Contacts of the helix formed by residues 207 - 223 (chain B) in PDB entry 5A36
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 ASP 207 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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204B ASN* 3.7 6.6 + - - +
205B LYS 3.4 0.2 - - - -
206B ASP* 1.3 80.0 - - + +
208B PRO* 1.3 58.8 - - - +
209B ILE* 3.9 5.9 + - - +
210B GLY* 3.1 30.8 + - - -
211B ASN* 2.8 38.9 + - - +
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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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181B LYS 3.7 12.8 - - - +
182B ASP* 3.5 23.3 - - + +
205B LYS 3.3 12.1 - - - +
206B ASP 3.2 10.3 - - - +
207B ASP* 1.3 87.6 - - - +
209B ILE* 1.3 60.7 + - + +
211B ASN* 3.2 1.1 + - - +
212B ILE* 2.9 34.8 + - - +
235B VAL* 3.7 35.9 - - + -
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Residues in contact with ILE 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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207B ASP* 3.2 5.5 + - - +
208B PRO* 1.3 78.3 - - + +
210B GLY* 1.3 64.1 + - - +
212B ILE* 3.5 4.1 + - - +
213B ASN* 3.0 46.8 + - - +
231B ALA* 4.0 13.9 - - + +
232B GLU* 3.8 36.1 - - + +
235B VAL* 3.4 36.1 - - + -
236B ASN* 5.1 0.4 - - - +
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Residues in contact with GLY 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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207B ASP* 3.1 26.7 + - - -
209B ILE* 1.3 79.9 - - - +
211B ASN* 1.3 52.0 + - - +
213B ASN* 3.7 4.6 - - - +
214B LEU* 2.7 39.1 + - - +
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Residues in contact with ASN 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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182B ASP 3.1 23.7 + - - +
183B GLY* 4.0 8.1 - - - +
184B LEU* 3.9 13.2 - - - +
187B CYS* 3.3 16.8 - - - -
203B LEU* 3.8 24.6 - - - +
204B ASN 2.9 30.6 + - - +
205B LYS* 4.7 0.4 - - - +
207B ASP* 2.8 31.6 + - - +
208B PRO* 3.4 5.4 - - - +
210B GLY* 1.3 73.0 - - - +
212B ILE* 1.3 62.7 + - - +
214B LEU* 3.5 5.2 - - - +
215B ALA* 3.0 19.1 + - - +
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Residues in contact with ILE 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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180B TRP 4.4 3.8 - - - +
181B LYS 3.8 20.6 - - - +
183B GLY* 3.6 18.4 - - - -
186B LEU* 4.6 8.0 - - + +
208B PRO 2.9 18.2 + - - +
209B ILE 3.8 3.1 - - - +
211B ASN* 1.3 74.8 - - - +
213B ASN* 1.3 53.1 + - - +
215B ALA* 3.2 7.8 + - - +
216B MET* 2.8 46.1 + - + +
229B LEU* 4.4 18.6 - - + -
231B ALA* 3.8 24.2 - - + -
234B ILE* 3.9 26.0 - - + -
235B VAL* 4.0 11.2 - - + -
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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
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209B ILE* 3.0 43.0 + - - +
210B GLY* 3.9 5.3 - - - +
212B ILE* 1.3 73.3 - - - +
214B LEU* 1.3 60.7 + - - +
216B MET* 3.3 24.8 - - - +
217B GLU* 2.8 31.0 + - - +
227B LYS* 5.0 2.6 - - - +
231B ALA* 4.2 8.6 - - - +
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Residues in contact with LEU 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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187B CYS* 4.6 1.3 - - - -
198B ILE* 4.0 21.1 - - + -
203B LEU* 3.9 28.9 - - + -
210B GLY 2.7 19.0 + - - +
211B ASN* 3.5 4.7 - - - +
212B ILE 3.2 0.2 - - - -
213B ASN* 1.3 74.0 - - - +
215B ALA* 1.3 66.2 + - - +
217B GLU* 3.2 7.4 + - + +
218B ILE* 3.0 47.0 + - + +
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Residues in contact with ALA 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B LEU* 3.8 30.3 - - + -
