Contacts of the helix formed by residues 210 - 220 (chain B) in PDB entry 4BL8
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 ASP 210 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151B ASN* 3.7 10.3 - - - +
153B GLN* 3.5 20.4 - - + +
208B ASP 3.1 5.0 + - - +
209B THR* 1.3 74.6 - - - +
211B TYR* 1.3 68.1 + - - +
212B SER* 3.2 13.7 + - - -
213B ILE* 3.0 32.7 + - - +
214B ALA* 3.1 18.7 + - - +
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Residues in contact with TYR 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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15B ASP* 4.8 13.2 - - + +
151B ASN* 3.6 26.9 + - + +
157B PHE* 4.1 22.0 - + - -
210B ASP* 1.3 78.7 - - - +
212B SER* 1.3 64.0 + - - +
214B ALA* 3.2 4.2 + - - +
215B GLU* 3.0 53.1 + - + +
228B ASN* 3.3 38.8 + - - -
231B TRP* 3.5 24.8 + + - -
232B ALA* 3.8 2.6 - - - +
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Residues in contact with SER 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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210B ASP* 3.2 15.5 + - - -
211B TYR* 1.3 86.6 - - - +
213B ILE* 1.3 62.0 + - - +
215B GLU* 4.0 7.9 - - - +
216B ALA* 3.3 23.7 + - - +
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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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149B MET* 3.8 21.5 - - + -
208B ASP* 3.7 26.0 - - + +
209B THR* 3.8 9.9 - - + +
210B ASP* 3.0 27.5 + - - +
212B SER* 1.3 78.1 - - - +
214B ALA* 1.3 64.3 + - - +
216B ALA* 3.6 4.0 + - - +
217B ALA* 3.2 21.8 + - - +
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Residues in contact with ALA 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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149B MET* 3.7 26.7 - - - +
150B PHE* 3.7 20.0 - - - +
151B ASN 4.3 1.8 - - - +
209B THR* 4.1 7.6 - - + -
210B ASP 3.1 8.2 + - - +
211B TYR* 3.7 7.2 - - - +
213B ILE* 1.3 77.5 - - - +
215B GLU* 1.3 65.7 + - - +
217B ALA* 3.2 6.9 + - - +
218B PHE* 3.1 24.9 + - - +
223B THR* 4.8 1.2 - - - +
226B THR* 4.6 4.9 - - - +
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Residues in contact with GLU 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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211B TYR* 3.0 47.0 + - + +
212B SER* 4.2 8.3 - - - +
213B ILE 3.4 0.2 - - - -
214B ALA* 1.3 76.8 - - - +
216B ALA* 1.3 62.5 + - - +
218B PHE* 3.7 3.2 + - - -
219B ASN* 3.1 40.1 + - - +
226B THR* 5.8 0.9 - - - -
228B ASN* 4.9 6.5 + - - +
232B ALA* 4.5 11.8 - - - +
235B ASN* 3.4 34.3 + - - +
236B ILE* 6.1 1.5 - - + +
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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 SER 3.3 17.0 + - - +
213B ILE* 3.9 4.3 - - - +
214B ALA 3.2 0.8 - - - -
215B GLU* 1.3 77.1 - - - +
217B ALA* 1.3 67.0 + - - +
219B ASN* 3.4 3.3 + - - -
220B LYS* 3.2 51.2 + - + +
222B GLU* 4.5 0.4 - - - -
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Residues in contact with ALA 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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149B MET* 3.5 29.8 - - + -
213B ILE 3.2 12.8 + - - +
214B ALA 3.2 8.5 + - - +
216B ALA* 1.3 81.4 - - - +
218B PHE* 1.3 61.6 + - - +
220B LYS* 3.3 0.7 + - - -
221B GLY 3.2 2.9 + - - -
222B GLU* 3.0 45.0 + - + +
223B THR* 3.8 8.5 - - + -
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Residues in contact with PHE 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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117B ILE* 3.5 41.5 - - + -
118B TYR* 3.9 10.5 - - - -
119B ASN* 3.8 21.6 + - + -
214B ALA 3.1 13.1 + - - +
215B GLU* 4.2 3.6 - - - +
217B ALA* 1.3 80.1 - - - +
219B ASN* 1.3 71.5 + - - +
221B GLY* 3.2 16.3 + - - -
223B THR* 3.5 24.5 - - + +
224B ALA 4.0 4.0 - - - -
225B MET 4.0 7.9 - - - -
226B THR* 3.8 22.2 - - + -
236B ILE* 3.7 30.5 - - + -
241B VAL* 3.9 13.1 - - + +
243B TYR* 4.0 7.4 - - + -
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Residues in contact with ASN 219 (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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215B GLU* 3.1 29.6 + - - +
216B ALA* 3.9 4.5 - - - +
217B ALA 3.3 0.4 - - - -
218B PHE* 1.3 94.2 - - - +
220B LYS* 1.3 60.4 + - + +
221B GLY 3.4 0.2 - - - -
235B ASN* 3.2 38.4 + - - +
236B ILE* 3.5 12.5 - - - +
239B SER* 3.3 34.7 + - - +
241B VAL* 3.4 9.1 - - - +
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Residues in contact with LYS 220 (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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216B ALA* 3.2 34.9 + - - +
217B ALA 4.0 2.7 - - - +
219B ASN* 1.3 79.5 - - + +
221B GLY* 1.3 60.6 + - - +
222B GLU* 3.3 27.8 + - + +
241B VAL* 5.1 2.0 - - - -
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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