Contacts of the strand formed by residues 215 - 220 (chain B) in PDB entry 3E88
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 215 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201B SER* 4.3 11.0 - - - +
204B LEU* 3.8 47.0 + - + +
205B GLN* 5.0 0.2 - - + -
213B THR 3.8 1.6 + - - -
214B ALA* 1.3 73.4 - - - +
216B LYS* 1.3 62.4 + - - +
217B TYR 3.2 25.1 - - - +
218B ALA* 3.8 22.4 - - + -
227B PHE* 4.0 19.3 - - + -
228B VAL 3.3 19.3 - - - +
229B MET* 4.1 7.2 - - + -
475B TYR* 3.7 25.6 + - + -
477B ALA* 3.8 7.8 - - - +
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Residues in contact with LYS 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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354A ASP* 4.6 6.1 + - - -
355A HIS* 4.4 23.4 + - - +
356A GLU* 4.5 21.8 + - - +
171B GLU* 4.5 4.4 + - - -
176B ARG* 6.2 0.2 - - - +
178B TYR* 3.3 45.8 + - + +
214B ALA 3.8 3.4 + - - -
215B LEU* 1.3 73.7 - - - +
217B TYR* 1.3 96.5 + - + +
228B VAL* 2.8 19.4 + - + +
229B MET* 4.9 0.9 - - - -
475B TYR* 4.1 1.2 - - - -
476B SER* 3.5 2.6 - - - -
477B ALA* 2.9 40.2 + - + +
478B SER* 4.6 11.2 + - - -
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Residues in contact with TYR 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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355A HIS* 5.3 5.0 + - - -
147B VAL* 4.4 20.4 - - + -
152B PHE* 4.0 24.7 - + - -
171B GLU* 2.6 32.8 + - - -
178B TYR* 5.6 0.4 - + - -
215B LEU* 3.2 11.6 - - - +
216B LYS* 1.3 115.1 - - + +
218B ALA* 1.3 60.7 + - - +
219B PHE* 4.2 15.0 - - + -
226B CYS 4.0 0.4 - - - +
228B VAL* 2.9 40.1 + - + -
475B TYR 3.4 4.7 - - - +
476B SER* 3.7 26.2 - - - -
477B ALA 5.3 0.9 - - - -
478B SER* 5.5 5.3 + - - -
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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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201B SER* 3.6 24.2 - - - +
215B LEU* 3.8 14.6 - - + -
217B TYR* 1.3 75.4 - - - +
219B PHE* 1.3 54.9 + - - +
226B CYS 3.5 6.5 - - - +
227B PHE* 4.8 2.5 - - + +
473B PHE* 4.0 13.2 - - + -
474B ASP* 2.7 29.6 + - - +
475B TYR* 2.7 30.2 + - + +
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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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146B LYS* 5.9 2.5 - - + -
147B VAL* 3.4 39.5 - - + +
148B THR* 3.9 26.5 - - - -
149B MET* 4.1 7.0 - - - -
152B PHE* 4.0 16.4 - + - -
180B MET* 4.5 7.0 - - + -
217B TYR* 4.3 9.0 - - + -
218B ALA* 1.3 75.8 - - - +
220B GLN* 1.3 72.5 + - - +
221B THR* 4.6 6.3 - - + -
225B LEU 3.9 0.2 - - - -
226B CYS* 2.9 65.4 + - + +
228B VAL* 3.8 20.4 - - + -
473B PHE* 3.9 6.2 - - - -
474B ASP* 4.1 11.2 - - - +
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Residues in contact with GLN 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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146B LYS* 4.0 23.7 + - - +
147B VAL 4.9 1.2 - - - +
148B THR* 6.2 0.3 - - - +
185B LYS* 3.1 17.1 + - - +
219B PHE* 1.3 83.3 - - - +
221B THR* 1.3 68.2 + - - +
224B ARG 3.4 11.7 - - - +
225B LEU* 3.8 11.4 - - + -
226B CYS 4.7 0.2 - - - +
469B HIS* 3.2 18.7 - - - +
470B PHE* 2.9 52.1 + - - +
473B PHE* 3.6 8.7 - - + +
474B ASP* 3.0 24.9 + - - +
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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