Contacts of the helix formed by residues 212 - 218 (chain B) in PDB entry 2BS3
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 LEU 212 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210B THR* 3.1 17.9 - - + +
211B LEU* 1.3 78.9 - - - +
213B ALA* 1.3 63.5 + - - +
214B CYS* 3.1 4.9 - - - -
215B HIS* 3.3 7.4 + - + +
216B ASP* 3.2 23.2 + - - +
225B GLN* 3.9 35.7 - - + +
228B ILE* 6.0 0.9 - - + -
1241B F3S 3.3 24.8 - - - -
120C HIS* 3.8 1.6 - - - -
122C ASP* 3.9 8.3 - - - +
188C TYR* 5.5 0.2 - - + -
192C VAL* 3.9 31.2 - - + +
206C ARG* 3.7 35.7 - - - +
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Residues in contact with ALA 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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160B ALA* 3.3 29.4 - - - +
211B LEU* 3.2 4.2 + - + -
212B LEU* 1.3 75.4 - - - +
214B CYS* 1.3 65.3 + - - +
216B ASP 3.3 0.7 + - - -
217B VAL* 3.1 29.3 + - - +
1241B F3S 3.4 5.9 - - - -
118C MET* 3.7 18.4 - - + -
120C HIS* 3.4 22.2 - - + +
123C THR* 3.9 7.0 - - - +
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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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157B CYS* 3.5 25.2 - - + +
160B ALA* 4.5 0.4 - - - +
173B ALA* 3.5 30.1 - - + -
212B LEU* 3.1 3.8 - - - -
213B ALA* 1.3 80.2 - - - +
215B HIS* 1.3 72.2 + - - +
217B VAL* 3.6 1.6 - - - +
218B CYS* 3.1 26.9 + - - +
224B LEU* 3.6 11.4 - - + +
228B ILE* 4.3 7.2 - - - -
1241B F3S 2.2 48.5 - - - -
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Residues in contact with HIS 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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212B LEU* 3.3 15.2 + - + +
214B CYS* 1.3 85.7 - - - +
216B ASP* 1.3 72.9 + - - +
217B VAL 3.4 0.9 + - - -
218B CYS* 3.8 11.1 + - - +
221B ASN* 5.5 4.6 - - - +
222B LEU 3.6 17.6 + - - +
223B PRO* 4.0 7.0 - - + -
224B LEU* 3.4 16.7 + - + -
225B GLN* 3.1 43.7 + - + +
226B SER* 5.4 0.7 - - - -
202C PRO* 6.2 2.2 - - + -
203C ASP* 2.8 31.0 + - - -
206C ARG* 3.7 12.1 - - - -
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Residues in contact with ASP 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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72B ARG* 5.0 7.3 + - - +
212B LEU 3.2 8.5 + - - +
213B ALA 3.3 2.9 + - - +
214B CYS 3.3 0.2 - - - -
215B HIS* 1.3 81.9 - - - +
217B VAL* 1.3 61.1 + - + +
218B CYS 3.7 0.2 - - - -
120C HIS* 2.6 38.0 + - + +
206C ARG* 2.7 40.1 + - - -
210C LYS* 5.6 0.3 + - - -
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Residues in contact with VAL 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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72B ARG* 4.5 21.3 - - + +
73B PRO* 4.1 28.7 - - + +
74B SER* 5.9 0.2 - - - -
156B CYS* 3.7 19.4 - - + +
157B CYS* 4.2 0.7 - - - -
160B ALA* 3.6 25.6 - - + -
213B ALA* 3.2 18.4 - - - +
214B CYS* 3.6 5.8 - - - +
216B ASP* 1.3 82.9 - - + +
218B CYS* 1.3 70.5 + - - +
219B PRO* 2.9 11.6 - - - +
118C MET* 4.6 4.5 - - + -
120C HIS* 5.8 0.4 - - + -
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Residues in contact with CYS 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 CYS 3.1 16.6 + - - +
215B HIS 3.8 7.3 + - - +
216B ASP 3.7 1.0 - - - -
217B VAL* 1.3 74.4 - - - +
219B PRO* 1.3 61.7 - - - +
220B LYS 3.1 16.2 - - - -
221B ASN* 2.9 26.2 + - - +
222B LEU* 3.7 26.2 - - - +
224B LEU* 4.2 8.5 - - + -
1242B SF4 2.2 47.1 - - - -
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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