Contacts of the strand formed by residues 215 - 221 (chain B) in PDB entry 3PEJ
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 GLN 215 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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207B TYR* 4.4 7.9 - - - +
208B THR 3.3 13.5 - - - +
209B LYS* 3.4 11.8 - - + +
214B GLU* 1.3 73.6 - - - +
216B TYR* 1.3 60.5 + - - +
230B LYS* 3.6 6.4 - - - +
231B ASP* 2.6 55.2 + - + +
233B ARG* 4.7 0.4 - - - +
234B GLY* 3.3 22.1 - - - +
235B ALA* 3.4 12.7 - - - +
236B THR* 2.8 20.8 + - - -
237B LEU* 2.9 47.2 + - - +
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Residues in contact with TYR 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B MET 5.2 2.7 - - - +
154B THR 6.1 0.2 - - - -
155B LYS* 3.6 57.6 + - + +
158B LEU* 5.1 8.7 - - + -
206B VAL 3.9 0.3 - - - +
207B TYR* 3.5 3.3 - - - -
208B THR* 2.8 44.9 + - + +
213B ASP* 3.3 33.4 + - + -
214B GLU* 3.2 37.9 + - + -
215B GLN* 1.3 77.3 - - - +
217B ILE* 1.3 65.8 + - - +
228B ILE* 4.5 3.1 - - + -
229B TYR* 3.3 24.5 - - - +
230B LYS* 3.5 19.8 - - + +
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Residues in contact with ILE 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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205B ILE* 3.7 25.4 - - + -
206B VAL 3.3 2.9 - - - +
207B TYR* 3.6 28.3 - - + -
216B TYR* 1.3 75.6 - - - +
218B TRP* 1.3 64.3 + - - +
219B GLU* 4.0 4.0 - - - +
227B THR 3.7 0.7 - - - +
228B ILE* 3.4 5.8 - - - +
229B TYR* 2.6 81.8 + - + +
231B ASP* 3.4 34.1 - - + +
232B PRO* 4.1 4.3 - - + -
233B ARG* 4.5 1.3 - - - +
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Residues in contact with TRP 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B TYR* 3.7 9.9 - - - -
158B LEU* 3.7 38.8 - - + -
162B LEU* 3.4 39.3 - - + +
194B PHE* 3.6 36.6 - + - -
195B TYR* 4.5 2.2 - - - -
204B VAL 3.5 3.1 - - - +
206B VAL* 2.7 61.6 + - + +
208B THR* 5.9 0.4 - - + +
216B TYR 4.3 0.2 - - - -
217B ILE* 1.3 74.3 - - - +
219B GLU* 1.3 68.7 + - - +
220B SER* 3.4 21.5 + - - -
226B PHE* 3.7 9.1 - + - +
227B THR 3.4 11.7 - - - +
228B ILE* 3.7 14.8 - - + -
1001B BC2 4.5 21.1 - - + -
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Residues in contact with GLU 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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203B LYS* 3.1 38.2 + - + +
204B VAL 3.5 4.0 - - - -
205B ILE* 3.6 25.4 - - + +
217B ILE* 4.0 4.0 - - + +
218B TRP* 1.3 75.4 - - - +
220B SER* 1.3 67.4 + - - +
221B THR* 5.4 3.1 - - - +
225B LYS 4.8 0.2 - - - -
226B PHE* 3.2 20.0 - - - +
227B THR* 3.2 26.8 + - - +
229B TYR* 3.5 27.6 + - + -
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Residues in contact with SER 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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77B TYR* 4.7 3.1 + - - -
85B MET* 5.8 1.1 - - - -
194B PHE* 4.6 5.6 - - - -
195B TYR* 5.6 2.2 - - - -
198B PHE* 3.4 22.7 - - - -
203B LYS* 3.4 6.1 - - - +
204B VAL* 2.8 42.3 + - - -
218B TRP* 3.4 27.5 + - - -
219B GLU* 1.3 77.6 + - - +
221B THR* 1.3 62.4 + - - +
225B LYS 3.6 5.4 - - - -
226B PHE* 4.0 5.4 - - - +
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Residues in contact with THR 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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85B MET* 3.4 12.8 - - - +
198B PHE* 3.8 3.1 - - - -
202B ASP 3.7 9.4 - - - +
203B LYS* 4.7 11.8 - - + +
219B GLU* 5.4 3.6 - - - +
220B SER* 1.3 75.2 + - - +
222B ALA* 1.4 65.1 + - + +
223B ASP* 3.1 36.2 + - - +
224B ALA* 3.2 12.9 + - - -
225B LYS* 2.8 18.2 + - - +
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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