Contacts of the helix formed by residues 210 - 229 (chain B) in PDB entry 5A6C
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
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Residue Dist Surf HB Arom Phob DC
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168B ARG* 4.6 7.4 + - - -
172B GLN* 5.2 2.4 - - - +
205B HIS* 3.2 38.0 + - - +
208B LEU* 3.9 22.0 - - - +
209B GLY* 1.3 76.1 + - - +
211B PHE* 1.3 61.7 + - - +
212B ARG 3.7 2.0 - - - -
213B ASP* 3.5 24.9 + - - +
214B ALA 3.5 3.5 + - - -
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Residues in contact with PHE 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B PRO* 4.2 9.9 - - + -
206B TYR* 3.6 44.4 - + - -
209B GLY* 3.2 29.9 + - - -
210B ASN* 1.3 70.8 - - - +
212B ARG* 1.3 62.2 + - - +
213B ASP 3.3 1.3 - - - -
214B ALA* 3.1 7.1 + - - +
215B VAL* 2.9 31.5 + - - +
244B ALA* 4.7 9.3 - - + +
247B PHE* 3.5 52.7 - + + -
248B LEU* 3.9 21.5 - - + -
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Residues in contact with ARG 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B ASN 3.7 0.2 - - - -
211B PHE* 1.3 78.2 - - - +
213B ASP* 1.3 62.7 + - - +
215B VAL* 3.0 12.4 + - + +
216B ILE* 2.9 34.7 + - + +
248B LEU* 4.7 16.6 - - + +
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Residues in contact with ASP 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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205B HIS* 3.8 31.0 + - + +
210B ASN* 3.5 25.7 + - - +
211B PHE 3.3 0.4 - - - -
212B ARG* 1.3 79.4 - - - +
214B ALA* 1.3 63.0 + - - +
216B ILE* 3.2 20.9 - - + +
217B ALA* 3.0 24.9 + - - +
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Residues in contact with ALA 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B GLY* 3.3 27.3 - - - +
205B HIS* 3.6 15.8 - - + +
206B TYR* 3.8 13.0 - - + +
210B ASN 3.5 4.2 + - - +
211B PHE* 3.1 13.0 + - - +
213B ASP* 1.3 78.6 - - - +
215B VAL* 1.3 57.7 + - - +
218B HIS* 2.9 45.1 + - + -
244B ALA* 4.9 5.8 - - + -
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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
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211B PHE 2.9 21.9 + - - +
212B ARG* 3.1 14.4 - - + +
214B ALA* 1.3 75.3 - - - +
216B ILE* 1.3 57.8 + - + +
218B HIS* 3.8 4.3 - - - +
219B GLU* 2.9 47.2 + - + +
241B LEU* 4.0 5.5 - - + +
244B ALA* 4.1 13.5 - - + -
245B TYR* 4.1 22.4 - - + +
248B LEU* 3.7 27.1 - - + -
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Residues in contact with ILE 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B PHE* 6.0 1.8 - - + -
212B ARG* 2.9 21.7 + - + +
213B ASP* 3.2 21.8 - - + +
215B VAL* 1.3 74.7 - - + +
217B ALA* 1.3 63.0 + - + +
219B GLU* 3.0 35.5 - - - +
220B GLN* 3.0 23.8 + - - +
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Residues in contact with ALA 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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198B PHE* 3.5 44.6 - - + +
201B LEU* 4.8 7.0 - - + -
202B GLY* 4.2 12.3 - - - +
205B HIS* 4.9 4.7 - - + -
213B ASP 3.0 14.1 + - - +
216B ILE* 1.3 78.4 - - + +
218B HIS* 1.3 66.8 + - - +
220B GLN* 3.2 5.2 + - - +
221B ARG* 3.0 19.6 + - - +
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Residues in contact with HIS 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B GLY* 3.6 14.8 + - - -
202B GLY* 3.2 17.5 + - - -
203B ASN* 3.3 36.2 + - - -
206B TYR* 4.7 5.2 - - + +
214B ALA* 2.9 35.4 + - + +
215B VAL 3.8 0.2 - - - +
217B ALA* 1.3 76.0 - - - +
219B GLU* 1.3 63.5 + - - +
221B ARG* 3.2 8.6 + - - +
222B LEU* 2.9 23.7 + - - +
237B ALA* 4.8 5.0 + - - +
240B ASN* 3.4 38.7 + - + +
241B LEU* 3.7 24.2 - - + +
244B ALA* 4.8 5.6 - - + -
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Residues in contact with GLU 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 VAL* 2.9 29.7 + - - +
216B ILE* 3.0 26.4 - - - +
218B HIS* 1.3 75.4 - - - +
220B GLN* 1.3 55.5 + - - +
222B LEU* 3.2 14.5 - - + +
223B LEU* 3.0 25.9 + - - +
241B LEU* 4.1 14.5 - - + +
245B TYR* 4.1 9.6 + - - +
257B TYR* 6.1 0.4 - - - +
