Contacts of the helix formed by residues 205 - 226 (chain B) in PDB entry 2B50
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 205 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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206B PRO* 1.4 78.4 - - - +
207B GLN* 3.2 18.8 - - - +
208B VAL* 3.0 48.4 - - + +
209B ALA* 3.1 26.3 + - - +
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Residues in contact with PRO 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B ASN* 1.4 93.4 - - - +
207B GLN* 1.3 60.6 + - - +
209B ALA* 3.4 4.3 + - + +
210B ASP* 3.1 32.3 + - - +
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Residues in contact with GLN 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B ASN* 3.2 12.0 - - - +
206B PRO* 1.3 77.0 - - - +
208B VAL* 1.3 59.6 + - + +
210B ASP* 3.0 11.3 - - - +
211B LEU* 2.9 56.2 + - + +
415B ARG* 3.2 40.2 + - - +
419B PHE* 3.6 14.5 - - - -
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Residues in contact with VAL 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B ASN* 3.0 33.8 - - + +
207B GLN* 1.3 73.7 - - - +
209B ALA* 1.3 61.7 + - - +
211B LEU* 3.9 6.9 - - - +
212B LYS* 3.3 21.3 + - - +
419B PHE* 3.7 50.7 - - + +
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Residues in contact with ALA 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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205B ASN 3.1 20.2 + - - +
206B PRO* 3.7 4.7 - - + +
208B VAL* 1.3 79.4 - - - +
210B ASP* 1.3 60.9 + - - +
212B LYS* 3.4 21.6 - - - +
213B ALA* 3.4 7.3 + - - +
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Residues in contact with ASP 210 (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 PRO* 3.1 21.1 + - - +
207B GLN* 3.0 20.3 + - - +
209B ALA* 1.3 73.5 - - + +
211B LEU* 1.3 67.6 + - - +
212B LYS 3.2 1.3 - - - -
213B ALA* 3.5 10.1 + - + +
214B PHE* 3.1 25.1 + - - +
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Residues in contact with LEU 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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207B GLN* 2.9 47.0 + - + +
208B VAL* 3.9 5.6 - - - +
210B ASP* 1.3 82.4 + - - +
212B LYS* 1.3 53.6 + - - +
214B PHE* 3.4 7.7 - - + +
215B SER* 2.8 39.3 + - - -
412B THR* 4.2 25.1 - - + +
415B ARG* 4.0 7.2 - - + +
416B ALA* 3.8 31.2 - - + +
419B PHE* 3.4 32.3 - - + -
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Residues in contact with LYS 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 VAL 3.3 11.3 + - - +
209B ALA* 3.4 13.9 - - - +
211B LEU* 1.3 77.1 - - - +
213B ALA* 1.3 58.8 + - - +
215B SER* 3.8 7.0 - - - -
216B LYS* 3.1 33.2 + - + +
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Residues in contact with ALA 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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209B ALA 3.4 9.1 + - - +
210B ASP* 3.6 13.0 - - + +
211B LEU 3.4 0.4 - - - -
212B LYS* 1.3 75.9 - - - +
214B PHE* 1.3 64.1 + - - +
216B LYS* 3.4 7.3 + - - +
217B HIS* 3.2 21.1 + - - +
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Residues in contact with PHE 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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210B ASP 3.1 14.3 + - - +
211B LEU* 3.4 10.8 - - + +
212B LYS 3.4 0.2 - - - -
213B ALA* 1.3 73.4 - - - +
215B SER* 1.3 64.6 + - - +
217B HIS* 3.2 9.3 + - + +
218B ILE* 3.1 51.8 + - + +
303B ILE* 5.5 3.4 - - + -
304B PRO* 6.3 2.5 - - + -
305B SER* 4.6 17.7 - - - -
409B ILE* 5.0 3.4 - - + -
412B THR* 4.1 21.5 - - + -
413B ILE* 3.7 33.9 - - + -
416B ALA* 4.0 15.7 - - + -
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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
----------------------------------------------------------
211B LEU 2.8 23.3 + - - -
212B LYS* 3.8 9.1 - - - -
214B PHE* 1.3 72.8 - - - +
216B LYS* 1.3 57.7 + - - +
218B ILE* 3.5 2.0 + - - +
219B TYR* 3.0 29.1 + - - +
382B SER 5.6 0.7 - - - +
385B ALA* 5.6 0.2 - - - +
386B LEU* 3.6 31.7 - - - +
416B ALA* 3.4 23.0 + - - +
420B HIS* 4.6 13.4 - - - +
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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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212B LYS* 3.1 22.3 + - + +
213B ALA* 3.7 7.4 - - - +
214B PHE 3.3 0.2 - - - -
