Contacts of the helix formed by residues 204 - 219 (chain E) in PDB entry 3J8B
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 PRO 204 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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202E SER* 3.1 12.7 - - - -
203E SER* 1.3 78.8 - - - -
205E LEU* 1.3 61.4 + - - +
206E GLN 3.0 0.4 - - - -
207E SER* 3.0 15.6 + - - -
208E LEU* 2.8 26.8 + - - +
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Residues in contact with LEU 205 (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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199E ASN 5.4 3.8 - - - +
200E SER* 5.5 2.2 - - - +
202E SER 3.7 11.9 + - - +
203E SER* 1.9 13.1 + - - +
204E PRO* 1.3 71.3 - - - +
206E GLN* 1.3 56.6 + - - +
208E LEU* 3.2 5.1 + - - +
209E GLN* 2.9 31.0 + - - +
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Residues in contact with GLN 206 (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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203E SER* 1.7 26.6 + - - +
205E LEU* 1.3 68.6 - - - +
207E SER* 1.3 65.0 + - - +
209E GLN* 3.2 8.7 + - - +
210E GLN* 2.9 23.5 + - - +
239E GLN* 5.5 11.2 - - + +
240E PRO* 4.9 1.6 - - + -
241E GLN* 3.3 42.0 - - + +
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Residues in contact with SER 207 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203E SER* 3.5 2.2 + - - -
204E PRO* 3.0 17.1 + - - +
206E GLN* 1.3 76.5 - - - +
208E LEU* 1.3 57.3 + - - +
210E GLN* 3.2 10.0 + - - +
211E ARG* 2.9 27.5 + - - +
245E ALA* 4.8 15.7 - - - +
246E ILE* 6.0 1.6 - - - -
247E GLN* 5.1 4.3 - - - +
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Residues in contact with LEU 208 (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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189E LEU* 5.0 14.4 - - + +
192E LEU* 5.7 6.5 - - + -
193E LYS* 5.4 12.1 - - + -
204E PRO 2.8 19.2 + - - +
205E LEU* 3.8 5.2 - - - +
207E SER* 1.3 69.9 - - - +
209E GLN* 1.3 66.3 + - - +
211E ARG* 3.2 6.9 + - - +
212E THR* 2.9 26.6 + - - -
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Residues in contact with GLN 209 (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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205E LEU 2.9 13.6 + - - +
206E GLN* 3.4 11.7 - - - +
208E LEU* 1.3 76.5 - - - +
210E GLN* 1.3 56.4 + - - +
212E THR* 3.3 5.5 + - - -
213E TRP* 2.8 32.1 + - - +
235E LEU* 4.0 20.5 - - + +
236E PHE* 6.1 0.7 - - - -
238E TYR* 5.4 6.5 - - + -
239E GLN* 5.9 7.2 - - + +
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Residues in contact with GLN 210 (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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206E GLN 2.9 12.1 + - - +
207E SER* 3.3 11.7 - - - +
209E GLN* 1.3 77.4 - - - +
211E ARG* 1.3 57.4 + - - +
213E TRP* 3.5 7.6 + - - +
214E LEU* 2.9 29.6 + - - +
236E PHE* 6.2 0.9 - - - +
245E ALA* 5.5 4.7 - - + +
247E GLN* 4.7 10.9 - - + +
248E THR* 4.1 24.5 - - - +
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Residues in contact with ARG 211 (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* 5.0 16.4 - - + -
185E ALA* 5.0 11.7 - - + +
189E LEU* 5.6 6.3 - - + -
207E SER 2.9 13.3 + - - +
208E LEU* 3.2 9.4 + - - +
210E GLN* 1.3 73.4 - - - +
212E THR* 1.3 60.2 + - - +
214E LEU* 3.1 7.1 + - - +
215E ILE* 2.9 29.2 + - - +
247E GLN* 5.1 9.8 - - + +
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Residues in contact with THR 212 (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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186E MET* 5.9 2.7 - - - +
189E LEU* 4.9 14.9 - - - +
208E LEU 2.9 16.9 + - - -
209E GLN* 3.6 5.8 - - - -
211E ARG* 1.3 72.0 - - - +
213E TRP* 1.3 67.6 + - - +
215E ILE* 3.0 8.6 + - - +
216E HIS* 2.9 25.7 + - - +
235E LEU* 4.8 5.2 - - - -
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Residues in contact with TRP 213 (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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209E GLN 2.8 18.1 + - - +
210E GLN* 3.6 8.1 - - - +
212E THR* 1.3 76.4 - - - +
214E LEU* 1.3 57.5 + - - +
216E HIS* 3.4 2.6 + - - +
217E TRP* 2.9 30.5 + - - +
232E ILE* 3.8 13.1 - - + +
235E LEU* 3.4 24.6 - - + +
236E PHE* 3.8 18.8 - - + +
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Residues in contact with LEU 214 (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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210E GLN 2.9 18.4 + - - +
211E ARG* 3.4 7.6 - - - +
212E THR 3.1 0.2 - - - -
213E TRP* 1.3 78.6 - - - +
215E ILE* 1.3 56.5 + - - +
217E TRP* 3.5 7.0 + - - +
218E SER* 2.9 29.6 + - - -
247E GLN* 6.4 1.6 - - + -
324E PHE* 6.4 2.0 - - + -
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Residues in contact with ILE 215 (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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182E TRP* 3.6 39.8 - - + +
185E ALA* 4.3 7.9 - - + -
186E MET* 4.5 10.5 - - + +
211E ARG 2.9 13.4 + - - +
212E THR* 3.0 10.7 + - - +
214E LEU* 1.3 74.3 - - - +
216E HIS* 1.3 58.6 + - - +
218E SER* 3.1 2.8 + - - -
219E LEU* 2.9 31.9 + - - +
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Residues in contact with HIS 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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212E THR 2.9 15.7 + - - +
213E TRP* 3.7 4.3 - - - +
215E ILE* 1.3 76.5 - - - +
217E TRP* 1.3 61.9 + - - +
219E LEU* 3.1 23.3 + - - -
229E ARG* 4.3 12.6 - - + +
231E ASN* 4.1 13.9 - - + -
232E ILE* 3.8 25.8 - - - +
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Residues in contact with TRP 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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213E TRP 2.9 18.6 + - - +
214E LEU* 3.7 8.3 - - - +
216E HIS* 1.3 76.8 - - - +
218E SER* 1.3 60.4 + - - +
219E LEU 4.6 2.1 - - - -
229E ARG* 5.8 0.9 - - - -
232E ILE* 3.9 14.7 - - + +
256E TYR* 6.1 6.1 - - + -
324E PHE* 5.4 7.4 - - + +
328E CYS* 5.1 10.4 - - - +
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Residues in contact with SER 218 (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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182E TRP* 4.5 14.1 - - - -
214E LEU 2.9 17.4 + - - -
215E ILE 3.1 4.0 + - - -
217E TRP* 1.3 78.3 - - - +
219E LEU* 1.3 58.5 + - - +
324E PHE* 5.8 4.3 - - - -
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Residues in contact with LEU 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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182E TRP* 5.4 4.5 - - + +
215E ILE 2.9 17.5 + - - +
216E HIS* 3.1 16.5 + - - +
217E TRP 4.6 2.2 - - - -
218E SER* 1.3 80.5 - - - +
229E ARG* 5.9 4.1 - - - +
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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