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Residues in contact with GLN 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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191B ARG* 5.8 2.2 - - - +
198B PHE* 3.4 41.3 - - + -
216B ILE* 3.0 30.0 + - - +
217B ALA 3.2 8.7 + - - +
219B GLU* 1.3 74.5 - - - +
221B ARG* 1.3 60.1 + - - +
223B LEU* 2.8 48.7 + - + +
224B ILE* 3.0 15.1 + - + +
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Residues in contact with ARG 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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192B ALA 5.1 1.4 + - - -
195B GLY* 3.3 40.9 + - - +
196B ARG* 4.2 9.3 - - - +
198B PHE* 3.9 3.0 - - + +
199B GLY* 3.7 20.9 - - - +
217B ALA 3.0 11.9 + - - +
218B HIS* 3.6 9.4 - - - +
220B GLN* 1.3 72.1 - - - +
222B LEU* 1.3 63.7 + - - +
224B ILE* 3.4 4.2 + - - +
225B ALA* 3.0 36.2 + - - +
230B ASP* 4.3 8.1 + - - -
233B ALA* 2.7 45.7 + - - +
236B ARG* 4.2 2.2 - - - +
237B ALA* 4.0 17.9 - - + +
377B GLU* 3.2 34.7 + - - +
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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 HIS 2.9 12.7 + - - +
219B GLU* 3.2 15.3 - - + +
221B ARG* 1.3 78.0 - - - +
223B LEU* 1.3 63.1 + - - +
225B ALA* 3.3 2.0 + - + -
226B LYS* 2.9 49.1 + - + +
234B GLU* 5.2 7.9 - - + +
237B ALA* 4.1 16.2 - - + -
238B TYR* 3.8 32.1 - - + -
241B LEU* 3.8 23.3 - - + -
257B TYR* 5.2 7.4 - - + +
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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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191B ARG* 3.9 25.6 - - - +
219B GLU 3.0 11.0 + - - +
220B GLN* 2.8 43.7 + - + +
222B LEU* 1.3 72.4 - - - +
224B ILE* 1.3 56.5 + - + +
226B LYS* 3.2 11.8 - - + +
227B GLU* 3.0 30.2 + - - +
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Residues in contact with ILE 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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191B ARG* 3.8 42.2 - - - +
192B ALA* 4.4 6.7 - - - +
194B GLN* 4.5 2.0 - - + -
195B GLY* 3.8 30.1 - - - +
198B PHE* 4.2 13.9 - - + -
220B GLN* 3.0 23.9 + - + +
221B ARG* 4.0 8.5 - - - +
223B LEU* 1.3 74.0 - - + +
225B ALA* 1.3 64.0 + - - +
226B LYS 2.9 5.9 + - - -
227B GLU* 3.1 20.9 + - - +
228B PHE* 3.0 41.9 + - + +
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Residues in contact with ALA 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 ARG* 3.0 32.6 + - - +
222B LEU* 3.8 6.5 - - + +
224B ILE* 1.3 78.1 - - - +
226B LYS* 1.3 55.7 + - - +
228B PHE* 3.7 1.7 + - - -
229B GLY* 3.1 6.9 + - - -
230B ASP* 2.9 41.1 + - + -
233B ALA 3.9 21.3 - - - +
234B GLU* 3.7 14.1 - - + +
237B ALA* 5.4 0.9 - - + -
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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 LEU* 2.9 40.3 + - + +
223B LEU* 3.2 14.4 - - - +
224B ILE 2.9 0.6 - - - -
225B ALA* 1.3 74.7 - - - +
227B GLU* 1.3 56.6 + - - +
228B PHE 3.0 9.3 + - - -
229B GLY* 3.2 11.3 + - - -
234B GLU* 4.4 14.1 + - - +
238B TYR* 4.4 15.2 + - - -
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Residues in contact with GLU 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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191B ARG* 3.2 56.0 + - - +
223B LEU* 3.0 19.1 + - - +
224B ILE* 3.1 21.5 + - - +
226B LYS* 1.3 73.0 - - - +
228B PHE* 1.3 69.2 + - + +
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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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183A SER* 4.3 15.7 - - - -
191B ARG* 4.1 11.7 - - + -
192B ALA* 3.9 34.3 - - + -
224B ILE* 3.0 23.0 + - + +
225B ALA* 4.3 4.7 - - - +
226B LYS 3.0 0.8 - - - -
227B GLU* 1.3 106.8 - - + +
229B GLY* 1.3 63.1 + - - +
230B ASP* 4.6 13.0 - - + +
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Residues in contact with GLY 229 (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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225B ALA 3.1 6.7 + - - -
226B LYS 3.2 10.3 + - - -
228B PHE* 1.3 80.3 - - - +
230B ASP* 1.3 63.4 + - - +
231B LYS* 3.3 11.1 + - - +
234B GLU* 4.2 9.4 - - - -
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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