Contacts of the helix formed by residues 207 - 219 (chain B) in PDB entry 3BQM
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 207 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173B PHE* 4.1 4.3 - - - -
174B SER 2.8 15.7 + - - +
175B THR* 2.8 38.6 + - - +
177B TYR* 3.5 15.1 + - + +
205B LEU* 4.7 6.3 - - - +
206B THR* 1.3 69.2 - - - +
208B THR* 1.3 58.9 + - - +
209B PHE 3.4 2.4 + - - -
210B GLY 3.6 0.3 + - - -
211B ALA* 3.0 28.6 + - - +
243B THR* 3.0 18.2 + - - +
244B ASP* 3.4 31.1 + - - +
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Residues in contact with THR 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B LEU* 5.4 0.2 - - + -
173B PHE* 3.6 27.5 - - + -
206B THR* 2.9 20.5 + - - +
207B ASN* 1.3 71.7 - - - +
209B PHE* 1.3 64.9 + - - +
211B ALA* 3.6 1.9 - - + +
212B ILE* 3.0 44.6 + - + +
236B ILE* 4.5 11.4 - - + -
238B THR* 4.8 4.0 + - + +
240B GLY 5.0 0.9 + - - -
242B ALA* 3.7 18.1 + - - +
244B ASP* 3.2 2.8 + - - -
258B ILE* 5.1 1.8 - - + -
277B PHE* 3.9 20.0 - - + -
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Residues in contact with PHE 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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208B THR* 1.3 75.3 - - - +
210B GLY* 1.3 63.8 + - - +
212B ILE* 3.5 1.9 + - - +
213B ASN* 2.9 34.0 + - - +
242B ALA* 4.3 3.4 - - + -
244B ASP* 3.1 40.4 + - - +
245B SER* 3.6 19.3 - - - +
246B GLY 3.4 20.9 - - - -
247B ASN* 3.6 29.6 - - - +
248B ILE* 4.0 9.6 - - + +
276B LYS* 3.6 33.0 - - + -
277B PHE* 3.5 29.4 - + - -
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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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177B TYR* 3.2 26.0 - - - -
209B PHE* 1.3 76.0 - - - +
211B ALA* 1.3 51.2 + - - +
213B ASN* 3.3 7.8 + - - +
214B TYR* 2.8 34.5 + - - +
244B ASP* 2.9 13.5 + - - -
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Residues in contact with ALA 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B LEU* 3.9 13.2 - - + +
173B PHE* 3.5 37.5 - - + -
177B TYR* 3.2 13.5 - - + -
207B ASN 3.0 19.0 + - - +
208B THR* 3.6 5.2 - - - +
209B PHE 3.3 0.2 - - - -
210B GLY* 1.3 72.8 - - - +
212B ILE* 1.3 60.9 + - - +
214B TYR* 3.2 5.1 + - - +
215B VAL* 3.0 31.2 + - - +
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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
----------------------------------------------------------
135B LEU* 3.8 20.4 - - + -
208B THR* 3.0 23.7 + - + +
211B ALA* 1.3 76.9 - - - +
213B ASN* 1.3 62.1 + - - +
215B VAL* 3.3 6.1 + - - +
216B ALA* 3.1 21.3 + - - +
234B LEU* 4.4 10.4 - - + +
236B ILE* 3.7 25.4 - - + -
248B ILE* 3.5 26.7 - - + -
251B ALA* 3.6 22.1 - - + +
256B ARG* 5.0 1.3 - - - -
277B PHE* 3.6 37.2 - - + +
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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
----------------------------------------------------------
209B PHE* 2.9 29.7 + - - +
210B GLY* 3.6 7.5 - - - +
212B ILE* 1.3 76.1 - - - +
214B TYR* 1.3 59.6 + - - +
216B ALA* 3.4 4.2 + - - +
217B THR* 3.0 33.7 + - + +
247B ASN* 2.8 30.0 + - - +
248B ILE* 4.1 9.5 - - - +
249B ASP 4.8 0.2 + - - -
250B ALA* 3.6 22.9 + - + +
251B ALA 5.1 0.5 + - - -
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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
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171B VAL* 3.7 23.3 - - + -
177B TYR* 3.6 45.4 + + + -
178B LYS* 4.5 0.2 - - - -
179B THR* 3.1 36.7 + - - -
210B GLY 2.8 20.9 + - - +
211B ALA 3.3 6.7 - - - +
213B ASN* 1.3 70.6 - - - +
215B VAL* 1.3 61.6 + - - +
217B THR* 4.2 4.3 - - - -
218B GLU* 2.8 54.7 + - + +
219B VAL* 3.5 8.0 + - + -
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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
----------------------------------------------------------
133B VAL* 3.9 29.4 - - + -
135B LEU* 4.0 26.9 - - + -
171B VAL* 4.2 11.7 - - + -
211B ALA 3.0 17.9 + - - +
212B ILE 3.6 8.1 - - - +
213B ASN 3.3 0.2 - - - -
214B TYR* 1.3 74.2 - - - +
216B ALA* 1.3 66.6 + - - +
219B VAL* 3.0 24.4 + - + -
220B PHE* 3.2 36.2 + - + -
234B LEU* 4.0 15.5 - - + -
254B ILE* 5.0 0.2 - - + -
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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
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212B ILE 3.1 16.6 + - - +
213B ASN* 3.7 5.6 - - - +
214B TYR 3.4 0.2 - - - -
215B VAL* 1.3 80.6 - - - +
217B THR* 1.3 58.9 + - - +
220B PHE* 4.0 17.7 - - - +
250B ALA* 3.3 39.2 - - + +
251B ALA* 4.0 10.1 - - + -
254B ILE* 4.1 13.7 - - + -
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Residues in contact with THR 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* 3.0 21.5 + - + +
214B TYR* 3.9 1.2 + - - -
216B ALA* 1.3 81.7 - - - +
218B GLU* 1.3 81.7 + - - +
219B VAL 3.7 0.4 - - - -
220B PHE 5.1 0.2 - - - +
221B ARG* 3.3 19.2 - - - +
250B ALA* 4.3 20.2 - - + -
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Residues in contact with GLU 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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179B THR* 5.2 0.5 + - - -
214B TYR* 2.8 47.9 + - + +
217B THR* 1.3 93.6 + - - +
219B VAL* 1.3 56.6 + - - +
221B ARG* 2.7 51.9 + - - +
224B LEU* 3.7 7.6 - - - +
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Residues in contact with VAL 219 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B VAL* 3.8 27.8 - - + -
169B ALA* 4.3 11.2 - - + -
171B VAL* 3.8 12.1 - - + -
179B THR* 3.6 23.1 - - + +
183B PHE* 3.6 18.1 - - + -
214B TYR* 3.8 13.7 - - + -
215B VAL* 3.0 29.1 + - + +
218B GLU* 1.3 82.3 - - - +
220B PHE* 1.3 61.5 + - - +
221B ARG* 2.9 9.6 + - - +
224B LEU* 3.9 20.6 - - + +
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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