Contacts of the helix formed by residues 213 - 228 (chain B) in PDB entry 3N6J
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 GLU 213 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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212B PHE* 1.3 82.7 - - - +
214B GLY* 1.3 68.6 + - - +
215B SER* 4.6 7.6 - - - +
216B LYS* 2.8 24.0 + - + +
217B GLU 3.1 9.0 + - - -
443B PRO* 4.7 5.4 - - - -
445B MSE 5.5 0.5 - - - +
446B VAL* 3.7 26.8 - - + +
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Residues in contact with GLY 214 (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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212B PHE 3.4 3.7 + - - -
213B GLU* 1.3 69.8 - - - +
215B SER* 1.3 51.4 + - - +
217B GLU* 2.8 8.1 + - - +
218B ILE* 2.6 41.5 + - - +
241B TRP* 3.8 31.2 - - - +
249B LEU* 3.8 10.8 - - - -
443B PRO* 5.1 2.0 - - - +
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Residues in contact with SER 215 (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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213B GLU* 4.6 7.2 + - - +
214B GLY* 1.3 74.0 - - - +
216B LYS* 1.3 59.0 + - - +
218B ILE* 3.5 12.7 - - - +
219B ASP* 3.0 30.9 + - - +
248B GLN* 6.0 0.9 - - - -
249B LEU* 4.3 15.1 - - - +
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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
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154B TYR* 4.1 13.6 - - - -
184B MSE 3.4 9.9 + - - -
185B ASP* 3.4 33.7 - - - +
186B THR* 3.9 14.1 + - - +
212B PHE* 4.1 27.4 - - + -
213B GLU* 2.8 17.4 + - + +
215B SER* 1.3 78.4 + - - +
217B GLU* 1.3 65.8 + - - +
219B ASP* 3.2 22.0 + - + +
220B THR* 3.2 15.4 + - - -
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Residues in contact with GLU 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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154B TYR* 4.0 18.0 - - + +
207B LEU* 4.3 2.0 - - + +
209B GLY* 2.9 13.1 - - - -
210B GLY* 2.7 23.3 + - - -
211B VAL* 2.8 30.7 + - - +
212B PHE* 2.8 33.5 + - + +
213B GLU 3.5 4.9 - - - +
214B GLY* 2.8 8.3 + - - +
216B LYS* 1.3 73.9 - - - +
218B ILE* 1.3 65.6 + - - +
220B THR* 3.2 14.4 + - - -
221B VAL* 3.3 14.6 + - - +
235B LEU* 4.5 17.3 - - + +
237B PRO* 4.6 1.2 - - - +
241B TRP* 4.4 13.5 + - + -
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Residues in contact with ILE 218 (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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214B GLY 2.6 27.5 + - - +
215B SER* 3.5 11.7 - - - +
217B GLU* 1.3 71.9 - - - +
219B ASP* 1.3 62.9 - - - +
221B VAL* 3.0 20.1 + - + +
222B ILE* 3.1 32.3 + - + +
235B LEU* 4.2 9.6 - - + +
241B TRP* 4.1 14.6 - - + -
249B LEU* 3.6 42.2 - - + +
250B CYS* 4.6 3.1 - - - -
253B LEU* 3.9 25.4 - - + -
257B LEU* 5.1 1.6 - - + -
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Residues in contact with ASP 219 (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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186B THR* 4.5 7.2 - - + +
215B SER 3.0 18.4 + - - +
216B LYS* 3.3 18.7 - - + +
217B GLU 3.2 0.2 - - - -
218B ILE* 1.3 76.7 - - - +
220B THR* 1.3 63.0 + - - +
222B ILE* 3.1 28.0 + - - +
223B GLU* 3.1 20.4 + - + +
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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
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154B TYR* 2.5 29.2 + - - +
186B THR* 3.5 31.1 + - + +
189B VAL* 4.0 26.7 - - + -
207B LEU* 3.8 16.8 - - + -
216B LYS* 3.2 9.4 + - - -
217B GLU 3.2 6.8 + - - -
219B ASP* 1.3 77.2 - - - +
221B VAL* 1.3 56.9 + - - +
223B GLU* 3.3 2.8 + - - +
224B LEU* 2.9 39.3 + - + +
