Contacts of the helix formed by residues 205 - 215 (chain B) in PDB entry 4BOS
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
---------------------------
Residue Dist Surf HB Arom Phob DC
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199B GLU* 3.7 26.9 - - - +
204B LYS* 1.3 79.4 - - - +
206B ASN* 1.3 54.6 + - - +
207B GLN* 3.9 5.1 + - - +
208B GLU* 3.0 40.3 + - - +
209B TYR* 2.7 32.6 + - - +
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Residues in contact with ASN 206 (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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190B VAL* 2.8 25.6 + - - +
191B ALA* 3.5 21.5 - - - +
194B PRO* 3.5 21.8 - - + +
197B TYR 2.7 27.5 + - - +
198B SER* 5.5 1.3 - - - -
199B GLU 5.0 2.8 - - - +
202B LEU* 3.6 11.5 - - - +
204B LYS 3.7 0.8 + - - -
205B THR* 1.3 72.2 - - - +
207B GLN* 1.3 60.8 + - - +
209B TYR* 3.1 4.5 + - - +
210B CYS* 3.0 32.4 + - - -
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Residues in contact with GLN 207 (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 ALA* 6.0 2.8 - - - +
205B THR* 3.3 5.3 + - - +
206B ASN* 1.3 79.6 + - - +
208B GLU* 1.3 68.2 + - + +
210B CYS* 3.4 9.3 + - - +
211B ASP* 3.1 37.1 + - - +
54C ARG* 2.3 34.7 + - - +
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Residues in contact with GLU 208 (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 GLU* 5.0 1.0 - - - +
204B LYS* 3.4 20.8 - - + +
205B THR* 3.0 48.5 + - - +
207B GLN* 1.3 79.8 - - + +
209B TYR* 1.3 58.1 + - - +
211B ASP* 3.5 6.5 + - - +
212B TRP* 2.9 29.1 + - - +
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Residues in contact with TYR 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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186B ILE* 4.9 0.2 - - + -
190B VAL* 4.2 17.0 - - + -
202B LEU* 3.7 54.1 - - + -
204B LYS* 3.9 19.0 - - + +
205B THR 2.7 15.6 + - - +
206B ASN 3.1 8.0 + - - +
208B GLU* 1.3 74.2 - - - +
210B CYS* 1.3 55.3 + - - +
212B TRP* 2.9 14.8 + + - +
213B ILE* 2.7 51.3 + - + +
219B TRP 5.5 0.9 + - - -
223B ILE* 3.7 19.4 - - + +
224B GLU* 2.3 41.7 + - - -
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Residues in contact with CYS 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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187B ALA* 3.4 33.7 - - + +
190B VAL* 3.9 9.2 - - - -
191B ALA* 3.7 13.2 - - - -
206B ASN* 3.0 35.1 + - - +
207B GLN* 3.4 11.9 + - - +
209B TYR* 1.3 76.2 - - - +
211B ASP* 1.3 64.7 + - - +
213B ILE* 3.5 10.5 - - - +
214B LYS* 3.3 34.8 + - - +
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Residues in contact with ASP 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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207B GLN* 3.1 25.9 + - - +
208B GLU* 3.8 5.9 - - - +
210B CYS* 1.3 78.2 - - - +
212B TRP* 1.3 64.8 + - - +
214B LYS* 3.3 15.9 + - - +
215B ARG* 3.5 14.5 + - - +
49C GLN 5.9 1.8 - - - +
51C GLU* 3.4 31.2 - - + +
54C ARG* 3.0 41.8 + - - -
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Residues in contact with TRP 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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199A GLU* 3.9 27.6 - - + -
200A ALA* 5.1 1.8 - - - -
203A GLY* 3.5 37.0 - - - -
204A LYS* 3.8 8.3 - - - -
204B LYS* 3.3 27.9 - - - +
208B GLU 2.9 18.5 + - - +
209B TYR* 2.9 21.7 + + - +
211B ASP* 1.3 77.4 - - - +
213B ILE* 1.3 68.6 + - + +
215B ARG* 3.1 37.4 + - - +
218B THR* 2.9 41.6 + - + +
219B TRP 5.0 6.2 + - - +
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Residues in contact with ILE 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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162B PHE* 4.2 9.6 - - + -
183B ARG* 3.0 51.5 + - + +
186B ILE* 3.9 25.8 - - + -
187B ALA* 4.2 4.9 - - + +
190B VAL* 5.9 0.2 - - + -
209B TYR* 2.7 31.7 + - + +
210B CYS* 3.5 18.4 - - - +
212B TRP* 1.3 78.0 - - + +
214B LYS* 1.3 60.8 + - - +
218B THR* 3.9 4.0 - - - +
219B TRP 4.2 15.0 - - - +
224B GLU* 3.5 35.9 - - + +
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Residues in contact with LYS 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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180B PRO* 6.1 0.3 - - - +
183B ARG* 4.0 24.1 - - + +
184B ARG* 3.8 25.1 - - + +
187B ALA* 3.7 25.1 - - + +
210B CYS* 3.3 27.5 + - - +
211B ASP* 3.3 8.7 + - - +
212B TRP 3.1 1.6 - - - -
213B ILE* 1.3 77.0 - - - +
215B ARG* 1.3 65.8 + - - +
216B ASP* 3.6 1.2 + - - -
51C GLU* 4.4 25.3 + - - +
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Residues in contact with ARG 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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200A ALA* 2.8 38.4 + - - +
201A ILE 4.2 3.0 + - - -
203A GLY* 3.3 17.0 - - - +
183B ARG* 3.1 24.8 + - - -
211B ASP 3.5 9.9 + - - +
212B TRP* 3.1 33.2 + - - +
214B LYS* 1.3 81.4 - - - +
216B ASP* 1.3 58.2 + - - +
217B ASP* 2.7 47.1 + - - +
218B THR* 3.7 14.2 + - + +
42C ARG* 4.0 4.3 - - - +
49C GLN* 3.2 53.2 + - + +
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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