Contacts of the helix formed by residues 214 - 232 (chain E) in PDB entry 1RBO
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 TRP 214 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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286B ASP* 5.6 6.1 - - - -
207E ASN 3.5 17.7 - - - +
208E SER* 3.1 28.5 + - - +
212E MET 3.9 0.4 + - - -
213E ARG* 1.3 74.4 - - + +
215E ARG* 1.3 94.9 + - + +
217E ARG* 3.2 17.7 + - - +
218E PHE* 3.0 45.2 + + + -
241E ASN 5.5 0.2 - - - +
252E LYS* 3.7 38.6 - - + +
253E ARG* 3.6 52.4 - - + +
256E PHE* 3.7 33.7 - + + -
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Residues in contact with ARG 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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161B LYS* 5.6 1.2 - - - +
258B ARG* 3.4 22.6 - - - +
285B ARG* 3.6 21.3 - - - +
286B ASP* 3.0 24.9 + - - +
287B ASN* 3.5 18.0 + - - +
288B GLY* 3.5 19.0 - - - +
58C SER* 4.8 7.5 + - - -
59C PRO* 4.6 2.8 + - - +
213E ARG* 3.4 2.2 - - + +
214E TRP* 1.3 105.1 - - + +
216E ASP* 1.3 65.2 + - - +
218E PHE* 3.4 3.1 + - - +
219E LEU* 3.1 39.9 + - - +
256E PHE* 3.4 50.3 - - + -
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Residues in contact with ASP 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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152B PRO 5.1 2.1 - - - +
153B HIS* 3.6 13.8 + - - -
157B VAL* 3.5 30.6 - - + +
161B LYS* 2.9 33.6 + - - +
285B ARG* 6.1 0.9 - - - -
182E ALA* 3.6 18.6 - - + -
213E ARG* 3.3 26.6 + - - +
214E TRP 3.3 0.4 - - - -
215E ARG* 1.3 78.3 - - - +
217E ARG* 1.3 62.8 + - - +
219E LEU* 3.4 2.8 + - - +
220E PHE* 3.1 29.2 + - + -
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Residues in contact with ARG 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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182E ALA* 3.8 10.0 - - - +
185E TYR* 3.8 12.6 - - + -
202E ASP* 2.9 40.3 + - - +
206E VAL* 3.4 25.7 + - - +
207E ASN* 2.9 29.9 + - - +
209E GLN* 5.4 0.2 + - - -
212E MET* 3.5 38.7 + - - +
213E ARG 3.2 4.6 + - - +
214E TRP* 3.2 16.4 + - - +
216E ASP* 1.3 80.3 - - - +
218E PHE* 1.3 76.1 + - + +
220E PHE* 3.4 1.0 + - - +
221E CYS* 2.9 49.2 + - - +
240E LEU* 5.1 0.4 - - + -
241E ASN 4.2 5.7 + - - -
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Residues in contact with PHE 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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214E TRP* 3.0 53.9 + + + +
215E ARG 3.7 4.9 - - - +
217E ARG* 1.3 99.2 - - - +
219E LEU* 1.3 57.6 + - - +
221E CYS* 3.9 1.2 - - - +
222E ALA* 3.0 30.5 + - - +
240E LEU* 3.7 49.4 - - + +
241E ASN 3.6 20.4 - - - -
242E ALA* 5.2 0.2 - - - -
253E ARG* 3.3 30.5 - - + -
256E PHE* 3.8 18.8 - + + -
257E ALA* 4.4 7.9 - - + -
260E LEU* 3.8 9.0 - - + +
265E VAL* 5.8 0.7 - - + -
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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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161B LYS* 4.0 22.9 - - + +
58C SER* 4.2 10.8 - - - +
59C PRO 4.0 7.6 - - - +
60C GLY 3.6 31.2 - - - +
61C TYR* 3.9 26.7 - - + -
65C ARG* 5.0 4.4 + - - +
215E ARG* 3.1 21.7 + - - +
216E ASP* 3.6 5.6 - - - +
217E ARG 3.2 0.2 - - - -
218E PHE* 1.3 79.3 - - - +
220E PHE* 1.3 63.7 + - + +
222E ALA* 3.3 7.3 + - - +
223E GLU* 3.2 18.0 + - - +
