Contacts of the strand formed by residues 216 - 222 (chain B) in PDB entry 2JIF
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 216 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146B ILE* 4.4 7.6 - - + -
150B ILE* 4.0 26.2 - - + -
162B TYR* 3.7 34.5 - - + -
166B LEU* 4.2 15.0 - - + -
170B LYS* 4.1 12.5 - - + +
171B VAL 3.2 6.7 + - - +
172B GLY* 3.3 4.9 - - - -
173B SER 2.8 25.9 + - - -
214B ALA* 3.8 5.0 - - - +
215B GLY* 1.3 80.0 - - - +
217B PHE* 1.3 68.3 + - - +
218B LEU* 4.8 1.6 - - + +
236B LEU* 4.1 17.0 - - + -
237B VAL 3.7 28.9 - - - +
238B ASP* 4.2 2.5 - - - +
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Residues in contact with PHE 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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173B SER* 3.5 29.8 - - - -
175B CYS* 3.7 18.6 - - - -
211B ALA* 3.8 21.1 - - + -
214B ALA* 3.4 27.8 - - + -
216B LEU* 1.3 76.7 - - - +
218B LEU* 1.3 60.6 - - - +
219B VAL* 4.0 10.1 - - + -
235B PHE 3.4 1.9 - - - +
236B LEU* 3.7 1.0 - - - -
237B VAL* 2.7 53.7 + - + +
239B ARG* 3.8 24.5 - - + -
244B LEU* 4.1 12.8 - - + -
246B ILE* 3.7 24.5 - - + -
263B LEU* 3.9 16.8 - - + -
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Residues in contact with LEU 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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146B ILE* 4.3 29.4 - - + +
149B LEU* 3.8 31.2 - - + -
150B ILE* 4.7 2.2 - - + -
173B SER 2.8 15.0 + - - +
174B PHE* 3.9 3.1 - - + -
175B CYS 2.9 28.4 + - - +
216B LEU* 4.2 2.6 - - + +
217B PHE* 1.3 69.6 - - - +
219B VAL* 1.3 59.4 + - - +
220B MET* 3.2 37.2 - - + +
234B SER* 4.0 14.1 - - - -
235B PHE 3.4 4.9 - - - +
236B LEU* 4.2 20.2 - - + +
276B LEU* 4.0 17.7 - - + -
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Residues in contact with VAL 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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175B CYS* 3.7 7.9 - - + +
190B THR* 4.9 2.0 - - + -
201B LEU* 3.9 17.9 - - + -
205B LYS* 4.2 11.7 - - - -
217B PHE* 3.8 15.7 - - + +
218B LEU* 1.3 77.8 - - - +
220B MET* 1.3 75.0 + - - +
221B ALA* 4.8 1.3 - - + -
233B THR 3.5 1.4 - - - +
234B SER* 3.3 3.5 - - - -
235B PHE* 2.8 43.7 + - - +
237B VAL* 3.6 26.2 - - + -
265B PHE* 3.8 32.3 - - + -
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Residues in contact with MET 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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149B LEU* 4.9 1.8 - - + -
174B PHE* 4.0 23.8 - - + -
175B CYS 3.1 13.0 + - - +
176B LEU* 3.5 34.3 - - + -
188B LEU* 3.7 11.2 - - + +
190B THR* 4.2 0.5 - - - -
205B LYS* 2.9 32.1 + - - -
218B LEU* 3.2 40.2 - - + +
219B VAL* 1.3 72.1 - - - +
221B ALA* 1.3 61.0 + - - +
232B ILE* 4.1 7.0 - - + -
233B THR 3.4 3.1 - - - +
234B SER* 3.5 19.5 - - - -
282B GLY 4.0 18.4 - - - +
285B TYR* 5.9 0.4 - - + -
286B ALA* 4.3 7.6 - - + +
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Residues in contact with ALA 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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188B LEU* 4.1 4.5 - - - -
190B THR* 3.3 27.4 - - + +
192B ALA* 4.0 11.7 - - + -
201B LEU* 4.0 11.0 - - + -
219B VAL 3.9 0.4 + - - -
220B MET* 1.3 75.4 - - - +
222B ASN* 1.3 62.5 + - - +
232B ILE* 4.3 1.3 - - - -
233B THR* 2.8 35.6 + - - +
235B PHE* 3.7 21.1 - - + -
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Residues in contact with ASN 222 (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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186B PHE 5.2 2.2 + - - -
188B LEU* 4.0 19.2 + - + +
189B LYS 5.7 0.4 - - - -
190B THR 2.8 14.8 + - - +
191B ARG* 3.3 9.2 - - - +
192B ALA 2.9 21.0 + - - +
221B ALA* 1.3 71.8 - - - +
223B VAL* 1.3 60.1 + - - +
224B ASP 3.0 29.8 + - - +
225B PRO* 3.8 26.9 - - + +
228B GLY* 2.8 27.4 + - - -
231B GLY* 3.2 13.4 - - - -
232B ILE* 3.9 11.7 - - + +
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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