Contacts of the helix formed by residues 205 - 214 (chain B) in PDB entry 1BK6
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 THR 205 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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495A ASP* 5.7 1.6 - - - +
498A TYR* 6.0 1.3 - - - +
204B SER* 1.3 72.8 - - - +
206B ASP* 1.3 64.8 + - - +
208B ARG* 3.6 27.1 + - - +
209B ASP* 2.5 39.9 + - - +
244B ARG 5.5 0.2 - - - +
245B GLY* 5.0 7.6 - - - -
247B LYS* 5.2 4.0 - - + -
248B PRO* 3.4 37.2 - - + +
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Residues in contact with ASP 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B SER* 3.7 15.5 + - - +
205B THR* 1.3 82.2 + - - +
207B TYR* 1.3 63.9 + - + +
209B ASP* 3.0 8.7 + - - +
210B TYR* 2.6 34.9 + - - +
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Residues in contact with TYR 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B SER 5.0 1.1 + - - -
166B THR* 4.1 10.8 - - + -
167B LYS* 3.6 34.6 + - + +
170B VAL* 3.7 39.8 - - + +
171B ASP* 5.3 0.7 + - - -
200B VAL* 3.3 25.6 - - + +
201B ALA* 4.4 0.9 - - - -
203B ASP* 3.7 32.1 - - + -
204B SER* 3.1 13.3 + - - +
206B ASP* 1.3 84.5 - - + +
208B ARG* 1.3 67.7 + - - +
210B TYR* 3.0 10.6 + + + +
211B VAL* 2.9 30.1 + - - +
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Residues in contact with ARG 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B ALA* 3.7 22.1 + - - +
204B SER 2.7 21.1 + - - +
205B THR* 3.6 20.4 + - - +
207B TYR* 1.3 72.6 - - - +
209B ASP* 1.3 100.0 + - - +
211B VAL* 3.6 3.3 + - - +
212B LEU* 3.2 23.7 + - + +
241B ASN 3.7 10.5 - - - +
242B LEU* 3.2 34.5 - - + +
244B ARG 3.2 23.8 + - - -
245B GLY* 3.4 13.3 - - - -
248B PRO* 2.6 31.5 + - - +
249B GLN 3.6 6.9 + - - -
250B PRO* 3.4 15.0 - - - +
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Residues in contact with ASP 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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205B THR* 2.5 25.5 + - - +
206B ASP* 3.0 8.2 + - - +
208B ARG* 1.3 106.1 + - - +
210B TYR* 1.3 59.7 + - - +
212B LEU* 3.2 7.6 + - - +
213B GLN* 2.8 46.4 + - - +
248B PRO* 5.0 5.0 - - - +
249B GLN 4.6 1.0 - - - +
250B PRO* 3.9 11.1 - - - +
251B ASP* 4.4 2.6 + - - +
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Residues in contact with TYR 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B VAL* 3.8 27.1 + - + -
173B ASP* 4.6 9.2 + - - -
175B VAL* 3.5 30.0 - - + +
176B PRO* 3.8 18.9 - - - +
200B VAL* 5.2 1.8 - - + -
206B ASP 2.6 17.0 + - - +
207B TYR* 3.0 18.1 + + + +
209B ASP* 1.3 73.1 - - - +
211B VAL* 1.3 65.0 + - + +
213B GLN* 3.0 17.3 + - + -
214B CYS* 3.0 32.6 + - - -
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Residues in contact with VAL 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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175B VAL* 4.5 19.1 - - + -
179B ILE* 5.1 0.9 - - + -
197B LEU* 4.3 21.1 - - + -
200B VAL* 3.9 25.4 - - + -
201B ALA* 4.3 12.6 - - + +
207B TYR 2.9 19.2 + - - +
208B ARG 3.8 4.7 - - - +
210B TYR* 1.3 75.6 - - + +
212B LEU* 1.3 64.8 + - - +
214B CYS* 3.2 10.9 + - - +
216B ALA* 3.5 33.2 + - + +
220B ILE* 5.4 0.7 - - + -
238B THR* 6.4 0.4 - - + -
242B LEU* 4.0 19.3 - - + -
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Residues in contact with LEU 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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208B ARG* 3.2 14.7 + - + +
209B ASP* 3.2 16.4 + - - +
211B VAL* 1.3 77.3 - - + +
213B GLN* 1.3 69.6 + - - +
215B ASN* 3.1 19.2 + - - -
216B ALA* 4.2 3.0 + - + +
217B MET* 3.9 32.7 + - + +
242B LEU* 3.9 27.4 - - + +
250B PRO* 4.1 26.2 - - + -
251B ASP* 4.4 11.0 - - + +
254B VAL* 3.9 23.7 - - + +
255B VAL* 4.1 9.9 - - + -
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Residues in contact with GLN 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 ASP* 2.8 41.0 + - - +
210B TYR* 3.0 9.8 + - + +
212B LEU* 1.3 80.1 + - - +
214B CYS* 1.3 58.8 + - - +
215B ASN* 3.1 8.5 + - - +
251B ASP* 3.6 29.7 + - - +
254B VAL* 4.8 6.3 - - - +
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Residues in contact with CYS 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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175B VAL* 4.0 11.4 - - + -
176B PRO* 5.0 9.4 - - + -
179B ILE* 3.5 29.0 - - + +
210B TYR* 3.0 47.6 + - - -
211B VAL 3.8 4.3 - - - +
212B LEU 3.2 1.2 - - - -
213B GLN* 1.3 77.7 - - - +
215B ASN* 1.3 68.8 + - - +
216B ALA 3.4 1.5 + - - -
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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