Contacts of the helix formed by residues 208 - 218 (chain B) in PDB entry 2BTO
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 208 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173B VAL* 3.2 15.6 - - - +
174B LEU 3.1 20.3 + - - +
176B SER* 3.9 14.3 - - - +
206B PHE 3.4 2.0 + - - -
207B ASP* 1.3 71.8 + - - +
209B GLU* 1.3 57.1 + - - +
211B LEU* 3.6 10.2 - - - +
212B PHE* 2.9 31.5 + - - +
229B LEU* 3.7 12.3 - - + +
1433B GTP 2.8 72.0 + - - -
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Residues in contact with GLU 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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176B SER* 3.5 15.4 - - - +
177B PRO* 3.7 24.1 - - + +
207B ASP* 3.1 14.7 + - - +
208B ASN* 1.3 80.0 - - - +
210B ALA* 1.3 62.7 + - - +
212B PHE* 3.5 5.1 - - + +
213B ASP* 3.1 33.5 + - - +
308B ALA* 3.6 12.8 - - + +
385B ARG* 3.0 33.5 + - - +
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Residues in contact with ALA 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* 3.0 8.5 + - - +
209B GLU* 1.3 76.3 - - - +
211B LEU* 1.3 59.8 + - - +
213B ASP* 3.1 8.5 + - - +
214B LEU* 2.9 36.2 + - + +
305B VAL 3.7 10.5 - - - +
306B PHE* 3.7 2.2 - - - -
307B ALA 3.4 42.8 - - - +
308B ALA* 3.7 5.9 - - - +
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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
----------------------------------------------------------
206B PHE* 4.4 7.0 - - + -
207B ASP 3.1 16.3 + - - +
208B ASN* 3.6 26.0 - - - +
210B ALA* 1.3 74.5 - - - +
212B PHE* 1.3 63.9 + - - +
214B LEU* 3.4 1.5 + - + -
215B ALA* 3.0 26.2 + - - +
229B LEU* 3.7 20.0 - - + +
232B LEU* 3.7 29.0 - - + +
233B ILE* 3.7 29.6 - - + -
306B PHE* 3.7 40.8 - - + -
1433B GTP 4.2 2.2 - - - +
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Residues in contact with PHE 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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176B SER* 5.4 6.5 - - - +
208B ASN 2.9 18.5 + - - +
209B GLU* 3.5 7.2 - - + +
211B LEU* 1.3 77.8 - - - +
213B ASP* 1.3 71.4 + - - +
215B ALA* 3.3 2.6 + - - +
216B HIS* 3.0 31.9 + + + +
222B GLU 5.3 1.8 - - - -
223B SER* 5.4 0.7 - - - -
224B PRO* 3.6 48.2 - - + +
229B LEU* 3.7 18.0 - - + +
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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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209B GLU* 3.1 22.4 + - - +
210B ALA* 3.1 10.3 + - - +
212B PHE* 1.3 88.1 - - - +
214B LEU* 1.3 54.0 + - + +
216B HIS* 3.0 6.7 + - - +
217B ARG* 2.6 50.3 + - + +
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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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210B ALA* 2.9 29.1 + - + +
211B LEU* 3.8 7.2 - - - +
213B ASP* 1.3 72.1 - - + +
215B ALA* 1.3 59.5 + - - +
217B ARG* 3.6 13.4 - - - +
218B LYS* 2.9 42.5 + - + +
219B TRP* 3.5 3.3 + - - -
232B LEU* 4.2 15.7 - - + -
279B LEU* 3.8 20.2 - - + -
303B GLY 3.2 28.5 - - - +
304B SER* 4.4 0.7 - - - +
305B VAL 4.2 7.9 - - - +
306B PHE* 3.8 36.1 - - + -
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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
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211B LEU 3.0 17.5 + - - +
212B PHE 3.7 3.4 - - - +
214B LEU* 1.3 76.9 - - - +
216B HIS* 1.3 59.7 + - - +
219B TRP* 3.1 44.9 - - + +
221B ILE* 3.3 15.0 + - + +
224B PRO* 4.1 19.1 - - + -
228B ASP* 4.5 7.6 - - + -
229B LEU* 4.2 8.3 - - + -
232B LEU* 4.6 5.1 - - + +
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Residues in contact with HIS 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 PHE* 3.0 23.8 + + + +
213B ASP* 3.6 5.6 - - - +
215B ALA* 1.3 76.2 - - - +
217B ARG* 1.3 66.4 + - + +
220B ASN* 3.0 26.6 + - - -
221B ILE 3.2 24.4 + - - +
222B GLU* 3.7 34.5 + - - -
224B PRO* 4.1 6.4 - - + +
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Residues in contact with ARG 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 ASP* 2.6 29.0 + - + +
214B LEU* 3.6 17.2 - - - +
216B HIS* 1.3 82.6 - - + +
218B LYS* 1.3 85.0 + - + +
219B TRP 3.1 1.6 + - - -
220B ASN* 3.6 10.6 + - - +
303B GLY* 2.6 44.0 + - - -
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Residues in contact with LYS 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 LEU* 2.9 32.8 + - + +
217B ARG* 1.3 100.4 - - + +
219B TRP* 1.3 74.5 + - + +
220B ASN* 4.4 5.0 - - - +
279B LEU* 3.9 28.3 - - + +
281B PRO* 3.8 15.6 - - - +
298B SER* 5.8 4.9 + - - -
301B ASP* 5.8 2.0 + - - -
303B GLY 4.3 6.5 - - - -
304B SER* 5.0 5.5 + - - -
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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