256E PHE* 3.5 28.5 - - + -
260E LEU* 4.2 7.6 - - + -
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Residues in contact with PHE 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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157B VAL* 5.2 3.1 - - + -
160B ASP* 3.6 42.2 - - + -
161B LYS* 3.8 26.7 - - + -
65C ARG* 3.9 28.5 - - + -
66C TYR* 3.4 34.2 - + - +
182E ALA* 3.7 27.8 - - + +
183E LYS* 3.8 21.5 - - + -
186E GLY* 4.4 1.1 - - - -
216E ASP* 3.1 26.5 + - + +
217E ARG 4.1 0.9 - - - +
219E LEU* 1.3 73.9 - - + +
221E CYS* 1.3 61.1 + - - +
223E GLU* 3.3 4.5 + - - +
224E ALA* 3.0 28.4 + - - +
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Residues in contact with CYS 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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182E ALA 5.4 0.2 - - - -
185E TYR* 3.9 12.8 - - - -
186E GLY* 4.5 7.2 - - - -
189E VAL* 4.2 11.1 - - + +
217E ARG* 2.9 34.3 + - - +
218E PHE 3.9 2.7 - - - +
220E PHE* 1.3 74.0 - - - +
222E ALA* 1.3 61.5 + - - +
224E ALA* 3.4 6.6 + - - +
225E LEU* 2.9 34.1 + - - +
238E HIS* 3.7 40.8 - - + +
240E LEU* 4.2 7.2 - - + -
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Residues in contact with ALA 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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61C TYR* 4.3 4.9 - - + -
218E PHE 3.0 18.2 + - - +
219E LEU 3.6 5.6 - - - +
220E PHE 3.3 0.2 - - - -
221E CYS* 1.3 73.3 - - - +
223E GLU* 1.3 66.9 + - - +
225E LEU* 3.4 11.1 + - - +
226E TYR* 3.0 46.1 + - + -
240E LEU* 6.0 0.6 - - - +
260E LEU* 4.2 24.0 - - + -
262E VAL* 4.3 8.5 - - + -
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Residues in contact with GLU 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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61C TYR* 3.5 21.7 - - + +
62C TYR 3.2 16.2 - - - +
63C ASP* 4.2 8.2 - - - +
64C GLY 3.5 4.8 + - - +
65C ARG* 2.9 59.7 + - - +
66C TYR* 3.2 28.6 + - + +
219E LEU 3.2 10.7 + - - +
220E PHE* 3.6 10.2 - - - +
221E CYS 3.3 0.2 - - - -
222E ALA* 1.3 79.1 - - - +
224E ALA* 1.3 61.6 + - - +
226E TYR* 3.5 2.1 + - - +
227E LYS* 3.1 23.9 + - + +
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Residues in contact with ALA 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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66C TYR* 4.0 8.9 - - + -
186E GLY* 3.1 31.0 - - - +
189E VAL* 4.0 5.4 - - + -
190E TYR* 3.8 21.9 - - + +
220E PHE 3.0 16.4 + - - +
221E CYS 3.7 4.0 - - - +
222E ALA 3.3 0.2 - - - -
223E GLU* 1.3 77.2 - - - +
225E LEU* 1.3 61.4 + - - +
227E LYS* 3.3 5.5 + - - +
228E ALA* 3.1 23.2 + - - +
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Residues in contact with LEU 225 (chain E).
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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189E VAL* 4.5 0.2 - - - +
193E LEU* 3.8 25.7 - - + +
221E CYS 2.9 20.2 + - - +
222E ALA* 3.8 9.4 - - - +
224E ALA* 1.3 72.7 - - - +
226E TYR* 1.3 82.2 + - + +
228E ALA* 3.4 2.3 + - - +
229E GLN* 3.0 35.7 + - - +
236E LYS* 3.8 24.2 - - + +
237E GLY* 4.3 2.2 - - - -
238E HIS* 3.9 32.1 - - + +
240E LEU* 6.1 0.9 - - + -
262E VAL* 3.9 26.7 - - + -
263E PRO* 4.8 4.5 - - + -
62F TYR* 6.1 0.2 - - - +
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Residues in contact with TYR 226 (chain E).
