Contacts of the helix formed by residues 215 - 234 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170E PRO* 4.1 23.7 - - - +
212E ASN* 3.0 22.7 + - - +
214E ASP* 1.4 79.7 - - - +
216E TYR* 1.4 59.9 + - - +
217E LYS 3.4 2.0 - - - -
218E ASP* 3.3 15.1 + - - +
219E SER* 3.1 26.0 + - - -
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Residues in contact with TYR 216 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211E LEU* 4.1 29.3 - - + +
212E ASN 2.8 17.7 + - - +
213E GLU* 3.6 23.8 - - - -
214E ASP 3.8 0.6 - - - -
215E SER* 1.4 69.8 - - - +
217E LYS* 1.4 105.4 + - + +
219E SER* 3.4 2.6 + - - -
220E THR* 3.0 43.9 + - + +
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Residues in contact with LYS 217 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216E TYR* 1.4 119.4 + - + +
218E ASP* 1.3 61.8 + - - +
220E THR* 3.2 8.2 + - - -
221E LEU* 3.1 30.8 + - - +
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Residues in contact with ASP 218 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170E PRO* 4.0 18.8 - - + -
214E ASP 3.6 7.8 - - - +
215E SER* 3.3 27.5 - - - +
216E TYR 3.3 0.4 - - - -
217E LYS* 1.3 83.2 + - - +
219E SER* 1.3 59.3 - - - +
221E LEU* 3.8 5.7 - - - +
222E ILE* 3.5 25.6 + - - +
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Residues in contact with SER 219 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168E THR 2.7 28.5 + - - -
170E PRO* 3.5 12.7 - - - +
173E LEU* 3.7 12.7 - - - +
211E LEU* 3.6 23.4 - - - +
215E SER* 3.1 17.6 + - - -
216E TYR 3.4 0.2 + - - -
218E ASP* 1.3 73.4 - - - +
220E THR* 1.4 60.2 + - - +
222E ILE* 3.1 7.3 + - - +
223E MET* 3.0 30.9 + - - +
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Residues in contact with THR 220 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208E LEU* 5.5 2.7 - - + -
211E LEU* 4.6 17.5 - - + -
216E TYR* 3.0 30.3 + - + +
217E LYS* 3.2 14.6 + - - +
219E SER* 1.4 74.8 - - - +
221E LEU* 1.4 55.3 + - - +
223E MET* 3.3 17.8 + - + +
224E GLN* 2.9 36.8 + - - +
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Residues in contact with LEU 221 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217E LYS 3.1 20.0 + - - +
218E ASP* 3.8 8.1 - - - +
219E SER 3.2 0.4 - - - -
220E THR* 1.4 76.2 + - - +
222E ILE* 1.4 61.3 + - + +
224E GLN* 3.6 12.0 - - - +
225E LEU* 3.4 26.4 + - - +
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Residues in contact with ILE 222 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170E PRO* 3.3 36.6 - - + +
173E LEU* 3.6 33.9 - - + +
174E GLY* 3.8 6.7 - - - +
177E LEU* 3.9 23.6 - - + -
218E ASP 3.5 17.2 + - - +
219E SER 3.1 6.1 + - - +
221E LEU* 1.4 75.3 - - + +
223E MET* 1.3 54.7 + - - +
224E GLN 3.2 0.2 - - - -
225E LEU* 3.0 11.6 + - + +
226E LEU* 2.8 34.6 + - + +
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Residues in contact with MET 223 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168E THR* 5.5 0.7 - - - -
173E LEU* 4.0 21.8 - - + -
201E PHE* 3.3 30.4 - - + +
204E ALA* 3.8 22.2 - - + -
205E ILE* 3.6 37.0 - - + -
208E LEU* 3.9 20.2 - - + -
211E LEU* 5.1 3.4 - - - -
219E SER* 3.0 23.0 + - - +
220E THR* 3.3 22.9 + - + +
222E ILE* 1.3 74.5 - - - +
224E GLN* 1.4 57.0 + - - +
226E LEU* 3.4 7.7 + - - -
227E ARG* 3.1 22.0 + - - +
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Residues in contact with GLN 224 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201E PHE* 5.5 0.2 - - - -
220E THR* 2.9 23.3 + - - +
221E LEU* 3.6 10.8 - - - +
223E MET* 1.4 74.4 - - - +
225E LEU* 1.4 51.8 + - + +
227E ARG* 3.2 7.7 + - - +
228E ASP* 2.8 48.4 + - - +
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Residues in contact with LEU 225 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177E LEU* 3.8 30.5 - - + -
221E LEU* 3.4 15.5 + - + +
222E ILE* 3.0 13.8 + - + +