187B CYS* 4.0 11.2 - - - -
190B ILE* 3.5 23.0 - - + +
211B ASN 3.0 13.4 + - - +
212B ILE 3.5 7.6 - - - +
214B LEU* 1.3 77.2 - - - +
216B MET* 1.3 63.2 + - - +
218B ILE* 4.7 2.0 - - - -
219B ALA* 3.0 26.2 + - - +
248B TYR* 4.4 2.5 - - - +
252B PHE* 5.4 1.8 - - + -
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Residues in contact with MET 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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42B LYS* 5.3 1.8 - - - +
186B LEU* 5.4 0.4 - - + -
212B ILE* 2.8 38.1 + - + +
213B ASN* 3.3 28.0 - - - +
215B ALA* 1.3 74.2 - - + +
217B GLU* 1.3 62.7 + - - +
219B ALA* 3.5 1.2 + - - +
220B GLU* 3.1 25.6 + - - +
225B ILE 4.5 0.9 - - - +
227B LYS* 3.9 33.4 - - + +
228B MET 4.1 0.4 - - - -
229B LEU* 3.6 46.7 - - + +
231B ALA* 4.5 3.8 - - + -
248B TYR* 3.4 28.5 + - + +
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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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213B ASN 2.8 21.9 + - - +
214B LEU* 3.2 9.6 + - + +
216B MET* 1.3 73.0 - - - +
218B ILE* 1.3 60.8 + - + +
220B GLU* 3.2 11.8 - - - +
221B LYS* 3.0 31.7 + - + +
227B LYS* 2.7 36.7 + - - +
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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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190B ILE* 4.1 23.6 - - + -
197B LEU* 4.0 35.0 - - + +
198B ILE* 3.9 21.8 - - + -
214B LEU* 3.0 47.5 + - + +
215B ALA* 3.9 3.8 - - - +
217B GLU* 1.3 76.4 - - + +
219B ALA* 1.3 62.9 + - - +
220B GLU 3.2 0.2 + - - -
221B LYS* 3.3 1.1 + - - -
222B HIS* 2.8 44.5 + - + +
223B LEU* 5.6 1.3 - - + -
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Residues in contact with ALA 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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190B ILE* 4.4 1.1 - - + +
215B ALA 3.0 18.3 + - - +
216B MET 4.0 0.7 - - - +
218B ILE* 1.3 76.8 - - - +
220B GLU* 1.3 57.5 + - - +
223B LEU* 2.9 26.3 + - + -
224B ASP 2.8 26.3 + - - -
225B ILE* 3.1 14.8 + - + +
248B TYR* 3.8 9.0 - - - +
252B PHE* 3.6 28.3 - - + -
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Residues in contact with GLU 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 MET 3.1 18.4 + - - +
217B GLU* 3.2 21.2 - - - +
219B ALA* 1.3 74.6 - - - +
221B LYS* 1.3 68.2 + - - +
224B ASP* 3.8 12.5 + - - -
225B ILE 3.1 18.8 + - - +
226B PRO* 4.6 7.1 - - + +
227B LYS* 3.6 31.8 + - + +
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Residues in contact with LYS 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 GLU* 3.0 23.2 + - + +
218B ILE* 4.5 0.9 - - - -
220B GLU* 1.3 82.4 + - - +
222B HIS* 1.3 82.3 + - + +
224B ASP* 4.9 0.5 + - - -
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Residues in contact with HIS 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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194B ARG* 4.7 11.6 + - - +
197B LEU* 3.6 41.9 - - + +
218B ILE* 2.8 34.0 + - + +
221B LYS* 1.3 92.5 + - + +
223B LEU* 1.3 63.8 + - + +
224B ASP* 3.4 5.1 + - - +
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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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190B ILE* 4.5 13.0 - - + -
194B ARG* 3.8 30.7 - - + +
197B LEU* 4.8 3.1 - - + -
218B ILE* 4.8 0.7 - - + +
219B ALA* 2.9 33.5 + - + +
222B HIS* 1.3 79.3 - - + +
224B ASP* 1.3 70.1 + - - +
225B ILE* 3.3 21.2 + - + +
252B PHE* 4.3 10.8 - - + -
255B ALA* 4.7 11.1 - - + +
256B PHE* 3.7 38.8 - - + -
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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