Contacts of the helix formed by residues 210 - 230 (chain B) in PDB entry 3EHN
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 ASN 210 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B SER* 4.2 3.8 + - - +
207B TYR* 3.1 15.0 + - - +
208B ASN* 2.8 11.5 + - + +
209B GLY* 1.3 67.0 - - - +
211B VAL* 1.3 60.4 + - - +
212B GLN* 3.1 14.7 + - - +
213B ASN* 2.9 51.8 + - - +
214B TRP* 3.3 16.2 + - - -
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Residues in contact with VAL 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B ILE* 4.8 5.4 - - + -
192B LEU* 3.3 48.0 - - + +
195B ILE* 4.4 10.1 - - + -
196B SER* 6.0 1.6 - - - -
197B TYR 3.5 23.1 + - - +
198B SER* 5.3 0.6 - - - +
199B VAL* 3.5 20.9 - - + -
209B GLY 2.7 17.0 + - - +
210B ASN* 1.3 70.3 - - - +
212B GLN* 1.3 68.9 + - - +
214B TRP* 3.0 19.9 + - + +
215B VAL* 3.0 12.7 + - + +
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Residues in contact with GLN 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B LEU 4.6 6.1 - - - +
193B ASN* 5.3 4.3 - - - +
195B ILE 4.9 10.0 + - - +
196B SER* 5.1 10.3 + - - +
210B ASN* 3.1 13.6 + - - +
211B VAL* 1.3 80.8 - - - +
213B ASN* 1.3 67.5 + - - +
215B VAL* 2.8 34.1 + - + +
216B LYS* 3.3 13.9 + - - +
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Residues in contact with ASN 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B TYR* 3.3 46.5 - - + +
210B ASN* 2.9 31.4 + - - +
212B GLN* 1.3 76.8 - - - +
214B TRP* 1.3 64.0 + - - +
216B LYS* 3.0 28.6 + - - +
217B LEU 3.1 9.9 + - - -
257B SER 5.1 4.3 + - - +
258B SER* 4.2 24.2 + - - +
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Residues in contact with TRP 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B PHE* 4.0 5.4 - + - -
47B GLN* 4.9 0.4 - - - -
138B ILE* 3.7 46.2 - - + +
141B ILE* 3.7 27.8 - - + +
142B VAL* 3.5 34.3 - - + -
192B LEU* 5.2 2.7 - - + -
204B ASP* 3.0 41.0 + - - -
206B ILE* 4.2 22.2 - - + -
207B TYR* 3.6 16.2 - + + +
209B GLY* 4.9 3.0 - - - +
210B ASN 3.3 23.3 - - - -
211B VAL* 3.0 17.3 + - + +
213B ASN* 1.3 79.1 - - - +
215B VAL* 1.3 54.6 + - - +
217B LEU* 3.6 22.6 + - + +
218B ALA* 3.0 26.5 + - - +
355B TRP* 4.5 2.9 - + - -
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Residues in contact with VAL 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B VAL* 3.9 12.6 - - + +
192B LEU* 4.3 22.9 - - + +
193B ASN* 3.3 28.9 - - - +
211B VAL* 3.0 19.1 - - + +
212B GLN* 2.8 26.8 + - + +
214B TRP* 1.3 74.7 - - - +
216B LYS* 1.3 65.5 + - + +
218B ALA* 3.0 15.8 + - - +
219B ASN* 3.1 30.7 + - - +
249B ASN 4.2 3.8 - - - +
250B GLY* 4.2 7.6 - - - -
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Residues in contact with LYS 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B GLN* 3.3 12.3 + - - +
213B ASN* 3.0 21.7 + - - +
215B VAL* 1.3 77.7 - - + +
217B LEU* 1.3 51.1 + - - +
219B ASN* 3.1 2.1 + - - -
220B SER* 2.5 41.5 + - - -
250B GLY* 4.3 14.6 - - - +
251B GLY 3.4 20.2 - - - +
252B VAL 4.0 15.3 - - - +
253B ILE* 3.9 15.0 - - + +
254B GLU 6.0 0.6 - - - +
255B ASP* 4.2 11.9 + - - -
258B SER* 3.7 30.3 + - - +
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Residues in contact with LEU 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B ILE* 4.6 2.2 - - + -
145B ILE* 3.7 31.9 - - + -
206B ILE* 5.2 0.4 - - + -
207B TYR* 3.8 28.9 - - + +
213B ASN 3.1 8.5 + - - +
214B TRP* 3.8 25.4 - - + +
