Contacts of the helix formed by residues 200 - 210 (chain B) in PDB entry 1BO6
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 ILE 200 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53B TRP* 3.9 21.8 - - + +
57B VAL* 5.3 0.4 - - + -
196B MET* 3.3 44.4 + - + +
197B LYS 4.8 0.8 + - - +
199B ASP* 1.3 72.3 - - - +
201B ARG* 1.3 77.8 - - + +
203B GLU* 3.1 3.2 + - + -
204B VAL* 2.8 47.9 + - + +
224B ILE* 3.7 36.6 - - + -
227B THR* 5.3 3.6 - - - +
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Residues in contact with ARG 201 (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* 3.4 6.0 - - - +
200B ILE* 1.3 80.5 - - + +
202B ARG* 1.3 61.7 + - - +
204B VAL* 3.5 2.5 + - - +
205B VAL* 3.0 37.0 + - + +
217B ALA* 4.9 4.6 - - - +
220B VAL* 3.8 21.3 - - + +
221B ASP* 2.7 42.2 + - - -
224B ILE* 3.7 21.7 - - + +
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Residues in contact with ARG 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B ASP* 2.5 36.8 + - - +
200B ILE 3.2 0.4 - - - -
201B ARG* 1.3 79.0 - - - +
203B GLU* 1.3 74.4 + - - +
205B VAL* 3.2 7.0 + - - +
206B LYS* 2.8 38.9 + - + +
292B ARG* 6.0 1.7 - - - +
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Residues in contact with GLU 203 (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 MET* 3.9 22.3 - - - +
192B PHE 4.9 0.2 + - - -
195B ASP* 3.4 42.9 - - - +
196B MET* 3.8 19.8 - - + +
199B ASP* 3.3 14.3 + - - +
200B ILE* 3.1 8.7 + - + +
202B ARG* 1.3 92.7 - - - +
204B VAL* 1.3 58.0 + - - +
206B LYS* 3.3 33.2 + - - +
207B LEU* 2.9 35.9 + - + +
292B ARG* 5.8 0.3 + - - -
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Residues in contact with VAL 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B VAL* 4.5 9.2 - - + -
196B MET* 6.1 0.2 - - + -
200B ILE* 2.8 47.5 + - + +
201B ARG 3.7 3.8 - - - +
203B GLU* 1.3 69.7 - - - +
205B VAL* 1.3 60.1 + - - +
207B LEU* 3.1 9.2 + - + +
208B ILE* 2.8 51.2 + - + +
220B VAL* 4.0 18.2 - - + -
223B ILE* 4.1 35.7 - - + -
224B ILE* 4.4 6.3 - - + -
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Residues in contact with VAL 205 (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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201B ARG* 3.0 27.1 + - + +
202B ARG* 3.6 6.5 - - - +
204B VAL* 1.3 74.8 - - - +
206B LYS* 1.3 64.3 + - - +
208B ILE* 3.4 8.8 + - - +
209B GLU* 3.0 50.9 + - - +
215B PRO* 4.2 13.7 - - + -
220B VAL* 3.7 22.7 - - + -
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Residues in contact with LYS 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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189B LEU* 4.3 17.5 - - + -
190B PHE 5.3 5.4 + - - +
191B MET* 3.2 27.5 - - + +
195B ASP* 5.3 3.2 + - - -
202B ARG* 2.8 24.6 + - + +
203B GLU* 3.3 32.9 + - - +
205B VAL* 1.3 77.6 - - - +
207B LEU* 1.3 57.3 + - - +
209B GLU* 3.3 8.8 + - - +
210B PHE* 2.9 26.9 + - + +
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Residues in contact with LEU 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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54B ILE* 4.0 24.9 - - + -
57B VAL* 3.8 25.4 - - + -
58B VAL* 4.5 4.9 - - + -
61B ILE* 3.9 13.0 - - + -
126B ILE* 3.8 30.1 - - + -
189B LEU* 3.9 6.3 - - + -
191B MET* 3.3 28.9 - - + -
196B MET* 5.1 6.1 - - + -
203B GLU* 2.9 18.8 + - + +
204B VAL* 3.1 6.0 + - + +
206B LYS* 1.3 74.5 - - - +
208B ILE* 1.3 66.4 + - - +
210B PHE* 3.0 5.0 + - + +
211B LEU* 2.9 28.8 + - + +
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Residues in contact with ILE 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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61B ILE* 3.7 27.4 - - + -
204B VAL* 2.8 28.1 + - + +
205B VAL 3.7 4.7 - - - +
207B LEU* 1.3 75.5 - - - +
209B GLU* 1.3 59.2 + - - +
211B LEU* 3.6 1.6 + - - +
212B GLU 3.4 2.8 + - - -
213B ARG* 2.8 58.2 + - + +
214B LYS 4.0 2.0 - - - +
215B PRO* 3.8 20.6 - - + -
219B LEU* 4.0 23.3 - - + -
220B VAL* 3.5 32.3 - - + -
223B ILE* 4.4 1.1 - - + -
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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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205B VAL* 3.0 37.7 + - - +
206B LYS* 3.7 6.8 - - - +
207B LEU 3.1 0.2 - - - -
208B ILE* 1.3 74.3 - - - +
210B PHE* 1.3 61.4 + - - +
211B LEU 3.1 1.8 - - - -
212B GLU* 2.9 21.1 + - - +
213B ARG 4.2 5.6 - - - +
215B PRO* 4.0 21.7 - - + +
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Residues in contact with PHE 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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41B LEU* 4.4 0.4 - - + -
124B LYS* 2.7 55.0 + - + -
125B MET 3.5 9.0 - - - -
126B ILE* 3.7 23.3 - - + -
186B SER 3.6 23.3 - - - -
187B ARG* 3.4 25.6 - - - -
189B LEU* 3.5 40.4 - - + -
206B LYS 2.9 17.0 + - - +
207B LEU* 3.0 3.8 + - + +
209B GLU* 1.3 76.9 - - - +
211B LEU* 1.3 67.5 + - + +
212B GLU* 3.3 2.1 + - - +
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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
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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