Contacts of the helix formed by residues 211 - 221 (chain B) in PDB entry 5V6Y
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 211 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152B ASN* 3.2 14.3 - - - +
154B GLN* 3.7 19.3 - - + -
209B ASP 3.4 3.9 + - - +
210B THR* 1.3 76.1 - - - +
212B TYR* 1.3 64.6 + - - +
213B SER* 3.3 10.3 + - - -
214B ILE* 3.1 36.1 + - - +
215B ALA* 3.2 23.9 + - - +
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Residues in contact with TYR 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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16B ASP* 4.3 13.3 - - + +
152B ASN* 3.4 20.0 + - + +
158B PHE* 4.0 23.3 - + - -
211B ASP* 1.3 78.4 - - - +
213B SER* 1.3 61.7 + - - +
215B ALA* 3.3 3.8 + - - +
216B GLU* 2.8 57.5 + - + +
229B ASN* 3.3 37.0 + - - -
232B TRP* 3.2 31.4 + + - -
233B ALA* 3.7 8.0 - - - +
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Residues in contact with SER 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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211B ASP* 3.3 13.4 + - - -
212B TYR* 1.3 85.9 - - - +
214B ILE* 1.3 62.9 + - - +
216B GLU* 3.8 7.8 - - - +
217B ALA* 2.8 32.6 + - - +
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Residues in contact with ILE 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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150B MET* 3.8 21.3 - - + -
209B ASP* 4.1 18.8 - - + +
210B THR* 4.1 9.0 - - + +
211B ASP* 3.1 24.9 + - - +
213B SER* 1.3 84.3 + - - +
215B ALA* 1.3 58.9 + - - +
217B ALA* 3.9 4.9 - - - +
218B ALA* 3.0 28.9 + - + +
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Residues in contact with ALA 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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150B MET* 3.4 28.8 - - - +
151B PHE* 3.6 17.7 - - - -
152B ASN 4.0 2.0 - - - +
210B THR* 4.2 5.1 - - + +
211B ASP 3.2 19.9 + - - +
212B TYR* 3.8 3.6 - - - +
214B ILE* 1.3 78.5 - - - +
216B GLU* 1.3 60.5 + - - +
218B ALA* 3.5 5.3 + - - +
219B PHE* 3.2 24.4 + - - +
224B THR* 4.9 0.5 - - - +
227B THR* 4.2 7.3 + - - +
229B ASN* 6.2 1.3 - - - +
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Residues in contact with GLU 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 TYR* 2.8 49.0 + - + +
213B SER* 3.9 7.2 - - - +
215B ALA* 1.3 77.1 - - - +
217B ALA* 1.3 57.3 + - - +
219B PHE* 4.1 1.9 - - - -
220B ASN* 3.0 52.4 + - - +
227B THR* 5.7 0.7 - - - -
229B ASN* 5.0 8.7 - - - +
233B ALA* 4.9 7.1 - - + +
236B ASN* 2.6 37.9 + - + +
237B ILE* 6.0 1.1 - - + -
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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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213B SER 2.8 18.4 + - - +
214B ILE* 3.9 5.4 - - - +
216B GLU* 1.3 77.4 - - - +
218B ALA* 1.3 58.0 + - - +
220B ASN* 4.6 3.8 - - - +
221B LYS* 2.9 55.1 + - + +
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Residues in contact with ALA 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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150B MET* 3.9 29.8 - - + -
214B ILE* 3.0 18.6 + - + +
215B ALA 3.9 3.8 - - - +
216B GLU 3.3 0.2 - - - -
217B ALA* 1.3 77.2 - - - +
219B PHE* 1.3 58.5 + - - +
221B LYS* 4.5 3.6 - - - +
222B GLY 3.3 1.6 + - - -
223B GLU* 2.7 50.3 + - + +
224B THR* 3.3 10.6 + - + -
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Residues in contact with PHE 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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118B ILE* 3.4 31.0 - - + -
119B TYR* 3.5 23.6 - - - -
120B ASN* 3.6 8.5 + - + -
215B ALA 3.2 14.7 + - - +
216B GLU* 4.2 2.7 - - - +
218B ALA* 1.3 78.1 - - - +
220B ASN* 1.3 74.1 + - - +
222B GLY* 3.1 13.0 + - - -
224B THR* 3.6 21.0 - - + +
225B ALA 3.5 23.8 - - - -
226B MET 4.1 6.3 - - - -
227B THR* 3.8 21.8 - - + -
237B ILE* 3.8 27.6 - - + -
242B VAL* 3.7 19.4 - - + +
244B TYR* 3.9 4.3 - - + -
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Residues in contact with ASN 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 GLU* 3.0 38.2 + - - +
217B ALA* 4.1 4.2 - - - +
219B PHE* 1.3 83.0 - - - +
221B LYS* 1.3 59.8 + - + +
222B GLY 3.3 0.4 - - - -
236B ASN* 3.2 34.1 + - - +
237B ILE* 3.4 22.2 - - - +
240B SER* 3.3 27.6 - - - +
242B VAL* 3.2 17.5 - - - +
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Residues in contact with LYS 221 (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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146B LYS* 5.3 0.7 + - - -
217B ALA* 2.9 42.7 + - + +
218B ALA* 4.3 5.6 - - - +
220B ASN* 1.3 78.1 - - + +
222B GLY* 1.3 61.4 + - - +
223B GLU* 3.3 18.1 + - + +
242B VAL* 5.2 0.4 - - - -
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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