Contacts of the helix formed by residues 210 - 231 (chain B) in PDB entry 2B7O
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 ALA 210 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208B SER* 3.2 6.6 + - - +
209B PRO* 1.3 78.1 - - - +
211B GLY* 1.3 52.5 + - - +
212B ALA* 3.4 2.5 - - - -
213B ARG* 2.6 46.4 + - + +
214B TYR* 3.6 23.0 - - + -
451B GLU* 4.0 16.6 - - - +
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Residues in contact with GLY 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B PHE* 5.8 0.2 - - - -
205B VAL* 3.3 33.5 - - - +
208B SER* 2.8 22.7 + - - -
209B PRO 3.2 0.6 - - - -
210B ALA* 1.3 74.2 - - - +
212B ALA* 1.3 53.8 + - - +
213B ARG 2.8 0.7 + - - -
214B TYR* 2.7 31.1 + - - +
215B GLU* 3.1 10.6 + - - +
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Residues in contact with ALA 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B VAL 4.6 0.2 + - - -
208B SER 4.9 0.4 + - - -
209B PRO 4.8 3.2 + - - +
210B ALA 3.4 1.5 - - - -
211B GLY* 1.3 73.0 - - - +
213B ARG* 1.3 61.3 + - - +
215B GLU* 3.9 18.4 + - - +
216B ALA* 5.0 1.4 + - - +
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Residues in contact with ARG 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B ALA* 2.6 31.2 + - + +
212B ALA* 1.3 74.6 - - - +
214B TYR* 1.3 93.5 + - + +
215B GLU 3.9 0.2 + - - -
216B ALA* 4.9 4.9 + - - +
217B LEU* 5.6 0.5 + - - +
451B GLU* 4.9 0.9 - - - -
455B LEU* 3.6 23.3 - - - +
458B GLU* 5.4 8.7 - - - +
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Residues in contact with TYR 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B PHE* 4.2 16.6 - + + -
205B VAL* 4.2 12.8 - - + -
210B ALA* 3.6 24.2 - - + -
211B GLY* 2.7 12.9 + - - +
213B ARG* 1.3 103.2 + - + +
215B GLU* 1.3 55.7 + - - -
216B ALA 3.4 2.9 - - - -
217B LEU* 3.3 6.2 + - + +
218B ALA* 3.0 28.1 + - - +
451B GLU* 2.7 51.0 + - + +
454B PHE* 3.5 43.5 - + + -
455B LEU* 3.4 27.7 - - + +
458B GLU* 6.3 2.2 - - + -
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Residues in contact with GLU 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B VAL* 3.5 26.7 - - + -
211B GLY 3.1 9.9 + - - +
212B ALA* 4.0 14.1 - - - +
213B ARG 3.6 1.2 - - - -
214B TYR* 1.3 77.1 - - - +
216B ALA* 1.3 58.6 + - - +
218B ALA* 3.3 2.2 + - - +
219B THR* 2.9 46.5 + - - +
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Residues in contact with ALA 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B ALA 5.0 1.2 + - - -
213B ARG 4.9 4.6 + - - +
214B TYR 3.4 0.4 - - - -
215B GLU* 1.3 81.6 + - - +
217B LEU* 1.3 57.6 + - - +
219B THR* 3.7 5.6 - - - +
220B GLU* 2.9 30.8 + - - +
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Residues in contact with LEU 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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112B VAL* 4.4 3.8 - - + -
115B TYR* 3.8 33.0 - - + -
213B ARG 5.6 0.6 + - - +
214B TYR* 3.3 10.1 + - + +
216B ALA* 1.3 75.4 - - - +
218B ALA* 1.3 61.2 + - - +
220B GLU* 3.1 6.2 + - + -
221B ILE* 2.9 34.3 + - + +
454B PHE* 3.5 31.4 - - + +
457B ALA* 3.8 28.0 - - + -
458B GLU* 3.5 28.0 - - + +
461B ARG* 4.1 14.8 - - - +
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Residues in contact with ALA 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B HIS* 2.9 33.5 + - + +
201B ASN 5.0 0.7 - - - +
202B ARG* 4.5 10.9 - - + -
205B VAL* 3.7 24.0 - - + -
214B TYR 3.0 17.9 + - - +
215B GLU* 3.3 4.9 + - - +
217B LEU* 1.3 77.8 - - - +
219B THR* 1.3 56.5 + - - +
221B ILE 3.4 0.2 + - - -
222B ASP* 3.0 15.4 + - - +
454B PHE* 3.8 14.7 - - + -
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Residues in contact with THR 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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202B ARG* 5.8 1.1 - - - +
215B GLU* 2.9 36.3 + - - +
216B ALA* 3.7 6.7 - - - +
218B ALA* 1.3 73.4 - - - +
220B GLU* 1.3 66.3 + - - +
222B ASP* 3.2 8.1 + - + +
223B ARG* 3.0 57.0 + - + +
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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
----------------------------------------------------------
115B TYR* 2.6 34.9 + - + +
216B ALA 2.9 19.6 + - - +
217B LEU* 3.1 8.7 + - - +
219B THR* 1.3 75.4 - - - +
221B ILE* 1.3 56.9 + - - +
223B ARG* 3.3 10.2 + - + +
224B GLY* 2.9 24.6 + - - -
461B ARG* 2.7 43.2 + - - -