215B SER* 1.3 76.3 - - - +
217B HIS* 1.3 61.8 + - - +
219B TYR* 3.4 34.4 + - - +
220B ASN* 3.0 44.3 + - - +
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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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213B ALA 3.2 13.6 + - - +
214B PHE* 3.2 11.8 + - + +
216B LYS* 1.3 76.8 - - - +
218B ILE* 1.3 69.5 + - + +
220B ASN* 3.2 12.3 + - + +
221B ALA* 3.0 19.1 + - + +
302B SER 2.7 29.4 + - - -
303B ILE* 4.6 2.9 - - - -
304B PRO* 3.4 28.2 - - + +
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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 PHE* 3.1 49.7 + - + +
215B SER 3.9 4.0 - - - +
216B LYS 3.4 0.2 - - - -
217B HIS* 1.3 80.4 - - + +
219B TYR* 1.3 63.1 + - - +
221B ALA* 3.2 7.8 + - - +
222B TYR* 3.1 18.2 + - - +
299B PHE* 3.6 10.8 - - + -
303B ILE* 4.5 20.6 - - + -
385B ALA* 3.4 32.8 - - + +
386B LEU* 3.9 18.8 - - + +
389B ALA* 3.9 12.8 - - + -
413B ILE* 4.4 9.9 - - + -
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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 SER 3.0 18.1 + - - +
216B LYS* 3.6 33.7 - - - +
218B ILE* 1.3 75.5 - - - +
220B ASN* 1.3 59.1 + - - +
222B TYR* 3.2 4.3 + + - +
223B LEU* 2.9 64.5 + - + +
381B ASP* 3.7 19.4 - - + +
382B SER* 3.7 45.0 + - - +
385B ALA* 3.8 11.4 - - + +
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Residues in contact with ASN 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 LYS* 3.0 33.8 + - - +
217B HIS* 3.2 11.9 + - + +
219B TYR* 1.3 78.7 - - - +
221B ALA* 1.3 57.7 + - - +
223B LEU* 3.4 18.1 + - - +
224B LYS* 2.9 32.2 + - - +
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Residues in contact with ALA 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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217B HIS* 3.0 13.5 + - + +
218B ILE* 3.3 12.8 - - - +
220B ASN* 1.3 77.0 - - - +
222B TYR* 1.3 59.1 - - - +
224B LYS* 4.6 2.9 - - - -
225B ASN* 2.8 36.7 + - - +
299B PHE* 3.7 15.9 - - + +
302B SER* 3.7 33.4 - - - +
303B ILE* 4.6 2.5 - - + -
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Residues in contact with TYR 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 11.0 + - - +
219B TYR* 3.2 10.3 - + - +
221B ALA* 1.3 75.8 - - - +
223B LEU* 1.3 77.0 + - + +
226B PHE* 3.2 59.4 + + + +
228B MET 5.1 1.7 + - - -
229B THR* 4.5 13.2 - - + -
230B LYS 4.5 3.1 + - - -
299B PHE* 3.6 13.7 - + + -
329B MET* 4.9 13.9 - - - +
332B SER* 5.0 1.9 + - - -
381B ASP* 2.8 47.2 + - + -
384B LEU* 3.8 21.7 - - + +
385B ALA* 3.6 32.3 - - + -
388B ILE* 5.0 2.5 - - + -
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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 TYR* 2.9 66.6 + - + +
220B ASN* 3.7 18.2 - - - +
222B TYR* 1.3 84.7 - - + +
224B LYS* 1.3 60.2 + - - +
225B ASN 3.7 0.3 + - - -
226B PHE 4.5 7.2 - - - +
229B THR* 4.5 15.9 - - + -
381B ASP* 5.1 1.1 - - + -
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Residues in contact with LYS 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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220B ASN 2.9 17.8 + - - +
221B ALA* 3.8 5.2 - - - +
223B LEU* 1.3 78.5 - - - +
225B ASN* 1.3 73.0 + - - +
226B PHE 5.3 0.7 - - - -
302B SER* 4.5 13.5 - - - +
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Residues in contact with ASN 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 ALA 2.8 25.7 + - - +
222B TYR 3.3 0.6 + - - +
224B LYS* 1.3 97.2 - - - +
226B PHE* 1.3 64.0 + - - +
227B ASN 3.9 0.3 + - - -
295B GLU* 3.7 24.8 - - - +
298B GLU* 3.2 22.5 + - + +
299B PHE* 3.7 27.2 - - + +
302B SER* 3.0 28.8 + - - -
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Residues in contact with PHE 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 TYR* 3.2 60.0 + + + +
223B LEU 4.5 7.1 - - - +
224B LYS 5.3 0.3 - - - -
225B ASN* 1.3 77.2 - - - +
227B ASN* 1.3 63.7 + - - +
228B MET* 3.3 18.1 + - - +
229B THR* 4.9 7.4 - - + +
292B THR 5.1 0.2 - - - -
295B GLU* 3.6 31.9 - - + +
296B LEU* 3.6 26.0 - - + -
299B PHE* 3.5 37.9 - + + -
329B MET* 3.5 33.4 - - + -
388B ILE* 4.8 0.4 - - + -
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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
------------------------------------------------------------
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