216B LYS* 1.3 72.5 - - - +
218B ALA* 1.3 60.8 + - - +
220B SER* 4.0 4.5 - - - -
221B LEU* 2.9 36.8 + - + +
253B ILE* 4.1 7.5 - - + +
260B ALA* 3.9 17.7 - - + -
355B TRP* 4.5 4.0 - - + -
356B PHE* 3.9 31.4 - - + -
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Residues in contact with ALA 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B ILE* 3.4 25.3 - - + +
185B LEU* 3.5 23.1 - - + +
188B SER* 5.4 0.4 - - - -
189B VAL* 3.7 22.2 - - + -
192B LEU* 5.8 0.2 - - + -
214B TRP 3.0 14.4 + - - +
215B VAL* 3.0 13.1 + - - +
217B LEU* 1.3 76.8 - - - +
219B ASN* 1.3 58.8 + - - +
222B MET* 3.4 23.2 + - - +
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Residues in contact with ASN 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B VAL* 3.2 29.5 - - - +
215B VAL* 3.1 17.5 + - - +
218B ALA* 1.3 75.8 - - - +
220B SER* 1.3 52.6 + - - +
221B LEU 3.1 2.0 - - - -
222B MET* 2.9 15.4 + - - +
223B LEU* 2.7 35.5 + - - +
243B LYS 4.9 0.3 - - - -
244B ALA* 3.7 19.9 + - - +
249B ASN* 2.6 32.0 + - - +
251B GLY 2.9 26.7 + - - +
252B VAL* 3.6 7.6 - - + -
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Residues in contact with SER 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B LYS 2.5 22.1 + - - -
217B LEU* 3.8 7.6 - - - -
219B ASN* 1.3 72.2 - - - +
221B LEU* 1.3 60.5 + - - +
223B LEU* 3.4 7.4 - - - +
224B ARG 3.4 12.3 + - - -
252B VAL* 3.2 11.9 - - - +
253B ILE* 2.6 43.5 + - - +
356B PHE* 3.2 37.8 - - - -
361B THR* 5.1 0.7 - - - -
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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
----------------------------------------------------------
141B ILE* 4.5 4.3 - - + +
144B ASN* 4.7 4.7 - - + -
145B ILE* 3.2 45.1 - - + +
148B LEU* 3.6 27.6 - - + -
181B MET* 5.8 0.2 - - - -
185B LEU* 4.1 24.7 - - + -
217B LEU* 2.9 22.1 + - + +
218B ALA 4.2 3.1 - - - +
220B SER* 1.3 75.5 - - - +
222B MET* 1.3 66.4 + - - +
223B LEU 3.2 0.2 - - - -
224B ARG* 3.1 29.7 + - - +
225B ILE* 3.0 30.9 + - + +
356B PHE* 4.4 4.2 - - + -
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Residues in contact with MET 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B LEU* 4.4 5.8 - - + +
185B LEU* 3.5 26.4 - - + +
186B SER* 3.3 40.2 - - - +
189B VAL* 3.5 18.2 - - + -
218B ALA 3.4 13.6 + - - +
219B ASN* 2.9 23.3 + - - +
221B LEU* 1.3 80.4 - - - +
223B LEU* 1.3 57.2 - - - +
225B ILE* 3.4 5.2 + - - +
226B VAL* 2.9 28.4 + - - +
240B TYR* 3.8 42.8 - - + +
243B LYS* 4.6 5.6 - - + -
244B ALA* 4.0 9.0 - - + -
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Residues in contact with LEU 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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219B ASN 2.7 11.2 + - - +
220B SER* 3.4 11.0 - - - +
221B LEU 3.2 0.2 - - - -
222B MET* 1.3 74.6 - - - +
224B ARG* 1.3 68.2 + - - +
226B VAL* 2.9 24.1 - - - +
227B VAL* 3.1 20.8 + - + +
241B ILE* 4.3 22.9 - - + -
244B ALA* 4.3 10.0 - - + +
245B LEU* 4.5 22.2 - - + -
252B VAL* 4.8 6.7 - - + -
356B PHE* 5.7 0.7 - - + -
361B THR* 4.3 20.6 - - + +
364B LEU* 3.7 31.9 - - + +
365B LYS* 4.7 5.6 - - + +
368B ALA* 6.0 0.4 - - + -
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Residues in contact with ARG 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B ILE* 5.3 7.5 - - - +
148B LEU* 4.8 5.9 - - + +
220B SER 3.4 7.5 + - - +
221B LEU* 3.1 32.2 + - + +