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Residues in contact with ILE 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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111B VAL* 5.0 9.4 - - + +
112B VAL* 3.9 39.3 - - + -
115B TYR* 3.6 37.8 - - + -
198B HIS* 3.4 36.3 - - + +
217B LEU* 2.9 35.4 + - + +
220B GLU* 1.3 72.9 - - - +
222B ASP* 1.3 57.6 + - - +
224B GLY* 3.2 2.1 + - - -
225B LEU* 2.9 35.5 + - + +
454B PHE* 4.4 3.4 - - + -
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Residues in contact with ASP 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B HIS* 3.7 8.9 + - + -
199B ASP* 5.1 1.7 - - - +
202B ARG* 3.7 29.6 + - - +
218B ALA 3.0 17.5 + - - +
219B THR* 3.6 8.1 - - + +
221B ILE* 1.3 77.5 - - - +
223B ARG* 1.3 58.6 + - - +
225B LEU* 3.3 8.2 + - - +
226B ARG* 2.7 78.3 + - - +
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Residues in contact with ARG 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 THR* 3.0 43.8 + - + +
220B GLU* 3.7 8.3 - - - +
221B ILE 3.2 0.2 - - - -
222B ASP* 1.3 75.3 - - - +
224B GLY* 1.3 60.4 + - - +
226B ARG* 3.8 7.6 - - - +
227B PHE* 2.9 31.8 + - - +
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Residues in contact with GLY 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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115B TYR* 4.6 14.4 - - - -
220B GLU 2.9 14.0 + - - -
221B ILE 3.2 4.0 + - - -
223B ARG* 1.3 76.5 - - - +
225B LEU* 1.3 60.2 + - - +
227B PHE* 3.4 11.0 - - - +
228B MSE 3.1 26.8 + - - +
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Residues in contact with LEU 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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111B VAL* 5.7 4.7 - - + -
194B LEU* 3.8 42.8 - - + +
195B HIS* 4.9 9.0 - - + +
198B HIS* 3.5 38.6 - - + -
221B ILE* 2.9 26.3 + - + +
222B ASP* 3.7 8.7 - - - +
223B ARG 3.3 0.2 - - - -
224B GLY* 1.3 76.1 - - - +
226B ARG* 1.3 64.6 + - + +
228B MSE 3.3 22.3 - - + +
229B SER* 3.2 23.6 + - - -
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Residues in contact with ARG 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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199B ASP* 5.3 0.8 + - - -
202B ARG* 3.7 22.4 - - - +
222B ASP* 2.7 55.7 + - - +
223B ARG* 4.0 8.0 - - - +
225B LEU* 1.3 73.9 - - + +
227B PHE* 1.3 60.2 + - - +
229B SER* 3.4 8.1 + - - -
230B ALA* 2.8 29.8 + - - +
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Residues in contact with PHE 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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223B ARG 2.9 19.3 + - - +
224B GLY* 3.4 11.9 - - - +
226B ARG* 1.3 73.4 - - - +
228B MSE 1.3 67.6 + - + +
230B ALA* 3.1 11.1 + - + +
231B CYS* 2.9 50.7 + - - -
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Residues in contact with MSE 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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194B LEU* 3.9 30.5 - - + -
224B GLY 3.1 17.2 + - - +
225B LEU* 3.3 21.5 - - + +
227B PHE* 1.3 80.3 - - + +
229B SER* 1.3 63.5 + - - +
231B CYS* 3.2 11.0 + - - +
233B VAL* 3.1 47.7 + - + +
235B ASP* 5.8 0.4 - - - +
238B LEU* 4.1 20.2 - - + -
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Residues in contact with SER 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 LEU 3.2 12.5 + - - -
226B ARG* 3.7 9.5 - - - -
228B MSE 1.3 74.1 - - - +
230B ALA* 1.3 62.2 + - - +
231B CYS 3.0 1.8 - - - -
232B GLY* 2.8 21.1 + - - -
233B VAL 3.6 17.1 + - - -
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Residues in contact with ALA 230 (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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226B ARG 2.8 20.7 + - - +
227B PHE* 3.1 14.6 + - + +
229B SER* 1.3 73.7 - - - +
231B CYS* 1.3 59.2 + - - +
232B GLY* 3.2 4.3 + - - -
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Residues in contact with CYS 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B PHE* 2.9 48.0 + - - +
228B MSE 3.5 12.1 - - - +
229B SER 3.0 0.8 - - - -
230B ALA* 1.3 74.8 - - - +
232B GLY* 1.3 58.1 + - - +
233B VAL* 3.5 9.1 + - + +
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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
------------------------------------------------------------
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