + - + +
219B SER* 3.3 6.3 + - - +
221B LEU* 1.4 75.5 - - + +
223B MET* 1.3 53.6 + - - +
225B LEU* 3.0 12.5 + - + +
226B LEU* 2.8 35.6 + - + +
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Residues in contact with MET 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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168B THR* 5.6 0.2 - - - -
173B LEU* 4.0 21.5 - - + -
201B PHE* 3.3 29.8 - - + +
204B ALA* 3.8 22.4 - - + -
205B ILE* 3.6 37.9 - - + -
208B LEU* 3.9 19.3 - - + -
211B LEU* 5.2 3.4 - - - -
219B SER* 3.0 23.5 + - - +
220B THR* 3.5 21.3 - - - +
222B ILE* 1.3 74.9 - - - +
224B GLN* 1.4 61.8 + - + +
226B LEU* 3.4 8.7 + - - +
227B ARG* 3.1 18.0 + - - +
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Residues in contact with GLN 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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201B PHE* 5.5 0.2 - - - -
220B THR* 3.0 20.1 + - - +
221B LEU* 3.4 26.5 - - + +
222B ILE 3.2 0.2 - - - -
223B MET* 1.4 75.2 - - - +
225B LEU* 1.4 52.7 + - + +
227B ARG* 3.2 6.7 + - - +
228B ASP* 2.8 45.5 + - - +
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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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177B LEU* 3.8 31.6 - - + -
221B LEU* 3.3 21.0 + - + +
222B ILE* 3.0 13.8 + - + +
224B GLN* 1.4 74.9 - - + +
226B LEU* 1.4 60.1 + - - +
228B ASP* 3.6 14.5 - - + +
229B ASN* 2.9 39.5 + - - +
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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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173B LEU* 3.9 32.1 - - + +
176B ALA 4.3 2.9 - - - -
177B LEU* 3.9 35.9 - - + +
180B SER* 4.6 0.4 - - - +
197B ALA* 3.8 37.4 - - + +
200B ALA* 4.4 11.9 - - + -
201B PHE* 4.4 12.8 - - + +
222B ILE* 2.8 23.3 + - + +
223B MET* 3.5 13.2 - - - +
225B LEU* 1.4 77.0 - - - +
227B ARG* 1.4 54.9 + - - +
229B ASN* 4.0 3.3 - - - +
230B LEU* 3.2 33.3 + - - +
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Residues in contact with ARG 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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201B PHE* 3.4 42.8 - - + -
223B MET 3.1 13.6 + - - +
224B GLN* 3.7 8.5 - - - +
226B LEU* 1.4 75.5 - - - +
228B ASP* 1.4 55.4 + - - +
230B LEU* 3.2 8.7 + - + +
231B THR* 2.7 49.6 + - - +
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Residues in contact with ASP 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B GLN* 2.8 28.3 + - - +
225B LEU* 3.4 18.7 + - + +
227B ARG* 1.4 79.7 - - - +
229B ASN* 1.4 58.2 + - - +
231B THR* 3.4 7.2 + - - -
232B LEU* 3.1 28.6 + - - +
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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
----------------------------------------------------------
177B LEU* 3.4 26.3 + - - +
180B SER* 4.9 0.6 + - - +
181B VAL* 3.6 23.2 - - - +
197B ALA* 5.8 0.7 - - + -
225B LEU* 2.9 21.1 + - - +
226B LEU* 4.0 5.4 - - - +
228B ASP* 1.4 74.8 - - - +
230B LEU* 1.3 55.8 + - - +
232B LEU* 3.3 10.3 + - - +
233B TRP* 2.8 64.8 + - + +
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Residues in contact with LEU 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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194B CYS* 3.9 30.7 - - + +
197B ALA* 3.7 13.7 - - + +
198B LYS* 3.5 43.1 - - + +
201B PHE* 5.1 5.6 - - + -
226B LEU 3.2 21.4 + - - +
227B ARG* 3.2 9.2 + - + +
229B ASN* 1.3 75.7 - - - +
231B THR* 1.4 53.5 + - - +
233B TRP* 3.7 5.7 - - + +
234B THR* 2.7 53.8 + - + +
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Residues in contact with THR 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 ARG* 2.7 36.1 + - - +
228B ASP* 3.6 8.4 + - - -
230B LEU* 1.4 71.1 - - - +
232B LEU* 1.3 61.2 + - - +
234B THR* 3.6 6.6 + - - -
235B SER* 3.2 23.7 + - - -
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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
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184B TYR* 5.3 2.4 + - + -
228B ASP 3.1 13.8 + - - +
229B ASN* 3.3 11.6 + - - +
231B THR* 1.3 77.2 - - - +
233B TRP* 1.3 79.9 + - + +
235B SER* 3.4 20.0 + - - -
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Residues in contact with TRP 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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180B SER* 3.6 33.7 - - - -
181B VAL* 3.9 10.3 - - + -
184B TYR* 3.4 63.0 + + + -
185B GLU* 6.1 1.8 - - + +
190B PRO* 5.9 1.0 - - - +
193B ALA* 3.6 28.0 - - + -
194B CYS* 3.7 31.5 - - - -
197B ALA* 4.2 8.3 - - + -
229B ASN* 2.8 51.7 + - + +
230B LEU* 3.4 4.9 + - - +
232B LEU* 1.3 90.9 - - + +
234B THR* 1.3 59.7 + - - +
235B SER 3.3 2.1 + - - -
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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
----------------------------------------------------------
194B CYS* 4.1 18.4 - - + -
230B LEU* 2.7 37.6 + - + +
231B THR* 3.6 8.1 + - - -
233B TRP* 1.3 75.5 - - - +
235B SER* 1.4 61.7 + - - +
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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
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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