Contacts of the strand formed by residues 207 - 215 (chain B) in PDB entry 5O67
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 ASN 207 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168B VAL* 3.7 2.8 - - - +
169B ASN* 3.0 61.6 + - - +
171B PRO* 4.3 0.8 - - - +
205B ASP 3.2 14.1 + - - -
206B VAL* 1.3 80.5 - - - +
208B PHE* 1.3 64.4 + - - +
229B ARG* 3.1 31.9 + - - +
230B VAL 3.3 15.0 - - - +
231B LYS* 3.8 16.2 - - + +
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Residues in contact with PHE 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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167B ASP 3.3 13.9 - - - +
168B VAL* 3.6 15.0 - - + -
207B ASN* 1.3 75.9 - - - +
209B GLY* 1.3 66.3 + - - +
210B ILE* 4.2 26.2 - - + -
229B ARG* 3.4 11.4 - - - +
230B VAL* 2.8 71.6 + - + +
265B TRP* 6.0 1.6 - + - -
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Residues in contact with GLY 209 (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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165B GLN 3.7 0.7 - - - +
166B PHE* 3.5 6.9 - - - +
167B ASP* 3.1 36.0 + - - +
208B PHE* 1.3 79.6 - - - +
210B ILE* 1.3 64.8 + - - +
228B VAL 3.5 9.4 - - - -
229B ARG* 3.8 17.8 - - - +
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Residues in contact with ILE 210 (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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164B TRP* 4.0 30.7 - - + -
165B GLN 3.5 3.8 - - - -
166B PHE* 4.1 22.0 - - + -
208B PHE* 4.2 23.1 - - + -
209B GLY* 1.3 77.4 - - - +
211B ALA* 1.3 63.7 + - - +
227B SER* 3.2 4.2 - - - -
228B VAL* 3.0 48.9 + - + +
230B VAL* 6.3 0.4 - - + -
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Residues in contact with ALA 211 (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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101B GLY 5.6 2.5 - - - +
102B PHE* 4.4 12.6 - - + -
163B ARG 3.9 0.6 - - - +
164B TRP* 3.4 11.0 - - - -
165B GLN* 3.0 39.6 + - + +
210B ILE* 1.3 78.6 - - - +
212B TYR* 1.3 61.0 + - - +
225B VAL* 4.0 13.2 - - + -
226B VAL 3.5 6.7 - - - +
227B SER* 3.4 16.8 - - - +
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Residues in contact with TYR 212 (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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163B ARG* 3.4 41.3 - - + -
164B TRP* 3.5 42.8 - + + -
211B ALA* 1.3 75.7 - - - +
213B LYS* 1.3 61.5 + - - +
214B PHE* 3.2 31.1 + - + -
225B VAL* 3.5 3.5 - - - -
226B VAL* 3.0 46.4 + - + +
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Residues in contact with LYS 213 (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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100B SER* 6.4 0.9 - - - -
102B PHE* 3.8 27.2 - - + -
104B GLY* 5.1 1.2 - - - -
162B ASN* 3.0 43.6 + - - +
163B ARG* 2.9 39.9 + - - +
212B TYR* 1.3 73.0 - - - +
214B PHE* 1.3 55.4 + - - +
215B LEU 3.7 9.4 - - - +
216B ASP* 3.3 23.6 - - - +
223B ASP* 3.6 30.3 + - - +
224B ALA 3.4 14.4 - - - +
225B VAL* 4.0 15.3 - - + -
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Residues in contact with PHE 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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163B ARG* 5.3 0.9 - - - -
212B TYR* 3.2 28.5 + - + -
213B LYS* 1.3 72.3 - - - +
215B LEU* 1.3 73.0 + - + +
224B ALA* 3.1 40.7 + - + -
225B VAL 3.8 0.7 - - - -
226B VAL* 3.8 26.7 - - + -
271B LEU* 3.7 24.0 - - + -
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Residues in contact with LEU 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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163B ARG* 5.2 0.2 - - - -
213B LYS* 3.4 10.5 + - - +
214B PHE* 1.3 91.9 - - + +
216B ASP* 1.3 68.4 + - - +
221B MET* 4.3 24.5 - - + -
222B PRO* 3.7 20.4 - - + +
223B ASP* 3.5 3.3 - - - -
224B ALA* 3.1 38.8 + - + -
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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