Contacts of the helix formed by residues 207 - 222 (chain B) in PDB entry 3DYQ
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 207 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185B LYS* 3.1 28.0 + - - -
205B LEU 4.2 0.9 + - - -
206B TRP* 1.3 77.0 - - - +
208B PRO* 1.3 81.0 - - + +
209B ASN* 3.2 13.4 - - - +
210B GLU* 2.6 27.3 + - - +
211B MET* 3.0 12.4 + - - +
255B ARG* 5.0 1.6 - - - +
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Residues in contact with PRO 208 (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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206B TRP 4.7 0.2 - - - +
207B GLU* 1.3 95.4 - - + +
209B ASN* 1.3 57.8 + - - +
211B MET* 3.1 20.7 + - + +
212B LEU* 2.8 35.5 + - + +
243B HIS* 4.0 31.0 - - + +
254B PHE* 4.1 4.8 - - + -
255B ARG* 5.2 4.0 - - - +
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Residues in contact with ASN 209 (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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185B LYS* 5.5 2.2 - - - +
186B TYR* 3.7 36.2 - - + +
207B GLU* 3.7 17.3 - - - +
208B PRO* 1.3 79.2 - - - +
210B GLU* 1.3 74.9 + - - +
212B LEU* 3.3 14.4 + - + +
213B SER* 3.0 25.0 + - - -
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Residues in contact with GLU 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B LYS* 3.5 51.7 + - + +
186B TYR* 4.9 0.7 - - - +
188B LEU* 4.0 4.6 - - + +
205B LEU 4.3 2.6 - - - +
206B TRP* 3.1 41.0 - - + -
207B GLU* 2.6 42.8 + - - +
209B ASN* 1.3 86.2 + - - +
211B MET* 1.3 57.2 + - - +
213B SER* 3.1 10.0 + - - -
214B CYS* 2.9 32.2 + - - -
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Residues in contact with MET 211 (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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203B VAL 4.4 1.1 - - - +
206B TRP* 3.5 22.0 - - + +
207B GLU 3.0 7.7 + - - +
208B PRO* 3.5 27.1 - - + +
210B GLU* 1.3 77.6 - - - +
212B LEU* 1.3 56.8 + - - +
214B CYS* 3.2 7.1 + - - +
215B LEU* 2.9 32.8 + - - +
254B PHE* 4.0 15.9 - - + -
255B ARG* 3.4 52.7 - - + +
258B PHE* 3.6 51.9 - - + -
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Residues in contact with LEU 212 (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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208B PRO* 2.8 26.1 + - + +
209B ASN* 3.5 14.6 - - + +
211B MET* 1.3 73.6 - - - +
213B SER* 1.3 55.8 + - - +
215B LEU* 3.2 6.3 + - + +
216B GLU* 2.9 30.9 + - - +
239B LEU* 3.4 44.8 - - + +
240B PHE* 4.3 24.5 - - + +
243B HIS* 3.9 17.9 - - + +
254B PHE* 3.6 24.2 - - + -
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Residues in contact with SER 213 (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 TYR* 3.0 31.9 + - - +
188B LEU* 3.9 17.6 - - - +
209B ASN 3.0 14.0 + - - -
210B GLU* 3.4 9.9 - - - -
212B LEU* 1.3 72.3 - - - +
214B CYS* 1.3 60.4 + - - +
216B GLU* 3.4 15.6 + - - +
217B HIS* 2.9 29.1 + - - +
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Residues in contact with CYS 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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188B LEU* 3.8 26.0 - - - -
192B THR* 4.6 2.0 - - - -
196B LEU* 3.6 30.2 - - + +
201B PHE* 4.5 8.5 - - - -
206B TRP* 5.7 4.0 - - - -
210B GLU* 2.9 20.5 + - - -
211B MET* 3.2 9.2 - - - +
213B SER* 1.3 74.9 - - - +
215B LEU* 1.3 66.6 + - - +
217B HIS* 3.2 2.8 + - - +
218B MET* 3.1 26.6 + - - +
258B PHE* 3.5 21.8 - - + -
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Residues in contact with LEU 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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211B MET 2.9 17.7 + - - +
212B LEU* 3.2 7.6 + - + +
214B CYS* 1.3 74.0 - - - +
216B GLU* 1.3 64.9 + - - +
218B MET* 3.0 29.7 + - + +