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Residues in contact with VAL 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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207B LEU* 3.9 16.8 - - + -
217B GLU 3.3 10.1 + - - +
218B ILE* 3.0 14.3 + - + +
220B THR* 1.3 78.6 - - - +
222B ILE* 1.3 61.6 + - + +
224B LEU* 3.4 3.3 + - - +
225B LYS* 3.1 21.7 + - - +
233B ILE* 3.6 27.2 - - + +
235B LEU* 3.9 26.7 - - + -
253B LEU* 5.6 3.4 - - + -
256B VAL* 3.8 21.3 - - + -
257B LEU* 4.1 19.3 - - + -
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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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218B ILE* 3.1 31.0 - - + +
219B ASP* 3.1 22.2 + - - +
221B VAL* 1.3 76.5 - - + +
223B GLU* 1.3 62.1 + - + +
225B LYS* 3.4 2.6 + - + +
226B LYS* 2.9 41.2 + - + +
253B LEU* 5.4 8.5 - - + -
256B VAL* 4.5 20.0 - - + -
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Residues in contact with GLU 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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186B THR* 3.6 16.2 - - + -
187B GLN* 5.5 0.7 - - - +
190B ILE* 3.5 21.0 - - + +
219B ASP* 3.1 15.1 + - + +
220B THR 3.6 4.5 - - - +
222B ILE* 1.3 75.6 - - + +
224B LEU* 1.3 55.3 + - - +
226B LYS* 3.5 10.3 - - - +
227B HIS* 2.7 58.4 + - - +
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Residues in contact with LEU 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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152B LEU* 4.0 22.7 - - + -
189B VAL* 4.3 7.9 - - + +
190B ILE* 4.7 11.2 - - + -
193B ALA* 3.6 20.6 - - + -
205B PHE* 4.9 8.7 - - + -
207B LEU* 4.8 4.5 - - + -
220B THR* 2.9 41.7 + - + +
221B VAL 3.4 6.5 - - - +
223B GLU* 1.3 76.3 - - - +
225B LYS* 1.3 57.1 + - - +
227B HIS* 4.5 2.0 - - - -
228B PHE* 2.8 61.2 + - + +
233B ILE* 3.6 21.3 - - + -
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Residues in contact with LYS 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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221B VAL 3.1 12.3 + - - +
222B ILE* 4.0 4.0 - - + +
224B LEU* 1.3 76.3 - - - +
226B LYS* 1.3 66.2 + - + +
228B PHE 3.2 22.2 - - - +
229B PRO* 3.2 29.1 + - + +
231B ALA 3.6 23.1 - - - -
232B ARG* 5.6 0.2 - - - +
233B ILE* 3.4 22.8 - - + +
255B ASP 3.6 22.6 + - - +
256B VAL* 3.8 26.0 + - + +
258B THR* 5.9 1.8 - - - -
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Residues in contact with LYS 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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222B ILE* 2.9 30.4 + - + +
223B GLU* 3.2 15.2 + - - +
225B LYS* 1.3 79.4 - - + +
227B HIS* 1.3 62.3 + - + +
228B PHE 3.6 0.2 + - - -
229B PRO* 3.8 11.2 - - - +
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Residues in contact with HIS 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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187B GLN* 4.2 14.1 + - - -
190B ILE* 3.6 36.8 - - + +
223B GLU* 2.7 45.5 + - - +
224B LEU* 4.5 0.4 - - - -
226B LYS* 1.3 74.7 - - - +
228B PHE* 1.3 87.4 + + + +
229B PRO* 3.6 6.3 - - - +
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Residues in contact with PHE 228 (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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190B ILE* 4.3 7.4 - - + -
193B ALA* 3.5 20.6 - - + -
194B ALA* 3.7 31.6 - - + -
197B LYS* 4.2 29.4 - - + -
205B PHE* 4.5 11.4 - + + -
224B LEU* 2.8 36.7 + - + +
225B LYS* 3.2 14.0 - - - +
227B HIS* 1.3 94.3 - + + +
229B PRO* 1.4 63.8 - - - +
230B ASP 3.3 2.9 + - - -
231B ALA* 3.7 29.6 + - + +
233B ILE* 5.6 0.5 - - - +
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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