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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55C HIS* 3.6 63.0 + + + +
56C HIS* 6.1 0.9 - - + -
61C TYR* 3.9 5.8 - + - +
63C ASP* 4.8 0.4 - - - +
222E ALA* 3.0 38.7 + - + +
223E GLU 3.9 3.4 - - - +
225E LEU* 1.3 90.9 - - + +
227E LYS* 1.3 61.9 + - - +
229E GLN* 3.5 16.2 + - - +
230E ALA* 3.1 24.8 + - - +
260E LEU* 2.9 27.8 + - + -
261E GLY 3.4 8.8 + - - -
262E VAL* 3.8 8.6 + - + +
263E PRO* 6.3 0.4 - - + -
53F ARG* 3.1 30.9 + - - -
62F TYR* 5.8 3.1 - + - -
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Residues in contact with LYS 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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45C GLU* 2.9 32.4 + - - -
48C HIS* 5.9 2.8 + - - +
52C TYR* 6.2 0.2 - - - +
55C HIS* 5.3 1.1 - - - -
64C GLY* 5.6 4.4 - - - -
66C TYR* 3.0 34.9 + - + +
67C TRP 4.4 2.2 - - - -
68C THR* 4.7 1.1 - - - -
190E TYR* 3.4 44.6 - - + -
223E GLU* 3.1 19.2 + - + +
224E ALA* 3.6 5.6 - - - +
226E TYR* 1.3 77.2 - - - +
228E ALA* 1.3 61.4 + - - +
230E ALA* 3.4 6.3 + - - +
231E GLU* 3.0 24.4 + - + +
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Residues in contact with ALA 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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190E TYR* 3.8 16.5 - - + +
193E LEU* 3.4 33.9 - - + -
194E ARG* 3.8 12.6 - - - +
224E ALA 3.1 15.7 + - - +
225E LEU 3.8 3.6 - - - +
227E LYS* 1.3 76.1 - - - +
229E GLN* 1.3 60.9 + - - +
231E GLU* 3.3 3.2 + - - +
232E THR* 3.0 32.3 + - - +
236E LYS* 4.3 2.7 - - + -
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Residues in contact with GLN 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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225E LEU* 3.0 22.4 + - - +
226E TYR* 3.8 16.5 - - + +
227E LYS 3.3 0.2 - - - -
228E ALA* 1.3 74.3 - - - +
230E ALA* 1.3 59.7 + - - +
233E GLY* 2.9 29.8 + - - -
234E GLU 3.3 24.2 - - - +
235E ILE* 3.5 14.5 - - + +
236E LYS* 3.0 38.3 + - + +
51F VAL* 4.2 10.8 - - + +
53F ARG* 5.6 2.8 - - - +
62F TYR* 3.8 25.4 + - - -
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Residues in contact with ALA 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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55C HIS* 5.6 7.2 - - + +
226E TYR 3.1 17.7 + - - +
227E LYS* 3.8 5.8 - - - +
229E GLN* 1.3 77.6 - - - +
231E GLU* 1.3 63.0 + - - +
233E GLY* 4.0 0.3 + - - -
10F LYS* 3.2 22.7 + - - -
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Residues in contact with GLU 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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190E TYR* 2.6 31.0 + - - -
194E ARG* 2.9 43.7 + - - +
227E LYS* 3.0 18.3 + - + +
228E ALA* 3.6 5.8 - - - +
229E GLN 3.3 0.2 - - - -
230E ALA* 1.3 78.2 - - - +
232E THR* 1.3 61.1 + - + +
4F TRP* 5.2 0.3 - - - -
5F PRO 4.0 4.5 - - - +
6F ILE* 3.6 30.7 - - - +
9F LEU* 4.2 13.7 + - + +
10F LYS* 3.3 19.9 + - - +
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Residues in contact with THR 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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193E LEU 4.3 4.7 - - - +
194E ARG* 3.5 35.7 - - + +
228E ALA 3.0 18.1 + - - +
231E GLU* 1.3 83.1 - - + +
233E GLY* 1.3 62.6 + - - +
234E GLU* 3.3 15.4 + - - -
236E LYS* 3.3 17.6 - - - +
9F LEU 4.4 9.4 - - - +
10F LYS* 3.5 4.2 - - - -
11F LYS* 2.8 31.4 + - - +
17F TYR* 4.7 10.1 - - - +
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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