219B TYR* 3.2 15.9 + - - -
239B LEU* 3.8 27.8 - - + -
254B PHE* 3.8 33.2 - - + -
257B CYS* 5.0 5.4 - - - -
258B PHE* 4.0 18.8 - - + -
261B ALA* 3.6 31.0 - - + -
290B ILE* 4.2 17.5 - - + -
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Residues in contact with GLU 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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212B LEU 2.9 15.5 + - - +
213B SER* 3.5 16.5 + - - +
215B LEU* 1.3 76.0 - - - +
217B HIS* 1.3 64.9 + - - +
219B TYR* 3.0 13.6 + - - +
220B HIS* 3.2 33.1 + - + -
232B PRO* 4.8 3.5 - - - +
235B LEU* 4.2 12.8 - - + -
236B ARG* 3.3 49.4 + - - +
239B LEU* 3.4 15.7 - - + +
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Residues in contact with HIS 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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188B LEU* 4.4 9.6 - - + -
193B ILE* 3.6 43.9 + - + +
196B LEU* 3.9 17.0 - - + -
197B ARG* 5.5 0.4 + - - -
213B SER 2.9 18.4 + - - +
214B CYS 3.2 3.8 + - - +
216B GLU* 1.3 76.7 - - - +
218B MET* 1.3 55.1 - - - +
220B HIS* 3.0 11.0 + - - +
221B ASP* 2.7 53.7 + - + +
265B TYR* 3.4 24.0 + - - -
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Residues in contact with MET 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B LEU* 4.0 15.9 - - + -
214B CYS 3.1 17.1 + - - +
215B LEU* 3.0 22.6 + - + +
217B HIS* 1.3 78.0 - - - +
219B TYR* 1.3 64.0 + - + +
222B LEU* 2.9 30.7 + - + +
258B PHE* 4.1 15.7 - - + -
261B ALA 4.3 1.6 - - - +
262B GLN* 3.9 35.0 - - + -
265B TYR* 3.7 49.6 - - + -
286B MET* 3.9 21.8 - - + -
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Residues in contact with TYR 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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215B LEU* 3.2 15.2 + - + -
216B GLU 3.0 9.7 + - - +
218B MET* 1.3 82.3 - - + +
220B HIS* 1.3 59.1 + - - +
223B GLY 3.6 0.3 + - - -
224B LEU* 3.0 45.8 + - + +
225B VAL* 3.2 10.3 + - + -
230B ILE* 4.0 18.2 - - + -
235B LEU* 3.7 28.3 - - + -
238B TRP* 3.6 11.2 - + - -
239B LEU* 5.5 0.4 - - + -
283B LEU* 3.8 22.0 - - + -
286B MET* 4.2 16.6 - - + -
287B THR* 2.9 37.9 + - - -
290B ILE* 3.3 27.9 - - + +
340B ILE* 4.4 11.7 - - + -
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Residues in contact with HIS 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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216B GLU* 3.2 41.5 + - + -
217B HIS* 3.0 11.5 + - - +
219B TYR* 1.3 77.8 - - - +
221B ASP* 1.3 58.1 + - - +
223B GLY* 3.0 22.2 + - - -
225B VAL* 3.5 39.7 - - + +
226B ARG* 5.2 2.3 + - - +
232B PRO* 4.4 19.9 - - + +
235B LEU* 4.0 7.4 - - + +
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Residues in contact with ASP 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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197B ARG* 3.4 15.7 + - - -
217B HIS* 2.7 44.9 + - + +
218B MET 4.0 2.5 - - - +
220B HIS* 1.3 74.3 - - - +
222B LEU* 1.3 57.4 + - - +
223B GLY 3.2 1.5 + - - -
265B TYR* 2.6 25.1 + - + +
269B TRP* 3.3 25.1 - - - -
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Residues in contact with LEU 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 MET* 2.9 23.8 + - + +
219B TYR* 6.1 0.2 - - + -
220B HIS 3.2 0.4 - - - -
221B ASP* 1.3 75.8 - - - +
223B GLY* 1.3 55.7 - - - +
224B LEU* 3.2 18.8 + - + +
226B ARG* 4.9 0.8 + - - -
265B TYR* 3.8 23.1 - - + -
268B VAL* 3.8 24.9 - - + -
269B TRP* 3.6 28.0 - - + -
274B GLN* 3.2 21.3 + - - +
279B GLN* 2.9 21.8 + - - +
282B ILE* 4.3 9.9 - - + -
286B MET* 3.9 30.3 - - + -
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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
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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