Contacts of the strand formed by residues 213 - 219 (chain B) in PDB entry 5BZZ
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 PRO 213 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200B PHE* 4.3 7.4 - - + -
211B CYS* 3.3 16.8 - - - +
212B ASN* 1.3 86.0 - - - +
214B GLN* 1.3 58.0 + - - +
228B ASN 4.2 0.5 - - - +
230B GLY* 2.7 33.5 + - - +
231B PRO* 3.9 17.0 - - + -
239B MET* 4.0 12.8 - - - -
241B PHE* 3.3 39.0 - - + -
257B PHE* 4.2 10.1 - - + -
258B PHE 3.2 8.3 - - - +
270B MET* 4.4 9.4 - - - -
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Residues in contact with GLN 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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212B ASN 4.8 1.3 - - - +
213B PRO* 1.3 74.3 - - - +
215B PHE* 1.3 82.8 + - - +
216B VAL* 4.1 4.9 - - - +
226B SER* 3.5 14.6 + - - -
227B SER* 3.0 33.6 + - - +
228B ASN 4.2 7.0 - - - +
229B SER* 4.4 13.7 - - - +
257B PHE* 3.3 5.9 - - - -
258B PHE* 2.7 68.4 + - + +
260B LYS* 5.6 3.1 - - + +
267B LYS* 4.3 11.5 + - + +
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Residues in contact with PHE 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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198B MET* 3.6 24.2 - - + -
214B GLN* 1.3 81.2 + - - +
216B VAL* 1.3 68.9 + - - +
217B VAL* 3.8 12.8 - - + -
225B TYR* 3.6 33.2 - + - -
226B SER* 3.6 0.2 - - - -
227B SER* 2.8 50.1 + - - -
241B PHE* 3.9 31.0 - + + -
242B GLU 6.0 0.9 - - - -
243B PHE* 3.6 21.5 - + - -
255B VAL* 4.6 1.1 - - + -
256B GLU 3.2 12.8 - - - +
257B PHE* 3.6 30.1 - + + -
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Residues in contact with VAL 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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214B GLN* 4.1 12.1 - - - +
215B PHE* 1.3 80.0 - - - +
217B VAL* 1.3 66.9 + - - +
218B CYS* 4.1 13.9 - - - -
223B LYS* 3.5 35.7 - - + -
225B TYR 3.4 5.6 - - - +
226B SER* 4.3 7.9 - - - +
254B LYS 3.8 0.5 - - - +
255B VAL* 3.5 4.3 - - - +
256B GLU* 3.0 36.2 + - + +
258B PHE* 3.8 23.8 - - + -
267B LYS* 5.0 6.1 - - - +
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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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195B PHE* 4.8 3.4 - - + -
215B PHE* 3.8 26.2 - - + -
216B VAL* 1.3 79.0 - - - +
218B CYS* 1.3 64.8 + - - +
223B LYS* 3.6 3.3 - - - +
224B ILE* 2.8 43.7 + - + +
225B TYR* 2.8 24.7 + - + +
243B PHE* 4.3 4.9 - - + -
247B LEU* 4.0 16.4 - - + -
249B VAL* 4.9 2.0 - - + -
253B ILE* 3.9 25.8 - - + -
254B LYS 3.4 3.4 - - - +
255B VAL* 4.3 12.1 - - + -
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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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216B VAL* 4.1 15.0 - - - -
217B VAL* 1.3 81.9 - - - +
219B GLN* 1.3 61.0 + - - +
220B LEU 4.4 10.2 - - - +
221B LYS* 5.0 6.1 - - - -
222B VAL 3.2 8.3 - - - +
223B LYS* 3.9 18.6 - - - -
224B ILE* 4.5 0.2 - - - -
252B ASP 4.0 0.3 - - - +
253B ILE* 3.5 7.6 - - - +
254B LYS* 2.8 54.9 + - + +
274B TRP* 5.6 0.2 - - + -
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Residues in contact with GLN 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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218B CYS* 1.3 74.9 - - - +
220B LEU* 1.3 81.2 - - + +
222B VAL* 2.8 27.4 + - - +
224B ILE* 4.0 25.7 - - + +
248B PRO 4.2 1.2 - - - +
249B VAL* 3.5 9.5 - - - -
250B CYS* 2.7 51.2 + - - +
252B ASP 3.8 6.1 - - - +
253B ILE* 3.7 7.7 - - + +
244C PRO* 2.7 39.4 + - + +
245C GLN* 5.3 2.8 - - - +
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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