Contacts of the strand formed by residues 201 - 208 (chain B) in PDB entry 3OFN
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 201 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148B VAL* 4.2 22.2 - - + -
163B ARG* 3.4 29.2 - - - +
188B GLN* 3.3 34.4 + - + +
191B TRP* 5.5 0.6 - - - +
192B ASN* 3.1 23.9 + - - -
199B LYS 3.8 0.8 + - - -
200B LYS* 1.3 69.2 - - - +
202B TYR* 1.3 66.2 + - - +
203B CYS* 3.6 9.7 - - - -
265B HIS* 3.8 11.9 - - + -
266B ALA 3.5 35.2 - - - +
267B LEU* 3.9 22.7 - - + -
324B THR* 4.6 6.5 - - - +
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Residues in contact with TYR 202 (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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106B LEU* 3.9 31.0 - - + -
192B ASN* 5.8 1.1 - - - -
197B GLU* 2.7 34.2 + - - -
200B LYS* 3.5 33.1 + - + +
201B LEU* 1.3 75.3 - - - +
203B CYS* 1.3 59.5 + - - +
204B VAL* 5.7 0.2 - - - -
230B TYR* 3.5 21.8 - - + +
259B PHE* 3.4 40.8 - + + -
264B LYS* 4.2 14.6 + - + -
265B HIS 3.4 19.0 + - - +
266B ALA* 3.2 4.8 - - + -
267B LEU 2.9 25.1 + - - -
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Residues in contact with CYS 203 (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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106B LEU* 5.8 0.4 - - - +
185B ILE* 3.7 44.4 - - + -
188B GLN* 4.2 8.3 - - - -
201B LEU 3.6 15.9 - - - -
202B TYR* 1.3 75.3 - - - +
204B VAL* 1.3 58.9 + - - +
230B TYR* 2.9 19.5 + - - -
231B SER* 3.0 22.7 - - - -
232B ILE* 2.7 33.4 + - - +
267B LEU* 3.4 15.0 - - - +
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Residues in contact with VAL 204 (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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185B ILE* 5.5 0.2 - - - -
202B TYR* 6.4 0.4 - - + -
203B CYS* 1.3 77.4 - - - +
205B TYR* 1.3 56.8 + - - +
232B ILE* 3.4 13.7 - - + +
234B VAL* 4.2 20.6 - - + -
252B ALA* 4.2 9.2 - - + +
255B ILE* 4.0 15.5 - - + -
256B GLY* 3.9 29.4 - - - +
259B PHE* 5.7 3.8 - - + -
266B ALA* 5.2 4.7 - - + -
267B LEU 2.6 14.9 + - - +
268B ILE* 3.1 27.1 - - + +
269B VAL* 2.7 35.3 + - - +
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Residues in contact with TYR 205 (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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178B THR* 3.7 14.9 - - + +
181B ALA* 5.0 2.2 - - + -
182B LEU* 6.4 1.1 - - + -
185B ILE* 4.2 22.0 - - + -
203B CYS 4.1 0.6 - - - -
204B VAL* 1.3 75.0 - - - +
206B VAL* 1.3 56.9 + - - +
207B ALA* 4.1 20.0 - - + -
210B GLN* 3.0 18.7 + - - -
215B VAL* 5.3 3.1 - - + -
218B LEU* 3.4 32.4 - - + +
222B LEU* 5.6 0.7 - - + -
231B SER* 5.8 1.3 - - - -
232B ILE 2.9 9.7 + - - -
233B ILE* 3.4 30.1 - - + -
234B VAL 2.8 31.4 + - - +
269B VAL* 3.7 23.1 - - + -
271B ASP* 2.6 39.5 + - + -
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Residues in contact with VAL 206 (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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204B VAL* 4.7 0.9 - - + -
205B TYR* 1.3 77.3 - - - +
207B ALA* 1.3 60.0 + - - +
208B VAL* 3.6 22.6 + - + -
234B VAL* 3.3 7.9 - - + +
248B ALA* 4.1 9.2 - - + +
249B PRO* 3.9 22.2 - - + -
252B ALA* 3.7 23.1 - - + -
268B ILE* 3.9 11.7 - - + -
269B VAL 2.7 21.0 + - - +
270B TYR* 3.7 20.9 - - + -
271B ASP* 2.9 30.3 + - - +
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Residues in contact with ALA 207 (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 TYR* 3.9 10.9 + - + -
206B VAL* 1.3 70.0 - - - +
208B VAL* 1.3 62.1 + - - +
209B GLY 3.9 0.4 - - - -
210B GLN* 3.7 13.0 - - + +
215B VAL* 3.6 34.1 - - + -
233B ILE* 5.3 0.2 - - + -
234B VAL 2.6 14.8 + - - +
235B ALA* 3.5 8.4 - - + +
236B ALA 3.1 29.6 + - - +
237B THR* 4.7 0.8 - - + -
248B ALA* 5.3 0.2 - - - +
271B ASP 3.6 4.9 - - - -
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Residues in contact with VAL 208 (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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206B VAL* 3.7 19.3 - - + +
207B ALA* 1.3 71.4 - - - +
209B GLY* 1.3 65.0 + - - +
210B GLN* 3.3 1.9 + - - +
236B ALA 3.5 2.0 - - - -
245B GLN* 3.4 36.8 - - + +
248B ALA* 4.3 4.0 - - + -
249B PRO* 3.6 30.3 - - + -
270B TYR* 5.9 0.9 - - + -
271B ASP 2.9 17.6 + - - +
272B ASP 3.8 14.4 + - - +
273B LEU* 6.0 0.2 - - + -
275B LYS* 3.5 17.9 - - - +
276B GLN* 3.8 22.7 - - - +
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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