224E GLN* 1.4 76.7 - - + +
226E LEU* 1.4 58.6 + - - +
228E ASP* 3.8 12.9 - - + +
229E ASN* 2.9 41.3 + - - +
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Residues in contact with LEU 226 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173E LEU* 3.8 32.1 - - + +
176E ALA 4.3 2.9 - - - -
177E LEU* 3.9 35.7 - - + +
180E SER* 4.6 0.9 - - - +
197E ALA* 3.9 41.2 - - + +
200E ALA* 4.4 10.8 - - + -
201E PHE* 4.4 14.4 - - + +
222E ILE* 2.8 23.5 + - + +
223E MET* 3.5 13.5 - - - +
224E GLN 3.3 0.2 - - - -
225E LEU* 1.4 75.7 - - - +
227E ARG* 1.4 55.2 + - - +
229E ASN* 4.0 3.1 - - + +
230E LEU* 3.1 28.2 + - - +
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Residues in contact with ARG 227 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198E LYS* 5.6 2.8 - - - +
201E PHE* 3.4 45.3 - - + -
202E ASP* 5.4 3.0 + - - -
223E MET 3.1 13.6 + - - +
224E GLN* 3.2 8.7 + - - +
226E LEU* 1.4 74.0 - - - +
228E ASP* 1.4 54.8 + - - +
230E LEU* 3.2 24.3 + - - +
231E THR* 2.7 51.3 + - - +
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Residues in contact with ASP 228 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224E GLN* 2.8 39.9 + - - +
225E LEU* 3.4 16.3 + - + +
227E ARG* 1.4 72.4 - - - +
229E ASN* 1.3 59.9 + - - +
231E THR* 3.5 6.8 + - - -
232E LEU* 3.1 27.7 + - - +
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Residues in contact with ASN 229 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177E LEU* 3.4 25.9 - - - +
180E SER* 5.0 0.6 + - - +
181E VAL* 3.6 23.4 - - - +
197E ALA* 5.9 0.9 - - + -
225E LEU* 2.9 23.0 + - - +
226E LEU* 4.0 4.9 - - + +
228E ASP* 1.3 77.2 - - - +
230E LEU* 1.4 58.8 + - - +
232E LEU* 3.3 9.4 + - - +
233E TRP* 2.9 59.1 + - + +
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Residues in contact with LEU 230 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194E CYS* 3.4 46.4 - - + +
197E ALA* 3.8 13.5 - - + +
198E LYS* 3.9 32.3 - - + +
201E PHE* 5.7 3.4 - - + -
226E LEU 3.1 18.9 + - - +
227E ARG* 3.2 27.3 + - - +
229E ASN* 1.4 73.3 - - - +
231E THR* 1.4 53.6 + - - +
233E TRP* 3.5 4.5 + - + -
234E THR* 2.7 47.7 + - + +
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Residues in contact with THR 231 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227E ARG* 2.7 41.1 + - - +
228E ASP* 3.7 8.4 - - - -
230E LEU* 1.4 70.1 - - - +
232E LEU* 1.3 63.1 + - - +
234E THR* 3.5 6.9 + - - -
235E SER* 3.2 25.9 + - - -
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Residues in contact with LEU 232 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184E TYR* 5.9 1.3 - - + -
185E GLU* 5.9 2.0 - - - +
228E ASP 3.1 16.7 + - - +
229E ASN* 3.3 9.4 + - - +
231E THR* 1.3 76.3 - - - +
233E TRP* 1.3 78.3 + - + +
235E SER* 3.4 7.3 + - - -
236E ASP* 3.1 29.6 + - + +
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Residues in contact with TRP 233 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180E SER* 3.6 33.4 - - - -
181E VAL* 3.9 11.4 - - + -
184E TYR* 3.4 60.8 + + + -
185E GLU* 4.6 4.3 + - + -
190E PRO* 6.0 1.0 - - - +
193E ALA* 3.6 27.6 - - + -
194E CYS* 3.7 32.5 - - - -
197E ALA* 4.2 8.5 - - + -
229E ASN* 2.9 46.0 + - + +
230E LEU* 4.0 4.3 - - - +
232E LEU* 1.3 94.6 - - + +
234E THR* 1.4 58.2 + - - +
235E SER 3.3 0.7 - - - -
236E ASP* 3.8 3.2 + - - +
237E GLN* 3.4 24.3 + - - +
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Residues in contact with THR 234 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194E CYS* 4.2 18.6 - - + -
230E LEU* 2.7 31.3 + - + +
231E THR* 3.5 8.8 + - - -
233E TRP* 1.4 75.2 - - - +
235E SER* 1.4 60.1 + - - +
237E GLN* 4.0 17.6 + - + +
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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
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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