223B LEU* 1.3 81.3 - - - +
225B ILE* 1.3 67.4 + - + +
226B VAL 2.9 0.3 + - - -
227B VAL* 3.1 3.5 + - - +
228B ARG* 3.0 37.0 + - - +
355B TRP 3.5 21.6 + - - -
356B PHE* 3.3 16.7 - - - +
360B GLU* 2.4 50.6 + - - +
364B LEU* 3.7 19.8 - - + +
455B LYS* 5.0 1.3 - - - +
459B LEU* 5.0 1.0 - - - +
462B ASN* 5.2 2.4 - - - +
465B GLU* 2.8 35.5 + - - +
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Residues in contact with ILE 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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148B LEU* 4.1 19.7 - - + -
178B TYR* 3.3 37.0 - - + +
181B MET* 4.0 25.6 - - + -
182B LEU* 3.5 24.5 - - + -
185B LEU* 3.5 31.2 - - + -
221B LEU* 3.0 16.1 + - + +
222B MET 3.6 5.4 - - - +
224B ARG* 1.3 74.6 - - - +
226B VAL* 1.3 66.1 + - - +
228B ARG* 3.2 20.7 + - - +
229B VAL* 3.2 11.7 - - + +
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Residues in contact with VAL 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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182B LEU* 4.7 4.2 - - + +
222B MET 2.9 31.3 + - - +
223B LEU* 2.9 12.5 + - - +
224B ARG 2.9 0.4 + - - -
225B ILE* 1.3 74.6 - - - +
227B VAL* 1.3 56.7 + - - +
229B VAL* 2.8 38.8 + - - +
230B HIS 3.3 4.5 + - - -
236B LEU 5.6 0.2 - - - +
237B ALA* 3.3 32.2 - - + +
240B TYR* 4.2 10.5 - - + -
241B ILE* 3.3 51.6 - - + +
373B LEU* 5.1 1.6 - - + -
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Residues in contact with VAL 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223B LEU* 3.5 15.7 - - + +
224B ARG 3.1 5.3 + - - +
226B VAL* 1.3 77.9 - - + +
228B ARG* 1.3 62.2 + - - +
229B VAL 3.0 1.4 + - - -
230B HIS* 3.2 24.9 + - + +
241B ILE* 5.2 0.2 - - + -
364B LEU* 3.4 44.9 - - + +
367B GLU* 3.3 43.3 - - + +
368B ALA* 5.1 8.1 - - + +
373B LEU* 5.7 0.7 - - - -
469B GLU* 5.3 0.4 - - - +
472B ARG* 3.5 16.0 + - - +
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Residues in contact with ARG 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B LEU* 4.7 7.3 - - - +
152B ASP* 3.1 27.3 + - - -
178B TYR* 3.0 31.7 + - + +
224B ARG* 3.0 24.5 + - - +
225B ILE* 3.2 15.0 - - - +
226B VAL 3.0 0.4 + - - -
227B VAL* 1.3 76.6 - - - +
229B VAL* 1.3 56.4 + - + +
231B PHE* 5.1 2.4 + - - +
465B GLU* 3.5 25.3 + - - -
468B THR* 3.3 14.5 - - - +
469B GLU* 2.8 27.7 + - - -
472B ARG* 3.4 29.5 + - - +
535B TRP* 3.3 45.8 - - + +
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Residues in contact with VAL 229 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B TYR* 4.1 12.8 - - + -
182B LEU* 5.7 2.7 - - + -
225B ILE* 3.2 13.0 - - + +
226B VAL* 2.8 31.2 + - - +
228B ARG* 1.3 83.7 - - + +
230B HIS* 1.3 50.0 + - - +
231B PHE 2.7 17.7 + - - -
232B ILE* 2.9 5.7 + - + +
233B ASP* 2.9 28.9 + - + +
236B LEU* 4.7 12.6 - - + -
237B ALA* 4.1 15.5 - - + +
534B TRP* 3.3 42.0 - - + -
535B TRP* 5.2 2.2 - - + -
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Residues in contact with HIS 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B VAL 3.3 4.7 + - - +
227B VAL* 3.2 27.0 + - + +
229B VAL* 1.3 73.4 - - - +
231B PHE* 1.3 96.5 + + - +
232B ILE 3.6 0.2 - - - -
233B ASP 4.0 12.1 - - - -
234B GLU* 4.5 16.1 + - + +
237B ALA* 4.1 9.6 - - + -
367B GLU* 2.7 37.3 + - + +
371B TYR* 3.6 22.8 - + + +
373B LEU* 4.1 28.3 - - + -
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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